**Meet the editor**

Mark T. Stauffer was born in 1957. He graduated in Chemistry from the University of Pittsburgh in 1979, worked in industry for 12 years, and returned to Pitt, receiving a PhD in Chemistry in 1998. He joined the chemistry faculty at Pitt-Greensburg in 2001, receiving tenure in 2007. Since 2001, he collaborated on projects in archaeology, foods, test kit evaluation, mine drainage,

and data analysis. He and his coauthors presented over 100 papers and posters at technical conferences and published 13 papers in peer-reviewed journals. He presents a short course on analytical data treatment at the annual Pittcon analytical chemistry conference. He conveys his enthusiasm for research and teaching via mentoring undergraduate research and through his courses in analytical chemistry.

## Contents

**Preface XIII**


Yanying Zhao, Xin Liu and Shuang Meng

#### **X** Contents


**Section 2 Molecular Spectroscopic Studies of Organic Materials 111**

Chapter 6 **Vibrational and Electronic Structure, Electron-Electron and Electron-Phonon Interactions in Organic Conductors**

**Investigated by Optical Spectroscopy 113**

Chapter 7 **Infrared and Raman Spectroscopic Characterization of**

Chapter 8 **Novel Pressure-Induced Molecular Transformations Probed by**

Chapter 9 **Conformational Analysis of Molecules: Combined Vibrational Spectroscopy and Density Functional Theory Study 189**

Partha P. Kundu and Chandrabhas Narayana

Chapter 10 **Geometric and Electronic Properties of Porphyrin and its**

**Section 3 Biological and Biomedical Applications of Molecular**

Chapter 11 **Applications of Molecular Spectroscopic Methods to the Elucidation of Lignin Structure 235**

Tatjana Dramićanin and Miroslav Dramićanin

Chapter 13 **Applications of 1H Nuclear Magnetic Resonance Spectroscopy**

Lara García‐Álvarez, Jesús H. Busto, Jesús M. Peregrina, Alberto

**Porphyrin and its Derivatives 141** Metin Aydin and Daniel L. Akins

**In Situ Vibrational Spectroscopy 163**

Andrzej Łapiński

**VI** Contents

Yang Song

**Derivatives 207**

**Spectroscopy 233**

**Breast Cancer 261**

Tingting You and Feng Xu

Chapter 12 **Using Fluorescence Spectroscopy to Diagnose**

**in Clinical Microbiology 281**

Avenoza and José Antonio Oteo

Metin Aydin and Daniel L. Akins


## Preface

The term *spectroscopy* is defined as the study of the interaction of matter with electromagnetic radiation (i.e., "light"). The effects of this relationship were known to the ancient Romans by a rainbow that was produced when light passed through a crystal. In the mid-seventeenth centu‐ ry, Sir Isaac Newton demonstrated that the production of a rainbow when sunlight fell on a clear crystal was due to the components of the sunlight itself and not any component of the crystal. Newton gave this rainbow a name for any diagram of light signal as a function of wave‐ length or frequency—a *spectrum* . Two centuries later, during the heyday of observational as‐ tronomy, astronomers utilized the emerging field of spectroscopy to characterize the stars of deep space via identification of their component elements. In this same timeframe, around 1859, two German scientists, Robert Bunsen (a chemist) and Gustav Kirchhoff (a physicist), discov‐ ered two main types of spectra, *absorption* (spectra yielding dark lines) and emission (spectra yielding bright lines), based on the processes of absorption of light by elements (and their atoms) and compounds (and their molecules or formula units) and the emission or discharge of radiation by these same entities. They also demonstrated how both absorption and emission spectra could be used for identification of elements within compounds, based on their observa‐ tion that every element, no matter the compound within which it is incorporated, produces its own unique spectrum with the same spectral features. Thus the foundation was laid for what would become, over the next century and a half or so, the development and utilization of spec‐ troscopic methods and techniques for identification, characterization, and quantitation of com‐ ponents of samples of myriad.

Spectroscopy is truly a multidisciplinary field in every aspect. The fundamental principles of spectroscopy, whether based on absorption, emission, or scattering of light, are rooted in the laws of physics, which concerns itself with the study of light as waves and particles (quantum theory). By definition, spectroscopy is the study of the interaction of light with matter; thus, spectroscopy is also firmly rooted in chemistry—the study of the composition, properties, and changes of matter. Matter in its various forms, in turn, makes up organic and inorganic compounds that figure prominently in the composition of various forms of life—the realm of biology—and the Earth, the domain of geology. Spectroscopy is used, then, to identify, characterize, and quantify the very elements and compounds that define the composition of the Earth and all life on it.

Despite its multidisciplinary nature, spectroscopy can be considered to reside well within the boundaries of chemistry. Spectroscopy may be used for elucidation of the structures of synthesized molecules (organic and inorganic chemistry), for qualitative identification or quantitative determination of a component of an interesting sample (analytical chemistry), for the study of physical processes and properties of elements and compounds (physical and theoretical chemistry), for characterization of various materials (organic, inorganic, and nu‐ clear chemistry), and in combination with electrochemical and chromatographic analytical methods (analytical chemistry).

Absorption and emission spectra are obtained for atoms of elements and molecules of com‐ pounds via methods and techniques that are atom specific or molecule specific. The spectra

may be a series of discrete lines, as in atomic spectra, or narrow to broad peaks due to intraand intermolecular forces, plus any sample/solution matrix effects, as in molecular spectra. Such spectra, which are usually plots of absorption, emission, or scattering signals as a func‐ tion of wavelength or frequency, can yield a wealth of information about the atoms or mole‐ cules being studied. Such information may be qualitative and useful for identification of functional groups as well as elucidation of the structure of a newly synthesized molecule. Information obtained from a spectrum may also be quantitative, via the relationship be‐ tween the intensity of a signal at a selected wavelength and the concentration of the analyte in a sample.

As the focus of this book is on *molecular* spectroscopic methods and techniques and their applications to a variety of research questions and issues, selected methods and techniques associated with this rather expansive branch of spectroscopy will be presented in a series of original research and review chapters. Such well-known methods as UV-visible spectropho‐ tometry, fluorescence spectrometry, infrared (IR) spectroscopy and its Fourier transform counterpart (FT-IR), Raman and FT-Raman spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy, along with X-ray diffraction (XRD) and photoelectron spectroscopy (PES), are widely used in research in many venues and are covered to varying extents in this text. Additionally, one cannot leave out the many computational and statistical methods used in conjunction with spectroscopic methods for analysis of data and results leading to characterization of samples and quantitation of analytes within samples. Such methods in‐ clude density functional theory (DFT) for quantum mechanical computations and chemo‐ metric methods for pattern recognition and classification, for example, principal component analysis (PCA) and hierarchical cluster analysis (HCA).

The goal of this book is to present an overview of applications of molecular spectroscopy to investigations of organic and inorganic materials, foodstuffs, biosamples and biomedicine, and novel characterization and quantitation methods. This text is a compilation of selected research articles and reviews covering current efforts in various applications of molecular spectroscopy. Sections 1 and 2 deal, respectively, with spectroscopic studies of inorganic and organic materials. Section 3 provides applications of molecular spectroscopy to biosam‐ ples and biomedicine. Section 4 explores spectroscopic characterization and quantitation of foods and beverages. Lastly, Section 5 presents research on novel spectroscopic methodolo‐ gies. Overall, this book should be a great source of scientific information for anyone in‐ volved in characterization, quantitation, and method development.

I am most grateful to Mr. Edi Lipović, the Publishing Process Manager who supervised and organized publishing of all materials; assisted me and the authors in completion of our work in an easy, timely manner; and provided helpful advice and guidance throughout the project. I thank the authors for their great contributions to this book. I express many thanks to the technical editor who prepared these manuscripts for publication.Finally, I thank my wife, Resa, who is also an analytical chemist, for her advice and support, the University of Pittsburgh at Greensburg for their support, and all the spectroscopists I have known throughout my career, for all they taught me about this fascinating field.

#### **Mark T. Stauffer, PhD**

University of Pittsburgh at Greensburg, Greensburg, Pennsylvania, United States of America **Applications of Molecular Spectroscopy to Inorganic Materials**

may be a series of discrete lines, as in atomic spectra, or narrow to broad peaks due to intraand intermolecular forces, plus any sample/solution matrix effects, as in molecular spectra. Such spectra, which are usually plots of absorption, emission, or scattering signals as a func‐ tion of wavelength or frequency, can yield a wealth of information about the atoms or mole‐ cules being studied. Such information may be qualitative and useful for identification of functional groups as well as elucidation of the structure of a newly synthesized molecule. Information obtained from a spectrum may also be quantitative, via the relationship be‐ tween the intensity of a signal at a selected wavelength and the concentration of the analyte

As the focus of this book is on *molecular* spectroscopic methods and techniques and their applications to a variety of research questions and issues, selected methods and techniques associated with this rather expansive branch of spectroscopy will be presented in a series of original research and review chapters. Such well-known methods as UV-visible spectropho‐ tometry, fluorescence spectrometry, infrared (IR) spectroscopy and its Fourier transform counterpart (FT-IR), Raman and FT-Raman spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy, along with X-ray diffraction (XRD) and photoelectron spectroscopy (PES), are widely used in research in many venues and are covered to varying extents in this text. Additionally, one cannot leave out the many computational and statistical methods used in conjunction with spectroscopic methods for analysis of data and results leading to characterization of samples and quantitation of analytes within samples. Such methods in‐ clude density functional theory (DFT) for quantum mechanical computations and chemo‐ metric methods for pattern recognition and classification, for example, principal component

The goal of this book is to present an overview of applications of molecular spectroscopy to investigations of organic and inorganic materials, foodstuffs, biosamples and biomedicine, and novel characterization and quantitation methods. This text is a compilation of selected research articles and reviews covering current efforts in various applications of molecular spectroscopy. Sections 1 and 2 deal, respectively, with spectroscopic studies of inorganic and organic materials. Section 3 provides applications of molecular spectroscopy to biosam‐ ples and biomedicine. Section 4 explores spectroscopic characterization and quantitation of foods and beverages. Lastly, Section 5 presents research on novel spectroscopic methodolo‐ gies. Overall, this book should be a great source of scientific information for anyone in‐

I am most grateful to Mr. Edi Lipović, the Publishing Process Manager who supervised and organized publishing of all materials; assisted me and the authors in completion of our work in an easy, timely manner; and provided helpful advice and guidance throughout the project. I thank the authors for their great contributions to this book. I express many thanks to the technical editor who prepared these manuscripts for publication.Finally, I thank my wife, Resa, who is also an analytical chemist, for her advice and support, the University of Pittsburgh at Greensburg for their support, and all the spectroscopists I have known

**Mark T. Stauffer, PhD**

University of Pittsburgh at Greensburg,

Greensburg, Pennsylvania, United States of America

analysis (PCA) and hierarchical cluster analysis (HCA).

volved in characterization, quantitation, and method development.

throughout my career, for all they taught me about this fascinating field.

in a sample.

X Preface

#### **Fourier Transform Infrared and Raman Characterization of Silica-Based Materials Fourier Transform Infrared and Raman Characterization of Silica-Based Materials**

Larissa Brentano Capeletti and Larissa Brentano Capeletti and João Henrique Zimnoch

João Henrique Zimnoch

Additional information is available at the end of the chapter Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/64477

#### **Abstract**

Fourier Transform Infrared and Raman are powerful techniques to evaluate silica and hybrid silica structure. It is possible to evaluate the silica network formation along the hydrolysis and condensation reactions in terms of siloxane rings formation and Si–O(– Si) angle deformation due to the introduction of organic groups, the employed synthetic route or encapsulated species interaction. The siloxane four- or six-membered rings imply in a more rigid or flexible network, respectively, in order to accommodate the organic groups. A structural analysis of the materials is of high importance, since interactions between the encapsulated molecules and the matrix are critical for the device performance, such as sensors. This type of device needs the permeation of an analyte to activate the encapsulated receptor molecules inside the silica structure. Fourier transform infrared spectrometry can be also used to determine parameters of the silica network as a function of the hydrophilicity/hydrophobicity degree and the siloxane ring structure with respect to thin film porosity. This silica structural analysis is reviewed along the text in a tentative of better exploring the data resulting from these powerful techniques. In addition, the functionalization of silica structures by the use of organoalkoxysilanes, which is important to the creation of high-specific materials, can be well described by these two complementary techniques. The Si–C bonds and the maintenance of the organic substituents such as methyl, octyl, octadecyl, vinyl, phenyl, aminopropyl, mercaptopropyl, isocyanatopropyl, iodopropyl, chloropropyl and glicydoxypropyl could be evaluated after the sol-gel synthesis process. The literature regarding silica vibrational spectroscopy is also explored creating a data bank of wave numbers for the most important bonds for different types of silica and hybrid silica materials obtained by different synthetic routes.

**Keywords:** hybrid silica, molecular imprinting, silica-based materials, FTIR, Raman

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

## **1. Introduction on silica-based materials**

Silica-based materials have a wide field of applications nowadays, since it is very flexible in terms of material characteristics and fabrication methods [1]. Different types of devices such as catalysts, chromatographic phases, sorbents, sensors, coatings, etc. can be produced with tuned properties to enhance activity and/or robustness.

In terms of catalysts, several different reactions can take advantage of the silica surface usage, resulting in heterogeneous processes. The hydrogen production, for example, needs high surface area supports, open porosity, nanostructure with uniform morphology, highly and relatively uniform dispersed active phase, which can be achieved by a silica matrix [2]. In addition, very complex structures can be designed as rattle-type magnetic silica composite with nonporous silica-coating magnetic iron oxide encapsulated in mesoporous silica hollow sphere which can also contain active metallic nanoparticles (**Figure 1A**), resulting in a Pt-based catalyst for hydrogenation that exhibits high activity, selectivity and excellent reusability [3]. Complex hierarchical structures can be also obtained with independent functionalization of macropore and mesopore networks on the basis of chemical and/or size specificity affords control over the reaction sequence in catalytic cascades [4]. The catalyst preparation strategies also include the addition of other metal oxides to the silica network: in desulfurization process, the prepared mixed oxide would take advantage of both titania, probably as the main active component, and silica, for its high thermal stability, excellent mechanical strength and high surface area [5] and the same approach can be employed for photocatalytic practices [6]. The mixed oxides can also be used as polymerization catalysts, where the presence of oxides such as WO3, CrO3 and MoO3 in the silica network decreased the necessary cocatalyst amount, suggesting that the support nature has a considerable influence on the process [7].

**Figure 1.** A) Rattle-type magnetic silica composite with nonporous silica-coating magnetic iron oxide encapsulated in mesoporous silica hollow sphere which can also contain active metallic nanoparticles [3]. B) Molecular imprinting process adapted with permission from Zhao et al. [9].

For chromatographic phases and sorbents, the main maneuvers are the so-called molecular imprinting or the silica functionalization with groups that retain the analytes. Taking into consideration the second approach, it is possible to design hybrid silica monoliths functionalized with, for example, aminopropyl or cyanopropyl groups and utilize them as selective stationary phase for microextraction by packed sorbent (MEPS). This method could determine drugs, such as antipsychotics in combination with antidepressants, anticonvulsants and anxiolytics in plasma samples from schizophrenic patients through liquid chromatographytandem mass spectrometry (LC-MS/MS) in the multiple reactions monitoring (MRM) mode [8]. On the other hand, the molecular imprinting is a methodology which creates cavities for the analytes encapsulating the analyte itself or a template within the silica network that is followed by an extraction process (**Figure 1B**) [9]. The resulting material is of high specificity, increasing the selectivity and performance of the sorbent/phase. This methodology has been employed to extract important compounds such as the β-N-methylamino-L-alanine amino acid from cyanobacteria which is hypothesized to be linked to amyotrophic lateral sclerosis and Parkinson dementia complex from people living in Guam island [10] and to pretreat, detect and analyze trace levels of toxic pyrethroid insecticides in soils [9].

**1. Introduction on silica-based materials**

properties to enhance activity and/or robustness.

process adapted with permission from Zhao et al. [9].

Silica-based materials have a wide field of applications nowadays, since it is very flexible in terms of material characteristics and fabrication methods [1]. Different types of devices such as catalysts, chromatographic phases, sorbents, sensors, coatings, etc. can be produced with tuned

4 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

In terms of catalysts, several different reactions can take advantage of the silica surface usage, resulting in heterogeneous processes. The hydrogen production, for example, needs high surface area supports, open porosity, nanostructure with uniform morphology, highly and relatively uniform dispersed active phase, which can be achieved by a silica matrix [2]. In addition, very complex structures can be designed as rattle-type magnetic silica composite with nonporous silica-coating magnetic iron oxide encapsulated in mesoporous silica hollow sphere which can also contain active metallic nanoparticles (**Figure 1A**), resulting in a Pt-based catalyst for hydrogenation that exhibits high activity, selectivity and excellent reusability [3]. Complex hierarchical structures can be also obtained with independent functionalization of macropore and mesopore networks on the basis of chemical and/or size specificity affords control over the reaction sequence in catalytic cascades [4]. The catalyst preparation strategies also include the addition of other metal oxides to the silica network: in desulfurization process, the prepared mixed oxide would take advantage of both titania, probably as the main active component, and silica, for its high thermal stability, excellent mechanical strength and high surface area [5] and the same approach can be employed for photocatalytic practices [6]. The mixed oxides can also be used as polymerization catalysts, where the presence of oxides such as WO3, CrO3 and MoO3 in the silica network decreased the necessary cocatalyst amount,

suggesting that the support nature has a considerable influence on the process [7].

**Figure 1.** A) Rattle-type magnetic silica composite with nonporous silica-coating magnetic iron oxide encapsulated in mesoporous silica hollow sphere which can also contain active metallic nanoparticles [3]. B) Molecular imprinting

For chromatographic phases and sorbents, the main maneuvers are the so-called molecular imprinting or the silica functionalization with groups that retain the analytes. Taking into consideration the second approach, it is possible to design hybrid silica monoliths functionalized with, for example, aminopropyl or cyanopropyl groups and utilize them as selective stationary phase for microextraction by packed sorbent (MEPS). This method could determine drugs, such as antipsychotics in combination with antidepressants, anticonvulsants and Different types of sensors can also be prepared taking advantages of silica materials' flexibility. Optical sensors use to employ the methodology of a receptor element encapsulation within the silica network and the structural properties and addition of organic groups can be correlated with the device performance [11]. They frequently include the encapsulation of an organic dye which can change color when in contact with the analyte [12]. The introduction of mixed oxides and organic groups can be of high importance in this field to avoid leaching of these dyes during usage [13]. It is also possible to manufacture different devices' configuration such as nanosensors for pH measurement [13], optical fibers for volatile organic compounds' detection [14], electrochemical [15], electrochemiluminescence [16] and biosensors [17]. Furthermore, silica is commonly used to protect or give special features to surfaces. In terms of protection, organosilanes are well known as corrosion protectors for metallic surfaces such as steel and aluminum alloys [18], where other metal such as cerium [19], metallic nanoparticles such as NiFe2O4 [20] and other compounds such as phosphonic acid [21] can also be added to the coating to enhance the protection. The surface characteristics are another feature that are able to be tuned by the silica coatings. In this field, it is possible to mention the superhydrophobicity that is widely explored with the possibility of self-cleaning surface creation [22, 23] and also the addition of antimicrobial properties is of high importance [24, 25].

Thus, the chapter shall be structured according to the following subitems:


## **2. Organic groups on silica surface**

Recent examples of the use of FTIR and FT-Raman spectroscopies in the monitoring of surface reactions between silanol groups and ligands for organic and organometallic compounds. The possibility of distinguishing liquid-like and crystalline configuration for long-chain alkyl groups from the C–H stretching vibrations position.

The organic groups' presence and interactions are monitored in different types of materials, as the ones discussed above. In terms of corrosion protection coatings, the organosilanes are widely known that due to their efficient properties as coupling agents, representing an interesting and environmentally friendly alternative in the field of surface treatments [26]. One of the employed organosilanes is the glycidyloxypropyltrimethoxysilane (GPS) that when mixed with methyltriethoxysilane can improve coating resistance, charge transfer resistance and present low-frequency impedance parameters. FTIR was employed by Foroozan et al. [18] to investigate the reaction between glycidyl groups of GPS molecules with silanol groups. It was possible to identify bands reflecting the epoxy ring breathing around ~910 and 840 cm−1 and also a new band appeared near 1730 cm−1 for C=O stretching that could be associated with the oxidation of the epoxide ring. The spectra confirmed a strong network reticulation as a result of the reaction between glycidyl groups of GPS molecules with hydrolyzed silanes. However, the complimentary results of water contact angles decreased probably due to higher amount of –CH–OH, produced in the reaction between glycidyl and silanol groups, so they reached an optimum point at which a more reticulated structure overcomes the silane layer hydrophilicity.

Silanol groups are also employed to investigate the grafting of catalytic compounds at the silica surface. Ochędzan-Siodłak et al. describes a catalytic system where metallocenes and postmetallocene compounds are immobilized in an ionic liquid modified silica surface. The modification process could be followed by the Si–OH stretching vibration, at 3700 cm−1, disappearing after the ionic liquid modified silane reaction with the silanol groups (**Figure 2A**) [27]. This strategy is becoming popular nowadays, where different organosilanes are first used to modify the surface with specific chemical groups with which is possible to graft the catalysts species or precursors itself [28, 29]. Similarly, the Si–OH vibration can be used to follow direct grafting of catalyst in the silica surface, where the silanol groups can react with a metallic center producing chemical bond between the catalyst compound and the silica surface. Li et al. [30] describes the grafting of a nickel complex in silica and alumina surfaces by following a band at 3745 cm−1, which is assigned to isolated surface hydroxyl groups drops gradually with reaction time and almost completely vanishes after 24 h and correspondingly the absorption bands at 3070–2877 cm−1 related to C–H stretching vibrations of the catalyst allyl groups steadily raise in intensity (**Figure 2B**). Capel-Sanchez et al. [31] also investigated the grafting by silanol groups and in the development of a single site titanium on an amorphous silica surface, they report that the titanium precursor is preferentially anchored over the silica surface by the bridging hydroxyl groups (broad band around 3500 and 3700 cm−1) over the isolated ones (~3700 cm−1).

**4.** *Silica molecular imprinting*. The use of FTIR and Raman in the monitoring of cavity interaction between templates/target molecules with functional groups from silica pores.

6 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**5.** *FTIR and Raman modes*. Discussion on the complementary information provided by sampling accessories and detection modes in the characterization/evaluation of hybrid silica materials, namely: attenuated total reflectance (ATR), DRIFTS, photoacoustic spectroscopy (PAS), infrared emission spectroscopy (IRES), micro-FTIR and Raman.

Recent examples of the use of FTIR and FT-Raman spectroscopies in the monitoring of surface reactions between silanol groups and ligands for organic and organometallic compounds. The possibility of distinguishing liquid-like and crystalline configuration for long-chain alkyl

The organic groups' presence and interactions are monitored in different types of materials, as the ones discussed above. In terms of corrosion protection coatings, the organosilanes are widely known that due to their efficient properties as coupling agents, representing an interesting and environmentally friendly alternative in the field of surface treatments [26]. One of the employed organosilanes is the glycidyloxypropyltrimethoxysilane (GPS) that when mixed with methyltriethoxysilane can improve coating resistance, charge transfer resistance and present low-frequency impedance parameters. FTIR was employed by Foroozan et al. [18] to investigate the reaction between glycidyl groups of GPS molecules with silanol groups. It was possible to identify bands reflecting the epoxy ring breathing around ~910 and 840 cm−1 and also a new band appeared near 1730 cm−1 for C=O stretching that could be associated with the oxidation of the epoxide ring. The spectra confirmed a strong network reticulation as a result of the reaction between glycidyl groups of GPS molecules with hydrolyzed silanes. However, the complimentary results of water contact angles decreased probably due to higher amount of –CH–OH, produced in the reaction between glycidyl and silanol groups, so they reached an optimum point at which a more reticulated structure overcomes the silane layer

Silanol groups are also employed to investigate the grafting of catalytic compounds at the silica surface. Ochędzan-Siodłak et al. describes a catalytic system where metallocenes and postmetallocene compounds are immobilized in an ionic liquid modified silica surface. The modification process could be followed by the Si–OH stretching vibration, at 3700 cm−1, disappearing after the ionic liquid modified silane reaction with the silanol groups (**Figure 2A**) [27]. This strategy is becoming popular nowadays, where different organosilanes are first used to modify the surface with specific chemical groups with which is possible to graft the catalysts species or precursors itself [28, 29]. Similarly, the Si–OH vibration can be used to follow direct grafting of catalyst in the silica surface, where the silanol groups can react with a metallic center producing chemical bond between the catalyst compound and the silica surface. Li et al. [30] describes the grafting of a nickel complex in silica and alumina surfaces by following a band at 3745 cm−1, which is assigned to isolated surface hydroxyl groups drops gradually with

**2. Organic groups on silica surface**

hydrophilicity.

groups from the C–H stretching vibrations position.

**Figure 2.** Monitoring of Si–OH stretching vibration, at 3700 cm−1, disappearing after (A) the grafting of a nickel complex in silica and alumina surfaces [27] and (B) the ionic liquid modified silane reaction with the silanol groups [30].

By using Raman spectroscopy, there is also the possibility of final conformation studies in the case of hybrid silica with long alkyl chains at the silica surface. Structure and order information about alkane-based systems can be obtained from multiple indicators in their Raman spectra, especially in the ν(C–H) region between 2750 and 3050 cm−1. Also, significant conformational order information exists for alkane systems in the ν(C–C) and δ(C–H) regions between 900 and 1500 cm−1. However, it is necessary some care about fluorescence phenomena interferences in Raman around this region [32]. Using this methodology, Brambilla et al. evaluated the gauche and trans conformation of hybrid silica with different octadecyl groups (octadecylsilane [ODS]) content by Raman spectroscopy. The two bands centered at 1080 and 1062 cm−1 are assigned, respectively, to *ν*(C–C) for *gauche* e *trans* conformation of the ODS alkyl chains. The ratio in intensity of these two bands was evaluated in order to monitor the influence of the TEOS/ODS molar ratio in the organic groups' behavior. For all ratios, the intensity between the two bands laid above 1, meaning there is a predominance of *trans* conformation in comparison to *gauche* one, indicating therefore an intense molecular organization in the hybrid silica prepared by the sol-gel method. In addition, it was found that the organization degree of alkyl chains decreases with the ODS content increase, with data from 29Si-NMR and FTIR detected in attenuated total reflectance (ATR) mode, corroborating to the findings [33].

## **3. Molecules within bulk silica**

The FTIR technique can also be employed to evaluate silica network characteristics such as hydrophilicity/hydrophobicity degree and siloxane ring structure regarding thin film porosity [34, 35]. In terms of sensors, these features may impact the analyte interaction and access to the encapsulated molecules, known as receptor elements, within the silica matrix. If the encapsulated molecules' interaction with the silica network occurs through their active sites, it is possible that these active sites are not available to further interact with the analyte. Reduced sensor performance can also occur if the silica network is nonpermeable. In this case, the silica network itself limits the pathways the analyte can travel to reach the encapsulated receptor molecules hindering the reaction. Consequently, both cases could reduce the sensor performance or completely disable it [36].

Silica materials have a prominent band corresponding to the Si–O–Si bond asymmetric stretching in the region from 1300 to 1000 cm−1. Literature reports that the maximum centers and relative intensities of the longitudinal optic (LO) and transversal optic (TO) modes of this bond are shifted with the introduction of chemical groups or organic molecules in the silica network [35]. So, a complete analysis of its components can be conducted, including the deconvolution of the LO and TO modes in their relative main contributions: the four-membered (SiO)4 and six-membered (SiO)6 siloxane rings (**Figure 3A**), resulting in a total of four components (LO6, LO4, TO6 and TO4) (**Figure 3B**). Usually, materials with higher content of chemical groups or organic molecules use to present higher formation of less stressed sixmembered ring, thereby allowing a better accommodation of the nonreactive organic groups [37]. Furthermore, there is a correlation between the formation of six-membered rings and an increase in the relative degree of crystallinity, as well as with the long-range organization in hybrid silica materials that is normally observed with an increase in the degree of matrix alkylation [38].

**Figure 3.** A) Two of the most common cyclical arrangements of SiO4 structural units in xerogels: four-membered siloxane ring (SiO)4 above and six-membered siloxane ring (SiO)6 below. B) Band deconvolution to asymmetric stretching ν(Si–O(–Si)) bond [39].

Using this approach, a series of silica-based acid-base optical sensors prepared by encapsulating pH indicators using three different sol-gel routes was investigated [36]. The employed routes were: nonhydrolytic, acid-catalyzed and base-catalyzed and the pH indicators were alizarin red, brilliant yellow and acridine. The FTIR spectra were performed for all the materials and the peak corresponding to the Si–O–Si asymmetric stretching was deconvoluted and their respective components analyzed and **Figure 4** assembles the results. For the acidic and nonhydrolytic routes, a positive correlation between the pH indicator content and the increase in (SiO)6 percentage was established, thereby indicating the silica network structure rearrangement in order to accommodate the indicator molecules. Using a basic route, the reached indicator contents were notably low and so this relationship was not observed. In addition, no relationship between the (SiO)6 percentage and the response time could be established in spite of less dense networks, with bigger rings, might render easier the analyte permeation. This behavior may indicate that the analyte probably accessed the receptor elements through the passages between the siloxane rings and not through the siloxane rings themselves [36].

**3. Molecules within bulk silica**

ance or completely disable it [36].

alkylation [38].

ν(Si–O(–Si)) bond [39].

The FTIR technique can also be employed to evaluate silica network characteristics such as hydrophilicity/hydrophobicity degree and siloxane ring structure regarding thin film porosity [34, 35]. In terms of sensors, these features may impact the analyte interaction and access to the encapsulated molecules, known as receptor elements, within the silica matrix. If the encapsulated molecules' interaction with the silica network occurs through their active sites, it is possible that these active sites are not available to further interact with the analyte. Reduced sensor performance can also occur if the silica network is nonpermeable. In this case, the silica network itself limits the pathways the analyte can travel to reach the encapsulated receptor molecules hindering the reaction. Consequently, both cases could reduce the sensor perform-

8 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Silica materials have a prominent band corresponding to the Si–O–Si bond asymmetric stretching in the region from 1300 to 1000 cm−1. Literature reports that the maximum centers and relative intensities of the longitudinal optic (LO) and transversal optic (TO) modes of this bond are shifted with the introduction of chemical groups or organic molecules in the silica network [35]. So, a complete analysis of its components can be conducted, including the deconvolution of the LO and TO modes in their relative main contributions: the four-membered (SiO)4 and six-membered (SiO)6 siloxane rings (**Figure 3A**), resulting in a total of four components (LO6, LO4, TO6 and TO4) (**Figure 3B**). Usually, materials with higher content of chemical groups or organic molecules use to present higher formation of less stressed sixmembered ring, thereby allowing a better accommodation of the nonreactive organic groups [37]. Furthermore, there is a correlation between the formation of six-membered rings and an increase in the relative degree of crystallinity, as well as with the long-range organization in hybrid silica materials that is normally observed with an increase in the degree of matrix

**Figure 3.** A) Two of the most common cyclical arrangements of SiO4 structural units in xerogels: four-membered siloxane ring (SiO)4 above and six-membered siloxane ring (SiO)6 below. B) Band deconvolution to asymmetric stretching

**Figure 4.** Comparison of (SiO)6 percentage () and encapsulated indicator content () in each sample [39].

It is remarkable that depending on the sol-gel route, the rate between hydrolysis and condensation reactions will change with the pH medium and can explain the behavior of the basiccatalyzed sensor material. Under basic conditions, the condensation reactions of silanol groups are strongly accelerated, and the particles are rapidly formed. Thus, the probability of rearrangement as a function of the presence of other molecules, as pH indicators for example, during the synthesis decreases, since the tridimensional network is quickly formed. When the condensation reactions are slower, such occurs in acid pH, the network can be more influenced by the addition of molecules to be encapsulated [39].

## **4. Silica molecular imprinting**

The molecular imprinting methodology involves a molecular recognition process where the analyte can recognize and preferentially bind to specific sites built by using a template of the target molecule during the matrix network formation. After an extraction process in order to remove the template, the resulting material is bulk silica with cavities that are morphologically and stereochemically compatible with the analyte. Therefore, an option of analytical technique to follow this procedure is FTIR. It is possible to track the template interaction with the silica network by the template bands appearance and/or SiO2 vibrations change.

With this approach, Morais et al. [40] describe the interactions of different drugs such as fluoxetine, gentamicin, lidocaine, morphine, nifedipine, paracetamol and tetracycline with silica matrix during the preparation of molecular imprinting materials. All these drugs present nitrogen atoms as primary, secondary or tertiary amines that can interact with silanol groups. The investigation was performed comparing the vibrations of bare drug with the encapsulated drug, before removal by extraction. The silica spectrum presents intense bands in the region of ~3500 cm−1 assigned to the O–H vibrations of silanol groups and adsorbed water; and in the region of 1200–800 cm−1, where the Si–O stretchings are observed. As a result of these strong bands and the frequently low concentrations of the encapsulated compounds, it is common to observe an overlapping of their signals by the silica ones avoiding this type of evaluation [36].

As an example, **Figure 5A** illustrates the spectra of lidocaine with its main bands at 1675 cm−1 is assigned to the ν(C=O) of the amide chemical group, 1655 and 1546 cm−1 attributed to δ(C– N–H) of the amine group and the band at 1476 cm−1 to the δ(C–CH3) of the methyl group; and **Figure 5B** shows the spectra of the lidocaine-silica composite where the main bands of the drug can still be observed. However, the bands assigned to the carbonyl stretching and amino bending modes were shifted to 1683 and 1639 cm−1, respectively, suggesting a potential medicine-silica network interaction through these chemical groups. Similar behavior was observed for the other drugs, considering the machine resolution of 4 cm−1. Most of the pharmaceutical presented infrared band shifts toward higher wave numbers (bathochromic shift) when encapsulated, indicating they are interacting with the silica structure, resulting in a rearrangement of the chemical groups, which was confirmed by the rotational isomerism of the molecule. In addition, some of the bands were shifted for lower wave numbers (hypsochromic shift) reflecting a tension increase in the molecule rotational conformation, since the encapsulation process may incur in difficulty of the functional groups vibrational movements demanding more energy. Most of the nitrogen-related bands, for all samples, had their wave numbers shifted. These results denote possibility of a hydrogen bonding interaction through electron donation between these groups and silica network, as illustrated by **Figure 6**. Among the studied drugs, the exception was tetracycline which presented a shift in the OH group deformation band and so indicating an interaction by this group [40].

Fourier Transform Infrared and Raman Characterization of Silica-Based Materials http://dx.doi.org/10.5772/64477 11

**Figure 5.** FTIR spectra of bare lidocaine (A) and the respective encapsulated system (B) [40].

condensation reactions are slower, such occurs in acid pH, the network can be more influenced

The molecular imprinting methodology involves a molecular recognition process where the analyte can recognize and preferentially bind to specific sites built by using a template of the target molecule during the matrix network formation. After an extraction process in order to remove the template, the resulting material is bulk silica with cavities that are morphologically and stereochemically compatible with the analyte. Therefore, an option of analytical technique to follow this procedure is FTIR. It is possible to track the template interaction with the silica

With this approach, Morais et al. [40] describe the interactions of different drugs such as fluoxetine, gentamicin, lidocaine, morphine, nifedipine, paracetamol and tetracycline with silica matrix during the preparation of molecular imprinting materials. All these drugs present nitrogen atoms as primary, secondary or tertiary amines that can interact with silanol groups. The investigation was performed comparing the vibrations of bare drug with the encapsulated drug, before removal by extraction. The silica spectrum presents intense bands in the region of ~3500 cm−1 assigned to the O–H vibrations of silanol groups and adsorbed water; and in the region of 1200–800 cm−1, where the Si–O stretchings are observed. As a result of these strong bands and the frequently low concentrations of the encapsulated compounds, it is common to observe an overlapping of their signals by the silica ones avoiding this type of evaluation [36].

As an example, **Figure 5A** illustrates the spectra of lidocaine with its main bands at 1675 cm−1 is assigned to the ν(C=O) of the amide chemical group, 1655 and 1546 cm−1 attributed to δ(C– N–H) of the amine group and the band at 1476 cm−1 to the δ(C–CH3) of the methyl group; and **Figure 5B** shows the spectra of the lidocaine-silica composite where the main bands of the drug can still be observed. However, the bands assigned to the carbonyl stretching and amino bending modes were shifted to 1683 and 1639 cm−1, respectively, suggesting a potential medicine-silica network interaction through these chemical groups. Similar behavior was observed for the other drugs, considering the machine resolution of 4 cm−1. Most of the pharmaceutical presented infrared band shifts toward higher wave numbers (bathochromic shift) when encapsulated, indicating they are interacting with the silica structure, resulting in a rearrangement of the chemical groups, which was confirmed by the rotational isomerism of the molecule. In addition, some of the bands were shifted for lower wave numbers (hypsochromic shift) reflecting a tension increase in the molecule rotational conformation, since the encapsulation process may incur in difficulty of the functional groups vibrational movements demanding more energy. Most of the nitrogen-related bands, for all samples, had their wave numbers shifted. These results denote possibility of a hydrogen bonding interaction through electron donation between these groups and silica network, as illustrated by **Figure 6**. Among the studied drugs, the exception was tetracycline which presented a shift in the OH group

network by the template bands appearance and/or SiO2 vibrations change.

10 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

deformation band and so indicating an interaction by this group [40].

by the addition of molecules to be encapsulated [39].

**4. Silica molecular imprinting**

**Figure 6.** Proposed interactions of the drugs with silica network [40].

In other approaches, hybrid silica networks have been used to improve both the process of molecular imprinting as the following usage of the material as an extraction matrix. Han et al. reports the functionalization of silica with amino groups provided by aminopropyltriethoxysilane to help interaction with the toxic herbicide pentachlorophenol [41]. By using FTIR to monitor this process, they were able to identify the N–H bond around 1560 cm−1 and C–H bond around 2935 cm−1, suggesting the –NH2 grafting onto the activated silica gel surface. In this case, imprinted and nonimprinted sorbents showed similar location and appearance of the major bands, reflecting the already mentioned problem of overlapping bands with the major bands of silica network. Similar behavior was observed by Chrzanowska et al., Ren et al. and Li et al. [42–44]. The first one employed the functionalization of silica nanoparticles surface with aminopropyl groups to promote the encapsulation of biochanin A, producing a selective solid-phase extraction of biochanin A, daidzein and genistein from urine samples [42]. Analogously, Ren et al. employed the same procedure with aminopropyl groups, although the target analyte was bisphenol A [44]. Finally, the later one made use of propylthiocyanate groups to modify the silica surface, creating a selective phase for selective removal of cadmium(II) competing with copper, zinc and lead in aqueous solution [43]. In all the cases, the assisting organic groups' bands were detected; however, the molecular imprinted and nonimprinted spectra were really similar.

#### **5. FTIR and Raman modes**

When analyzing hybrid silica materials, sometimes it is necessary to use complementary techniques to better evaluate the materials' characteristics. The same occurs for vibrational spectroscopy methods. A wide investigation was performed with a series of different hybrid silica prepared with tetraethoxysilane (C0), methyltriethoxysilane (C1), octyltriethoxysilane (C8), octadecyltrimethoxysilane (C18), vinyltrimethoxysilane (Vy), phenyltrimethoxysilane (Ph), mercaptopropyltrimethoxysilane (SHp), isocyanatepropyltriethoxysilane (NCOp), chloropropyltrimethoxysilane (Clp) and glycidoxypropyltrimethoxysilane (Gp) [45]. Using FTIR, the main bands of silica were well determined for all the hybrid silicas and they showed shifts depending on the organic group presenting at the network, although the organic groups' bands were barely seen. Using Raman spectroscopy, the organic groups were well described and some of the silica network bands were also observed.

The region around 3600–3000 cm−1 is attributed to hydroxyl groups ν(O–H) stretching modes. The shoulder at ~3600 cm−1 matches the OAH vibrations associated with alcohols that are a subproduct of sol-gel reaction, while the maximum at ~3425 cm−1 is related to surface –OH participating of hydrogen bonds. Water is also described here as a shoulder at ~3230 cm−1, which is also observed at ~1630 cm−1. As mentioned before, silica presents a characteristic region of peaks from 1250 to 700 cm−1 that can provide structural characteristics of the network. Specially, when related to the main bands between 1250 and 1000 cm−1 corresponding to the asymmetric ν(Si–O–H) and their deconvolution on LO at ~1130 cm−1 and TO at 1047 cm−1 modes. The Si–O(H) bond stretching appears at slightly different positions in the FTIR (~950 cm−1) and Raman (~980 cm−1) spectra. The symmetric mode of ν(Si–O–Si) band is found at ~791 (FTIR) and ~799 cm−1 (Raman), while the Si–O− rocking mode was observed at ~540 cm−1 (IR). Finally, the Raman spectra also show the siloxane ring breathing mode (with 3 or 4 SiO units) located at ~490 cm−1 [45].

The silica-related bands presented wave number shifts depending on the employed organic group in the different hybrid silicas. For Si–O(–Si) LO mode, the largest shift occurs from the nonhybrid to the hybrid samples. In this case, shifts to lower wave numbers use to be related to the network deformation in order to accommodate the organic groups within the inorganic silica matrix resulting in larger siloxane rings and greater Si–O–Si angles and longer Si–O bond lengths. LO and TO mode shifts occur mainly near the surface of the material, which can be better detected employing attenuated total reflectance (ATR) mode of FTIR spectroscopy. In addition, the organic groups' introduction can originate from heterogeneous regions that may introduce local deformations in the network resulting in the differences observed for Si–O bond lengths and Si–O–Si angles in the different hybrid materials. Another interesting behavior is reported to Si–O(H) band, considering that, in a general way for this case, the wave number shifts result from hydrogen bond formation with the silanol groups. A significantly higher wave number occurred for C18 while the lower ones occurred for Clp and Gp [45]. The very hydrophobic C18 organic chain can hinder hydrogen bond formation by comparison with the other samples, thus, the Si–O bond length is decreased and the wave number is shifted to higher values. However, the groups Clp and Gp can facilitate hydrogen bond formation with the silanol groups and, as a consequence, the Si–O bond length is increased and the vibrational wave number is decreased [46].

silane to help interaction with the toxic herbicide pentachlorophenol [41]. By using FTIR to monitor this process, they were able to identify the N–H bond around 1560 cm−1 and C–H bond around 2935 cm−1, suggesting the –NH2 grafting onto the activated silica gel surface. In this case, imprinted and nonimprinted sorbents showed similar location and appearance of the major bands, reflecting the already mentioned problem of overlapping bands with the major bands of silica network. Similar behavior was observed by Chrzanowska et al., Ren et al. and Li et al. [42–44]. The first one employed the functionalization of silica nanoparticles surface with aminopropyl groups to promote the encapsulation of biochanin A, producing a selective solid-phase extraction of biochanin A, daidzein and genistein from urine samples [42]. Analogously, Ren et al. employed the same procedure with aminopropyl groups, although the target analyte was bisphenol A [44]. Finally, the later one made use of propylthiocyanate groups to modify the silica surface, creating a selective phase for selective removal of cadmium(II) competing with copper, zinc and lead in aqueous solution [43]. In all the cases, the assisting organic groups' bands were detected; however, the molecular imprinted and

12 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

When analyzing hybrid silica materials, sometimes it is necessary to use complementary techniques to better evaluate the materials' characteristics. The same occurs for vibrational spectroscopy methods. A wide investigation was performed with a series of different hybrid silica prepared with tetraethoxysilane (C0), methyltriethoxysilane (C1), octyltriethoxysilane (C8), octadecyltrimethoxysilane (C18), vinyltrimethoxysilane (Vy), phenyltrimethoxysilane (Ph), mercaptopropyltrimethoxysilane (SHp), isocyanatepropyltriethoxysilane (NCOp), chloropropyltrimethoxysilane (Clp) and glycidoxypropyltrimethoxysilane (Gp) [45]. Using FTIR, the main bands of silica were well determined for all the hybrid silicas and they showed shifts depending on the organic group presenting at the network, although the organic groups' bands were barely seen. Using Raman spectroscopy, the organic groups were well described

The region around 3600–3000 cm−1 is attributed to hydroxyl groups ν(O–H) stretching modes. The shoulder at ~3600 cm−1 matches the OAH vibrations associated with alcohols that are a subproduct of sol-gel reaction, while the maximum at ~3425 cm−1 is related to surface –OH participating of hydrogen bonds. Water is also described here as a shoulder at ~3230 cm−1, which is also observed at ~1630 cm−1. As mentioned before, silica presents a characteristic region of peaks from 1250 to 700 cm−1 that can provide structural characteristics of the network. Specially, when related to the main bands between 1250 and 1000 cm−1 corresponding to the asymmetric ν(Si–O–H) and their deconvolution on LO at ~1130 cm−1 and TO at 1047 cm−1 modes. The Si–O(H) bond stretching appears at slightly different positions in the FTIR (~950 cm−1) and Raman (~980 cm−1) spectra. The symmetric mode of ν(Si–O–Si) band is found at ~791

Finally, the Raman spectra also show the siloxane ring breathing mode (with 3 or 4 SiO units)

rocking mode was observed at ~540 cm−1 (IR).

nonimprinted spectra were really similar.

and some of the silica network bands were also observed.

(FTIR) and ~799 cm−1 (Raman), while the Si–O−

located at ~490 cm−1 [45].

**5. FTIR and Raman modes**

As mentioned before, the characterization of the organic groups of hybrid network is better done using Raman spectroscopy than FTIR. The last one can observe only some bands, while Raman presents a series of them showing the complementarity of both techniques for hybrid materials' characterization. **Table 1** compiles some important assignments regarding the organic groups and their respective wave numbers detected by both techniques, when applicable [45].

The complementary use of FTIR and Raman spectroscopies can be also employed to deeply investigate the processes taking place during sol-gel process and there are other types of detection modes for these vibrational techniques as DRIFTS, PAS, IRES, micro-FTIR and Raman which can help.

DRIFT spectroscopy is primarily used on samples where most of the reflected radiation is diffused. It is important that the specular reflectance is reduced to a minimum because it distorts the DRIFT spectrum and lowers the band intensities [47]. During the last years, it has become the most effective technique for studying the processes taking place at the gas-solid interface [48]. Ivanovski et al. investigated the region of the OH stretching vibrations of silica gel activated at different temperatures for the purpose of checking the availability of the OH groups for further reaction with 3-aminopropyltrimethoxysilane (APTMS) molecules and whether chemisorption was successful, finding evidence whether chemisorption of APTMS involves all available methoxy groups. It is also possible to investigate the conformation of the aminopropyl groups (APS) backbone on the silica gel surface and the possible proton transfer between the NH2 groups of APS and OH from silica gel detected by the formation of NH3 + and SiO− which is spectroscopically detectable through the appearance of the δ(NH3 + ) vibrations at 1668 cm−1 [49]. In addition, Bukleski et al. developed a direct quantitative method of quantification of maximal chemisorption of 3-aminopropylsilyl groups on silica gel using DRIFT spectroscopy, as (APS) modified silica gel plays an important role as a precursor for further modifications, where APS acts as a spacer or bridging molecule. By integrating the spectra in the frequency range of the *ν*(CH2)/*ν*(CH3) vibrations between 3014 and 2808 cm−1, the mass fraction of APTMS of 19.04% was found to correspond to a maximal concentration of APS on silica gel of 2.23 μmol m−2, which was confirmed by elemental analysis for carbon [47].


\*asym: asymmetric; sym: symmetric; bend: bending; term: terminal; def: deformation; R: Raman; and I: infrared.

**Table 1.** Organic group bands detected by the complementary techniques of FTIR and Raman [45].

The photoacoustic spectroscopy (PAS) FTIR is a broad-applicable mid-infrared solution when samples present opacity problems [50]. It is a unique extension of IR spectroscopy which combines the utility of interferometry with the standard sample-gas microphone of the photothermal technique for depth-profile analysis of materials. Its signal generation processes automatically and reproducibly isolates a layer extending beneath the sample surface which has suitable optical density for analysis without physically altering the sample. PAS involves measurement of acoustic wave (pressure oscillations) in a hermetically sealed cell fitted with a very sensitive microphone. The microphone signal, when plotted as a function of wavelength, contains a spectrum proportional to the absorption spectrum of the sample. The wave generation follows absorption of light, which is modulated at a frequency in the acoustic range, by the sample. Most FTIR instruments provide modulation frequencies between 50 and 500 Hz in the 400–4000 cm−1 wave number span [51]. Therefore, this approach can be employed to evaluate silica samples as described by Gao et al. to widely explore a polyethylene-*co*-Znacrylic acid hybrid material prepared by the sol-gel process. They could identify both vibrations for silica and the organic group. By investigating the silica bands it is noted that not only silica but also other forms of silicon groups are formed via the sol-gel reaction, while the existence of the Si–OH group indicates that the condensation reaction was not completely finished. However, analyzing the peaks referring to the organic groups, it was reported that –CH2– and –CH3 positions in the region of 2800–3000 cm−1 remain the same after hybrid material fabrication, indicating no chemical bond between silicon and these two groups forms after the sol-gel reaction. The band at 1700 cm−1 is the C=O stretching mode from the –COOH group was also noticed for both materials. This is due to unneutralized acrylic acid. While the transparency of the hybrid is a result of strong organic-inorganic interaction, and a high degree of mixing, no evidence of hydrogen bonding is observed from the FTIR peak position [52].

DRIFT spectroscopy, as (APS) modified silica gel plays an important role as a precursor for further modifications, where APS acts as a spacer or bridging molecule. By integrating the spectra in the frequency range of the *ν*(CH2)/*ν*(CH3) vibrations between 3014 and 2808 cm−1, the mass fraction of APTMS of 19.04% was found to correspond to a maximal concentration of APS on silica gel of 2.23 μmol m−2, which was confirmed by elemental analysis for carbon

14 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Assignment C1 C8 C18 Vy Ph SHp NCOp Clp Gp**

C–H(2) asym 2932 R 2930 R 2928 R 2939 R 2962 R 2926 R

C–H(2) sym 2861 R 2850 R 2894 R 2897 R 2901 R 2894 R

1278 R

Ring breath 737 I 1260 R

2926 I 2918 I 2942 I 2945 I 2960 I 2935 I

2856 I 2848 I 2880 I

[47].

C–H(3) asym 2979 R 2955 I 2957 I C–H(3) sym 2916 R 2884 R 2883 R

1280 I CH2 bend 1463 R 1460 R

C–H arom 3058 R Si–C 1412 R 1122 R

C–C 1064 R 1062 R 1013 R 999 R

C–H bend 1432 i

Ring def 698 I

S–H 2574 R C–S 652 R

C=N 1553 I N=C=O 1449 R

H–C–Cl def 1412 R C–Cl(H)trans 645 R

**Table 1.** Organic group bands detected by the complementary techniques of FTIR and Raman [45].

OC–H 1456 R \*asym: asymmetric; sym: symmetric; bend: bending; term: terminal; def: deformation; R: Raman; and I: infrared.

C=C 1603 R =C–H term 3072 R =C–H term bend 1412 R

(Si)C–H 2991 R

1457 I 1468 I

Infrared emission spectroscopy (IRES) is a method in which a sample is energized by heating and so on, and the infrared light emitted from the sample is measured to obtain a spectrum. It utilizes the contrast between the sample and the base material with possibility of an improved signal-to-noise ratio compared to absorption spectroscopy. Ideally only photons emitted by the sample are detected ("zero background"), free from the noise produced by the continuum lamp in an absorption experiment. This improvement in sensitivity is particularly useful for the spectroscopy of transient molecules because of their intrinsically low concentrations [53]. In the case of hybrid silicas, this methodology can be successfully employed to evaluate the thermal stability of materials. Brambilla et al., for example, describe the behavior of octadecylsilane (ODS) hybrid silicas prepared by grafting and sol-gel methods with a spectra series from 100 to 900°C between 4000 and 500 cm−1. The decrease of physically adsorbed water band and the surface silanol interactions, leading to an increase in the band at 3747 cm−1, attributed to isolated silanol groups was observed. For temperatures higher than 450°C up to 900°C, the band assigned to isolated silanol groups (3747 cm−1) is reduced due to condensation reactions and structural reorganization with generation of siloxane groups. Concerning the ν(C–H) stretching region, the bands at 2963, 2929 and 2855 cm−1 are reduced in the range of 250–550°C, as a result of the thermal degradation of ODS chains. **Figure 7** presents the relative band area for this vibration. It was possible to compare the thermal stability of hybrid materials prepared by grafting (GR100) and sol-gel method (SG10A), confirm the higher thermal stability of the first one [54].

**Figure 7.** Relative area of ν(C–H) bands versus temperature for grafting prepared (GR100) and sol-gel prepared (SG10) hybrid silicas [54].

Finally, micro-Raman and micro-FTIR modes have less sensibility, however, they are key methods employed when spatial resolution of a few micrometers is necessary. It can be employed, for example, to evaluate radial distribution of the fictive temperature in pure silica optical fibers [55], porous silica supports for individual living cells [56] and phenyl-bridged polysilsesquioxane positive and negative resist for electron beam lithography where the technique helped to propose a description of the tone switching mechanisms [57].

#### **6. Final remarks**

Observing all the procedures and results described above, it is noticeable that a vibrational spectrum is not collected only to simply evaluate peak positions anymore. Nowadays, it is possible to obtain deep information about materials' formation, evolution and structure, as well as to acquire spatial resolution spectra or in high-resolution modes with low signal/noise ratios. The reaction chemical processes following methods are getting more and more specific, as collected data are more and more exploited in order to give the maximum results information, bringing fast advance in the materials characterization field.

## **Author details**

prepared by grafting (GR100) and sol-gel method (SG10A), confirm the higher thermal stability

16 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 7.** Relative area of ν(C–H) bands versus temperature for grafting prepared (GR100) and sol-gel prepared (SG10)

Finally, micro-Raman and micro-FTIR modes have less sensibility, however, they are key methods employed when spatial resolution of a few micrometers is necessary. It can be employed, for example, to evaluate radial distribution of the fictive temperature in pure silica optical fibers [55], porous silica supports for individual living cells [56] and phenyl-bridged polysilsesquioxane positive and negative resist for electron beam lithography where the

Observing all the procedures and results described above, it is noticeable that a vibrational spectrum is not collected only to simply evaluate peak positions anymore. Nowadays, it is possible to obtain deep information about materials' formation, evolution and structure, as well as to acquire spatial resolution spectra or in high-resolution modes with low signal/noise ratios. The reaction chemical processes following methods are getting more and more specific, as collected data are more and more exploited in order to give the maximum results informa-

technique helped to propose a description of the tone switching mechanisms [57].

tion, bringing fast advance in the materials characterization field.

of the first one [54].

hybrid silicas [54].

**6. Final remarks**

Larissa Brentano Capeletti and João Henrique Zimnoch\*

\*Address all correspondence to: jhzds@iq.ufrgs.br

Chemistry Institute, Federal University of Rio Grande do Sul, Porto Alegre, Brazil

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#### **Investigations of Phonons in Zinc Blende and Wurtzite by Raman Spectroscopy Investigations of Phonons in Zinc Blende and Wurtzite by Raman Spectroscopy**

Lin Sun, Lingcong Shi and Chunrui Wang Lin Sun, Lingcong Shi and Chunrui Wang

Additional information is available at the end of the chapter

Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/64194

#### **Abstract**

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22 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

The importance of phonons and their interactions in bulk materials is well known to those working in the fields of solid‐state physics, solid‐state electronics, optoelectronics, heat transport, quantum electronic, and superconductivity. Phonons in nanostructures may act as a guide to research on dimensionally confined phonons and lead to phonon effects in nanostructures and phonon engineering. In this chapter, we introduce phonons in zinc blende and wurtzite nanocrystals. First, the basic structure of zinc blende and wurtzite is described. Then, phase transformation between zinc blende and wurtzite is presented. The linear chain model of a one‐dimensional diatomic crystal and macroscopic models are also discussed. Basic properties of phonons in wurtzite structure will be considered as well as Raman mode in zinc blende and wurtzite structure. Finally, phonons in ZnSe, Ge, SnS2, MoS2, and Cu2ZnSnS4 nanocrystals are discussed on the basis of the above theory.

**Keywords:** phonons, zinc blende, wurtzite, Raman spectroscopy, molecular vibration

## **1. Zinc blende and wurtzite structure**

Crystals with cubic/hexagonal structure are of major importance in the fields of electronics and optoelectronics. Zinc blende is typical face‐centered cubic structure, such as Si, Ge, GaAs, and ZnSe. Wurtzite is typical hexagonal close packed structure, such as GaN and ZnSe. In particular, II–VI or III–V group semiconductor nanowires always coexist two structures, one cubic form with zinc blend (ZB) and another hexagonal form with wurtzite (WZ) structure. Sometimes, this coexistence between zinc blende and wurtzite structure leads to form twinning crystal during the phase transformation between zinc blende and wurtzite [1, 2].

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

#### **1.1. Basic structure of zinc blende and wurtzite**

The crystal structure of zinc selenide in the zinc blende structures is shown in **Figure 1**, which is regarded as two face‐centered cubic (fcc) lattices displaced relative to each other by a vector a <sup>4</sup> <sup>+</sup> <sup>a</sup> <sup>4</sup> <sup>+</sup><sup>a</sup> <sup>4</sup> , where a is lattice constant. Close‐packed planes of zinc blende are {111} along <111>, and the stacking is …ABCABCA…; the adjacent plane separation is 3/3a. Along <100>, the sacking is …ABABAB…; the adjacent plane separation is a/2. Along <110>, the sacking is …ABABABA…; the adjacent plane separation is 2/4a. Zinc blende structures have eight atoms per unit cell.

**Figure 1.** Zinc blende crystal structure.

**Figure 2** is wurtzite structure of zinc selenium. Close‐packed planes of wurtzite are {0001} along <0001>, and the stacking is …ABABA…. Adjacent plane spacing is c/2. Wurtzite structures have four atoms per unit cell. In zinc blende, the bonding is tetrahedral. The wurtzite structure may be generated from zinc blende by rotating adjacent tetrahedra about their common bonding axis by an angle of 60° with respect to each other.

**Figure 2.** Wurtzite crystal structure.

#### **1.2. Phase transformation between zinc blende and wurtzite**

**1.1. Basic structure of zinc blende and wurtzite**

a <sup>4</sup> <sup>+</sup> <sup>a</sup>

<sup>4</sup> <sup>+</sup><sup>a</sup>

atoms per unit cell.

**Figure 1.** Zinc blende crystal structure.

**Figure 2.** Wurtzite crystal structure.

bonding axis by an angle of 60° with respect to each other.

The crystal structure of zinc selenide in the zinc blende structures is shown in **Figure 1**, which is regarded as two face‐centered cubic (fcc) lattices displaced relative to each other by a vector

24 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

<111>, and the stacking is …ABCABCA…; the adjacent plane separation is 3/3a. Along <100>, the sacking is …ABABAB…; the adjacent plane separation is a/2. Along <110>, the sacking is …ABABABA…; the adjacent plane separation is 2/4a. Zinc blende structures have eight

**Figure 2** is wurtzite structure of zinc selenium. Close‐packed planes of wurtzite are {0001} along <0001>, and the stacking is …ABABA…. Adjacent plane spacing is c/2. Wurtzite structures have four atoms per unit cell. In zinc blende, the bonding is tetrahedral. The wurtzite structure may be generated from zinc blende by rotating adjacent tetrahedra about their common

<sup>4</sup> , where a is lattice constant. Close‐packed planes of zinc blende are {111} along

Research into controlling nanowire crystal structure has intensified. Several reports address the diameter dependency of nanowire crystal structure, with smaller diameter nanowires tending toward a WZ phase and larger diameter nanowires tending toward a ZB phase. Allowing for ZnSe, two phases, zinc blende (ZB) and wurtzite (WZ), exist, and the (111) faces of ZB phase are indistinguishable from and match up with the (001) faces of WZ phase, the subtle structural differences of which lead to the attendant small difference in the internal energies (∼5.3 meV/atom for ZnSe). The WZ‐ZB phase transformation is considered to be caused by the crystal plane slip. Take the formation of ZnSe longitudinal twinning nanowires, for example [3]. Structurally, the (001) planes of WZ and the (111) planes of ZB are their corresponding close packing planes. ABAB stacking for WZ and ABCABC stacking for ZB are shown in **Figure 3a** and **b**, respectively. It was noteworthy that the arrangement of atoms in A/B packing planes was different in WZ phase. So the phase transition could not be realized until the smaller Zn atoms moved to the interspaces provided by three neighboring bigger Se atoms, within the plane B. In this case, the new layers B' were obtained, and then, the slip occurs between neighboring planes A and B' by 1 <sup>3</sup> <sup>+</sup> <sup>2</sup> <sup>3</sup> <sup>b</sup> , that is <120> direction, indicated in **Figure 3a**.

**Figure 3.** Phase transformation between zinc blende and wurtzite. (a) The arrangement of atoms in WZ phase; (b) The arrangement of atoms in ZB phase; (Se is shown with the bigger sphere and Zn is shown in little one.) (c) The stacking sequence schematic model showing the phase transformation process from WZ phase to ZB phase.

Generally, there are three equivalent directions to realized the slip, which are <120>, <210>, and <110>. Such a displacement could be indicated in **Figure 3c**, and the ZB structure could be obtained through the slip between every second close‐packed layer in the WZ sequence to form the ABC stacking.

## **2. Linear‐chain model and macroscopic models**

To the simple double lattice, lattice vibration can be described by the one‐dimensional diatomic model. The linear‐chain model of a diatomic crystal is based upon a system of two atoms with masses, *m* and *M*, placed along a one‐dimensional chain as depicted in **Figure 4**. The separation between the atomics is "*a*", and the vibration in the vicinity of their equilibrium position is treated as the simple harmonic vibration. The properties of optical phonon can be described based on the macroscopic fields. It is the model based on the Huang and Maxwell equations, which has great utility in describing the phonons in the uniaxial crystals such as wurtzite crystals.

**Figure 4.** One‐dimensional diatomic linear‐chain model.

#### **2.1. Polar semiconductors**

Polar semiconductor is the crystal that consists of different ions. In polar semiconductor, the lattice vibration is associated with the electric dipole moment and electric field generation. Assume that the vibration frequency is *ω*, wave vector is q , then the intensity of polarization can be written as follows,

$$
\vec{P} = \vec{P}\_0 e^{l(\alpha t - \vec{q} \cdot \vec{r})} \tag{2-1}
$$

Solve the simultaneous formula (2‐1) and Maxwell equations can obtain,

$$\vec{E} = \frac{\alpha^2 \vec{P} - \vec{q}c^2 \langle \vec{q} \cdot \vec{P} \rangle}{\varepsilon\_o \langle q^2 c^2 - \alpha^2 \rangle} \tag{2-2}$$

To longitudinal polarity lattice mode, p //q , formula (2‐2) can be simplified as follows,

$$
\vec{E}\_L = -\frac{\vec{P}}{\varepsilon\_0} \tag{2-3}
$$

To transverse polarity lattice mode, p ⊥ q , formula (2‐2) can be simplified as follows,

$$
\vec{E}\_r = \frac{o\rho^2}{\varepsilon\_0 (q^2 \varepsilon^2 - o^2)} \vec{P} \tag{2-4}
$$

As was apparent above, polar optical phonon vibrations produce electric fields and electric polarization fields that may be described in terms of Maxwell's equations and the driven‐ oscillator equations. Assume that the mass of the ions are M+, M−, the charges are ±Ze, displacements are u±, the force constant is *k*,

$$M\_{\downarrow}\ddot{\vec{\mu}}\_{\downarrow} = -k\vec{u} + Ze\vec{E}\_{\epsilon} \tag{2-5}$$

$$\mathbf{M}\_{-}\ddot{\vec{\mu}}\_{-} = k\vec{u} - \mathbf{Z}e\vec{\mathbf{E}}\_{e} \tag{2-6}$$

where Ee is the effect electric field, <sup>u</sup> = u <sup>+</sup> − u <sup>−</sup>, then

$$
\vec{M}\ddot{\vec{\mu}} = -k\vec{\mu} + Z\varepsilon\vec{E}\_e \tag{2-7}
$$

where M = M+M− M+ + M− is reduced mass.

based on the macroscopic fields. It is the model based on the Huang and Maxwell equations, which has great utility in describing the phonons in the uniaxial crystals such as wurtzite

26 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Polar semiconductor is the crystal that consists of different ions. In polar semiconductor, the lattice vibration is associated with the electric dipole moment and electric field generation. Assume that the vibration frequency is *ω*, wave vector is q , then the intensity of polarization

> w - × = r r r r ( ) 0

> > w

( )

22 2

( ) *P qc q P <sup>E</sup>*

Solve the simultaneous formula (2‐1) and Maxwell equations can obtain,

w

e

0

*L*

e

To transverse polarity lattice mode, p ⊥ q , formula (2‐2) can be simplified as follows,

w

 <sup>=</sup> r r <sup>2</sup> 22 2 <sup>0</sup> ( ) *<sup>T</sup> E P*

 w


To longitudinal polarity lattice mode, p //q , formula (2‐2) can be simplified as follows,

e = <sup>r</sup> <sup>r</sup>

0

*i t qr P Pe* (2‐1)

*q c* (2‐2)

*<sup>P</sup> <sup>E</sup>* (2‐3)

*q c* (2‐4)

crystals.

**Figure 4.** One‐dimensional diatomic linear‐chain model.

**2.1. Polar semiconductors**

can be written as follows,

The lattice vibration is associated with the electric dipole moment generation, which can be described as follows,

$$
\vec{P} = \frac{1}{\Omega} (Ze\vec{u} + a\vec{E}\_\circ) \tag{2-8}
$$

where Ω is the volume of the primitive cell, and is the electron polarization. Under the effective field approximation, the effective field can be described as follows,

$$
\vec{E}\_c = \vec{E} + \frac{\vec{P}}{3\varepsilon\_0} \tag{2-9}
$$

Replace the value of p in formula (2‐9) with (2‐8),

$$
\vec{E}\_c = \frac{\Im \varepsilon\_0 \Omega \vec{E} + Z e \vec{\mu}}{\Im \varepsilon\_0 \Omega - \alpha} \tag{2-10}
$$

Then, take formula (2‐7) and (2‐9) into (2‐10),

$$
\ddot{\vec{\mu}} = A\vec{\mu} + B\vec{E} \tag{2-11}
$$

28 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

$$
\vec{P} = C\vec{E} + D\vec{u} \tag{2-12}
$$

where

$$A = -\frac{k}{\overline{M}} + \frac{Z^2 e^2}{\overline{M}(3\varepsilon\_0 \Omega - a)}\tag{2-13}$$

$$B = \frac{3\varepsilon\_0 \Omega Z e}{\overline{M}(\Im \varepsilon\_0 \Omega - a)}\tag{2-14}$$

$$C = \frac{3\varepsilon\_0 \alpha}{3\varepsilon\_0 \Omega - \alpha} \tag{2-15}$$

$$D = \frac{3\varepsilon\_0 Z e}{3\varepsilon\_0 \Omega - a} \tag{2-16}$$

formula (2‐11) and (2‐12) are the Huang equations, which are the basic equations of describing the vibrations of long wave in the polar crystals. From the formula (2‐14) and (2‐16), one can find that,

$$B = \frac{\Omega}{\overline{M}} D \tag{2-17}$$

When the system is under the high‐frequency electric field, formula (2‐12) reduces to

$$
\vec{P} = \mathbf{C}\vec{E}\tag{2-18}
$$

For <sup>∞</sup> =1+ 0 , formula (2‐18) can be written as follows,

$$\mathbf{C} = \varepsilon\_0 [\varepsilon(\infty) - 1] \tag{2-19}$$

Compute the curl of formula (2‐11) and solve the simultaneous equations of (2‐12) and electrostatic equations ∇ × E = 0,

$$A = -a\_0^2\tag{2-20}$$

When the system is under the static electric field, u¨ = 0, and formula (2‐11) reduces to

$$
\vec{\mu} = -\frac{B}{A}\vec{E}\tag{2-21}
$$

Take formula (2‐21) into (2‐12),

= +

=- +

28 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

*k Ze <sup>A</sup>*

e

<sup>W</sup> <sup>=</sup> W - 0 0

3

*Ze <sup>B</sup>*

e

e a

e

e

When the system is under the high‐frequency electric field, formula (2‐12) reduces to

= r r

= ¥ e e

> = w

Compute the curl of formula (2‐11) and solve the simultaneous equations of (2‐12) and

, formula (2‐18) can be written as follows,

 <sup>=</sup> W - 0 0 3 3

e

 <sup>=</sup> W - 0 0 3 3

(3 )

e

 a

W - 2 2 <sup>0</sup> (3 )

> a

 a

> a

formula (2‐11) and (2‐12) are the Huang equations, which are the basic equations of describing the vibrations of long wave in the polar crystals. From the formula (2‐14) and (2‐16), one can

where

find that,

For <sup>∞</sup> =1+

 0

electrostatic equations ∇ × E = 0,

r r <sup>r</sup> *P CE Du* (2‐12)

*M M* (2‐13)

*<sup>M</sup>* (2‐14)

*C* (2‐15)

*Ze <sup>D</sup>* (2‐16)

<sup>W</sup> *B D* <sup>=</sup> *<sup>M</sup>* (2‐17)

*P CE* (2‐18)

<sup>0</sup> *C* [ ( ) 1] (2‐19)

<sup>2</sup> *A* <sup>0</sup> (2‐20)

$$
\vec{P} = (\mathbf{C} - \frac{BD}{A})\vec{E} \tag{2-22}
$$

Replace the electrostatic equation,

$$
\vec{P} = [\varepsilon(0) - 1] \varepsilon\_0 \vec{E} \tag{2-23}
$$

And take formula (2‐23) and (2‐20) into (2‐22),

$$BD = [\varepsilon(0) - \varepsilon(\infty)]\varepsilon\_0 \alpha\_0^2 \tag{2-24}$$

Solve the simultaneous equations of (2‐17) and (2‐24) can obtain

$$B = (\frac{\Omega}{\overline{M}})^{\frac{1}{2}} \{ [\varepsilon(0) - \varepsilon(\infty)] \varepsilon\_0 \}^{\frac{1}{2}} o\_0 \tag{2-25}$$

$$D = (\frac{\tilde{M}}{\Omega})^{\frac{1}{2}} \langle [\varepsilon(0) - \varepsilon(\infty)] \varepsilon\_0 \rangle^{\frac{1}{2}} a\_0 \tag{2-26}$$

Solve two simultaneous Maxwell and Huang equations,

$$
\nabla \times \vec{E} = -\mu\_0 \frac{\partial \vec{H}}{\partial t} \tag{2-27a}
$$

$$
\nabla \times \overrightarrow{H} = \frac{\partial}{\partial t} \left( \varepsilon\_0 \overrightarrow{E} + \overrightarrow{P} \right) \tag{2-27b}
$$

$$
\nabla \cdot \vec{D} = 0 \tag{2-27c}
$$

$$
\nabla \cdot \vec{H} = 0 \tag{2-27d}
$$

Assume the solution forms are

$$
\vec{u} = \vec{u}\_0 e^{i(q \cdot r - \omega t)} \tag{2-28a}
$$

$$
\vec{P} = \vec{P}\_0 e^{i(q \cdot r - \omega t)} \tag{2-28b}
$$

$$
\vec{E} = \vec{E}\_0 e^{i(q \cdot r - \alpha t)} \tag{2-28c}
$$

$$
\overrightarrow{H} = \overrightarrow{H}\_0 e^{i(q \cdot r - \omega t)} \tag{2-28d}
$$

Take (2‐28) into the Huang and Maxwell equations,

$$
\vec{P}\_0 = \mathbf{I} - \frac{BD}{A + o\nu^2} + \mathbf{C} \,\mathbf{J} \,\vec{E}\_0 \tag{2-29}
$$

$$[(\vec{q} \cdot \vec{E}\_0)] \varepsilon\_0 + \mathbb{C} - \frac{BD}{A + o\nu^2} \mathbf{l} = \mathbf{0} \tag{2-30}$$

To the longitudinal wave, <sup>q</sup> · E0 ≠ 0, (2‐30) reduces to

$$
\varepsilon\_0 + \mathbb{C} - \frac{BD}{A + \alpha^2} = 0 \tag{2-31}
$$

Take (2‐19) (2‐20) (2‐25) (2‐26) into (2‐31)

$$
\alpha\_{\rm LO}^2 = \frac{\varepsilon(0)}{\varepsilon(\infty)} \alpha\_0^2 \tag{2-32}
$$

Equation (2‐23) is the dispersion relations of longitudinal wave, which is commonly called Lyddane‐Sachs‐Teller (LST) relationship. LST relation indicates that the frequency of longitu‐ dinal wave is a constant and independent on the wave vector.

Similarly, to the transverse wave, <sup>q</sup> · E0 = 0, solve the simultaneous equations of Maxwell and Huang equations,

$$\frac{q^2}{\mu\_0 a o} = o\left(\varepsilon\_0 + C - \frac{BD}{A + o^2}\right) \tag{2-33}$$

Replace the values of *A*, *B*, *C*, and *D* into (2‐33),

$$\frac{c^2}{\alpha^2}\boldsymbol{q}^2 = \boldsymbol{\varepsilon}\{\boldsymbol{\alpha}\} + \frac{\boldsymbol{\varepsilon}(\boldsymbol{0}) - \boldsymbol{\varepsilon}\{\boldsymbol{\alpha}\}}{\alpha\_0^2 - \alpha^2}\boldsymbol{\alpha}\_0^2\tag{2-34}$$

Equation (2‐34) is the dispersion relations of transverse wave. One can find that the frequency of transverse is dependent on the value of wave vector q , but independent on its direction [4, 5].

#### **2.2. Dispersion relations**

(2‐28a)

(2‐28b)

(2‐28c)

(2‐28d)

Assume the solution forms are

Take (2‐28) into the Huang and Maxwell equations,

To the longitudinal wave, <sup>q</sup> · E0 ≠ 0, (2‐30) reduces to

Take (2‐19) (2‐20) (2‐25) (2‐26) into (2‐31)

Huang equations,

w

× +- =

w

+

w

 w

Equation (2‐23) is the dispersion relations of longitudinal wave, which is commonly called Lyddane‐Sachs‐Teller (LST) relationship. LST relation indicates that the frequency of longitu‐

Similarly, to the transverse wave, <sup>q</sup> · E0 = 0, solve the simultaneous equations of Maxwell and

æ ö = +- ç ÷ è ø +

0 2

w

0 (0)

+- = <sup>+</sup> <sup>0</sup> <sup>2</sup> <sup>0</sup> *BD <sup>C</sup>*

e

e <sup>=</sup> ¥ 2 2

w

w e

*<sup>q</sup> BD <sup>C</sup>*

dinal wave is a constant and independent on the wave vector.

m w

0

2

*<sup>A</sup>* (2‐29)

*<sup>A</sup>* (2‐31)

( ) *LO* (2‐32)

*<sup>A</sup>* (2‐33)

0 0 <sup>2</sup> ( )[ ] 0 *BD qE C <sup>A</sup>* (2‐30)

=- + + r r 0 0 <sup>2</sup> [ ] *BD <sup>P</sup> C E*

e

30 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

r r

e

One‐dimensional diatomic model can be regarded as the simple double lattice. In the simple linear chain model, it is assumed that only nearest neighbors are coupled, and that the interaction between these atoms is described by Hooke's law; the spring constant *α* is taken to be that of a harmonic oscillator. Thus, the kinematical equations are established,

$$\mathbf{m}\ddot{\mathbf{u}}\_{2n} = -\beta(2\ddot{\mathbf{u}}\_{2n} - \ddot{\mathbf{u}}\_{2n+1} - \ddot{\mathbf{u}}\_{2n-1}) \tag{2-35a}$$

$$\mathbf{M}\ddot{\mathbf{\ddot{u}}}\_{2n+1} = -\mathcal{J}(2\mathbf{\ddot{u}}\_{2n+1} - \mathbf{\ddot{u}}\_{2n+2} - \mathbf{\ddot{u}}\_{2n})\tag{2-35b}$$

where *m* and *M* are the mass of the adjacent atoms 2 <sup>1</sup>, <sup>u</sup> 2n, <sup>u</sup> 2n + 1, , <sup>u</sup> 2n + 2 are the displacements of the atoms at the position of 2*n*‐1, 2*n*, 2*n* + 1, and 2*n* + 2, respectively. is the force constant. The solution forms of (2‐35) can be written as follows

$$
\vec{u}\_{2n} = A\_1 e^{l[(\omega t - (2n)\vec{a} \cdot \vec{q})} \tag{2-36a}
$$

$$
\overrightarrow{u}\_{2n+1} = A\_2 e^{l[(\omega t - (2n+1)\overline{a}\cdot\overline{q}]} \tag{2-36b}
$$

where q is the phonon wave vector and ω is its frequency. Take formulas (2‐36a) and (2‐36b) into formulas (2‐35a) and (2‐35b),

$$-m o^2 A\_1 = \beta (e^{-\tilde{\alpha} \cdot q} + e^{\tilde{\alpha} \cdot q}) A\_2 - 2\beta A\_1 \tag{2-37}$$

$$-M\alpha^2 A\_z = \beta(e^{-\vec{u}\cdot\vec{q}} + e^{\vec{u}\cdot\vec{q}})A\_1 - \mathcal{D}\beta A\_z \tag{2-38}$$

Eliminating *A*1 and *A*2,

$$\rho \alpha^2 = \beta \frac{M+m}{Mm} \left\{ 1 \pm \left[ 1 - \frac{4Mm}{\left(M+m\right)^2} \sin^2(\vec{a} \cdot \vec{q}) \right]^{p\_2'} \right\} \tag{2-39}$$

The relationship between frequency and wave vector is commonly called dispersion relation [5].

#### **3. Basic properties of phonons in wurtzite structure**

In this section, we discuss the phonon effects in wurtzite structure. The crystalline structure of a wurtzite material is depicted in **Figure 2**. There are four atoms in the unit cell. Thus, the total number of optical modes in the long‐wavelength limit is nine: three longitudinal optic (LO) and six transverse optic (TO). In these optical modes, there are only three polar optical vibration modes. According to the group theory, the wurtzite crystal structure belongs to the space group C6v <sup>4</sup> , and the phonon modes at Γ point of the Brillouin zone are represented by the following irreducible representations:

$$
\Gamma = \mathfrak{D}A\_1 + \mathfrak{D}B + \mathfrak{D}E\_1 + \mathfrak{D}E\_2
$$

Due to the anisotropy of wurtzite structure, the vibrational frequency of oscillates parallel and perpendicular to the optical axis is denoted by ωeT and ωoT, and the corresponding dielectric constants are denoted by ε es, εe∞ and <sup>ε</sup> os, εo∞. The corresponding components can be written as the form of Huang equations, and the dispersion relation can be obtained by solving two simultaneous equations of Maxwell and Huang equations.

$$\frac{\sigma^2 \boldsymbol{c}^2}{\boldsymbol{\alpha}^2} = \boldsymbol{\varepsilon}\_0 = \frac{\boldsymbol{\alpha}\_{\circ T}^2 \boldsymbol{\varepsilon}\_{\boldsymbol{\alpha}} - \boldsymbol{\alpha}^2 \boldsymbol{\varepsilon}\_{\boldsymbol{\alpha}\boldsymbol{\alpha}}}{\boldsymbol{\alpha}\_{\circ T}^2 - \boldsymbol{\alpha}^2} \tag{3-1}$$

$$\frac{q^2c^2}{\alpha^2} = \mathcal{E}\_o = \frac{(\frac{\alpha^2\_{\ell\Gamma}\mathcal{E}\_{os} - \alpha^2\mathcal{E}\_{co}}{\alpha\mathcal{o}\_{\ell\Gamma}^2 - \alpha^2})(\frac{\alpha\mathcal{o}\_{\ell\Gamma}^2\mathcal{E}\_{os} - \alpha^2\mathcal{E}\_{oo}}{\mathcal{o}\_{\ell\Gamma}^2 - \alpha^2})}{(\frac{\alpha\mathcal{o}\_{\ell\Gamma}^2\mathcal{E}\_{os} - \alpha^2\mathcal{E}\_{oo}}{\mathcal{o}\_{\ell\Gamma}^2 - \alpha^2})\cos^2\theta + (\frac{\alpha\mathcal{o}\_{\ell\Gamma}^2\mathcal{E}\_{os} - \alpha^2\mathcal{E}\_{oo}}{\mathcal{o}\_{\ell\Gamma}^2 - \alpha^2})\sin^2\theta} \tag{3-2}$$

where ε <sup>o</sup> and is the dielectric constants of ordinary and extraordinary wave, is the included angle between wave vector and optical axis.

When the wave vector is parallel to the optical axis, θ=0, formula (3‐2) reduce to

Investigations of Phonons in Zinc Blende and Wurtzite by Raman Spectroscopy http://dx.doi.org/10.5772/64194 33

$$\varepsilon\_{\theta} = \frac{\alpha\_{\circlearrow}^2 \varepsilon\_{\circlearrow} - \alpha^2 \varepsilon\_{\circlearrow}}{\alpha\_{\circlearrow}^2 - \alpha^2} \tag{3-3}$$

which is the same as formula (3‐1). When the wave vector is perpendicular to the optical axis, θ = 90 , formula (3‐2) reduces to

$$
\varepsilon\_{\theta} = \frac{\alpha\_{\ell\ell}^2 \varepsilon\_{\rm es} - \alpha^2 \varepsilon\_{\rm oo}}{\alpha\_{\ell\Gamma}^2 - \alpha^2} \tag{3-4}
$$

Formula (3‐4) indicates that the extraordinary wave is transverse wave when the wave vector is perpendicular to the optical axis.

When q ≫ ω/c, formulas (3‐1) and (3‐2) can be rewritten as follows,

$$
\alpha = \alpha\_{\rho \Gamma} \tag{3-5}
$$

and

w b

[5].

C6v

irreducible representations:

constants are denoted by ε

<sup>+</sup> ì ü = ±- í ý <sup>×</sup>

The relationship between frequency and wave vector is commonly called dispersion relation

In this section, we discuss the phonon effects in wurtzite structure. The crystalline structure of a wurtzite material is depicted in **Figure 2**. There are four atoms in the unit cell. Thus, the total number of optical modes in the long‐wavelength limit is nine: three longitudinal optic (LO) and six transverse optic (TO). In these optical modes, there are only three polar optical vibration modes. According to the group theory, the wurtzite crystal structure belongs to the space group

<sup>4</sup> , and the phonon modes at Γ point of the Brillouin zone are represented by the following

= ++ + 1 12 2 22 2 *A BE E*

Due to the anisotropy of wurtzite structure, the vibrational frequency of oscillates parallel and perpendicular to the optical axis is denoted by ωeT and ωoT, and the corresponding dielectric

as the form of Huang equations, and the dispersion relation can be obtained by solving two

w e we

> ww

¥ - = = - 2 2 2 2 2 0 2 2

*oT os o oT*

> w e we


( )( )

*eT es e oT os o oT oT eT es e oT os o eT oT*

2 22 2

 ww

> w w

2 2

¥ ¥

*q c* (3‐2)

 w e we

<sup>o</sup> and is the dielectric constants of ordinary and extraordinary wave, is the included

¥ ¥

q

( )cos ( )sin

2 2 2 2

e

ww

When the wave vector is parallel to the optical axis, θ=0, formula (3‐2) reduce to


2 2 22 22 2 22 2 2

r r <sup>1</sup> 2 2 <sup>2</sup>

*M m Mm*

32 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**3. Basic properties of phonons in wurtzite structure**

G

es, εe∞ and <sup>ε</sup>

w

w e we

simultaneous equations of Maxwell and Huang equations.

q

 w e we

> w w

e

angle between wave vector and optical axis.

w

where ε

î þ +

2 <sup>4</sup> 1 [1 sin ( )] ( )

*a q Mm M m* (2‐39)

os, εo∞. The corresponding components can be written

 q

*q c* (3‐1)

$$(\frac{\alpha \alpha\_{\rm \ell 1}^2 \mathfrak{z}\_{\rm cs} - \alpha^2 \mathfrak{z}\_{\rm cs \bullet}}{\alpha \alpha\_{\rm \ell \top}^2 - \alpha^2}) \cos^2 \theta + (\frac{\alpha \alpha\_{\rm \ell 1}^2 \mathfrak{z}\_{\rm cs} - \alpha^2 \mathfrak{z}\_{\rm cs \bullet}}{\alpha \alpha\_{\rm \ell \top}^2 - \alpha^2}) \sin^2 \theta = 0 \tag{3-6}$$

Formula (3‐5) indicates that frequency of ordinary phonon is independent on the wave vector *q*. Formula (3‐6) indicates that the frequency of extraordinary phonon is dependent on the orientation of the wave vector, but independent on its value.

It is most convenient to divide uniaxial crystals into two categories: (a) the electrostatic forces dominate over the anisotropy of the interatomic forces and (b) the short‐range interatomic forces are much greater than the electrostatic forces. It has been turned out that crystals with the wurtzite symmetry fall into the first category. In this case, ωeT − ωoT <sup>≪</sup> ωeL − ωoT and ωoL − ωoT , <sup>ε</sup> e∞ ≈ εo∞ = ε∞, formula (3‐5) reduces to

$$(\frac{\alpha\_{el}^2 - \alpha^2}{\alpha\_{el}^2 - \alpha^2})\cos^2\theta + (\frac{\alpha\_{el}^2 - \alpha^2}{\alpha\_{oT}^2 - \alpha^2})\sin^2\theta = 0\tag{3-7}$$

thus,

$$
\rho \alpha^2 \approx \left. \phi\_{\iota \Gamma}^2 \sin^2 \theta + \left. \phi\_{\iota \Gamma}^2 \cos^2 \theta \right| \tag{3-8}
$$

and

$$
\rho \alpha^2 \approx \alpha\_{\rm d}^2 \sin^2 \theta + \alpha\_{\rm eT}^2 \cos^2 \theta \tag{3-9}
$$

## **4. Raman mode in zinc blende and wurtzite structure**

Raman spectroscopy is a non‐destructive technical tool used to gain information about the phonon behavior of the crystal lattice through the frequency shift of the inelastically scattered light from the near surface of the sample. It is well known that different crystal phases have different vibrational behaviors, so the measured Raman shifts of different phases are mostly unique and can be seen as fingerprints for the respective phases. This provides the possibility of detecting different phases in a sample. It has been developed to be a versatile tool for the characterization of semiconductors leading to detailed information on crystal structure, phonon dispersion, electronic states, composition, strain, and so on of semiconductor nano‐ structures.

In a zinc blende structure, the space group of the cubic unit cell is *F*43*m*(Td 2) containing four formula units. The primitive unit cell contains only one formula per unit cell, and hence, there are three optical branches to the phonon dispersion curves. As there is no center of inversion in the unit cell, the zone‐center transverse optic (TO) and longitudinal optic (LO) optic modes are Raman active. The optic mode is polar so that the macroscopic field lifts the degeneracy, producing a non‐degenerate longitudinal mode that is at a higher frequency than the two transverse modes.

The wurtzite crystal structure belongs to the space group C6v 4 and group theory predicts zone‐ center optical modes are *A*1, 2*B*1, *E*1, and 2*E*2. The *A*1 and *E*1 modes and the two *E*2 modes are Raman active, whereas the *B* modes are silent. The *A* and *E* modes are polar, resulting in a splitting of the LO and the TO modes [6].

## **5. Phonons in ZnSe, Ge, SnS2, MoS2, and Cu2ZnSnS4 nanocrystals**

In addition to the attached references, this chapter is primarily written on the basis of our research works. Here, we select ZnSe, Ge nanowires and CdSe/Ge‐based nanowire hetero‐ structures, two‐dimensional semiconductors SnS2 and MoS2, and candidate absorber materials of thin‐film solar cells Cu2ZnSnS4. These examples will help us to understand the phonons behaviors in nanostructures.

It is well known that ZnSe has two structures: cubic zinc blende (ZB) and hexagonal wurtzite (WZ) due to the difference of the stacking sequence of successive layers, whereas Ge has diamond structure. SnS2 and MoS2 belong to the wide family of compounds with layered structures. SnS2 crystal is isostructural to the hexagonal CdI2‐type structure. MoS2 usually consists of a mixture of two major polytypes of similar structure, 2H (hexagonal) and 3R (rhombohedral), with the former being more abundant. As for quaternary Cu2ZnSnS4 (CZTS), the parent binary II‐VI semiconductors adopt the cubic zinc blende structure, and the ternary I‐III‐VI2 compounds can be generated by mutating the group II atoms into pairs of group I and III atoms. The quaternary CZTS materials are formed by replacing the two In (III) atoms with Zn (II) and Sn (IV), respectively (see **Figure 5**).

**Figure 5.** Evolution of multinary compounds.

and

structures.

transverse modes.

w w

34 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**4. Raman mode in zinc blende and wurtzite structure**

In a zinc blende structure, the space group of the cubic unit cell is *F*43*m*(Td

The wurtzite crystal structure belongs to the space group C6v

splitting of the LO and the TO modes [6].

behaviors in nanostructures.

 qw

Raman spectroscopy is a non‐destructive technical tool used to gain information about the phonon behavior of the crystal lattice through the frequency shift of the inelastically scattered light from the near surface of the sample. It is well known that different crystal phases have different vibrational behaviors, so the measured Raman shifts of different phases are mostly unique and can be seen as fingerprints for the respective phases. This provides the possibility of detecting different phases in a sample. It has been developed to be a versatile tool for the characterization of semiconductors leading to detailed information on crystal structure, phonon dispersion, electronic states, composition, strain, and so on of semiconductor nano‐

formula units. The primitive unit cell contains only one formula per unit cell, and hence, there are three optical branches to the phonon dispersion curves. As there is no center of inversion in the unit cell, the zone‐center transverse optic (TO) and longitudinal optic (LO) optic modes are Raman active. The optic mode is polar so that the macroscopic field lifts the degeneracy, producing a non‐degenerate longitudinal mode that is at a higher frequency than the two

center optical modes are *A*1, 2*B*1, *E*1, and 2*E*2. The *A*1 and *E*1 modes and the two *E*2 modes are Raman active, whereas the *B* modes are silent. The *A* and *E* modes are polar, resulting in a

In addition to the attached references, this chapter is primarily written on the basis of our research works. Here, we select ZnSe, Ge nanowires and CdSe/Ge‐based nanowire hetero‐ structures, two‐dimensional semiconductors SnS2 and MoS2, and candidate absorber materials of thin‐film solar cells Cu2ZnSnS4. These examples will help us to understand the phonons

It is well known that ZnSe has two structures: cubic zinc blende (ZB) and hexagonal wurtzite (WZ) due to the difference of the stacking sequence of successive layers, whereas Ge has diamond structure. SnS2 and MoS2 belong to the wide family of compounds with layered

**5. Phonons in ZnSe, Ge, SnS2, MoS2, and Cu2ZnSnS4 nanocrystals**

 q

» + 2 22 2 2 sin cos *oL eT* (3‐9)

2) containing four

4 and group theory predicts zone‐

We use Raman spectroscopy to identify crystal structure of ZnSe one‐dimensional material (**Figure 6**). In sample S3, the Raman peaks at 204 and 251 cm‐1 are attributed to the scatterings of the transverse optic (TO) and longitudinal optic (LO) phonon modes of ZnSe, respectively. A strong peak at 232 cm‐1, between the TO and LO phonons, is thought to be surface mode. The Raman peak at ∼176 cm‐1 is attributed to the hexagonal phase *E*1(TO) mode of ZnSe, which is inhibited in Raman spectrum (RS) of ZB ZnSe. Compared with S3, Raman peaks at 205.6 (TO mode) and 252 cm‐1 (LO mode) of S1 show tiny blue‐shift. However, in S1, there is no Raman peak corresponding to the surface mode, as well as *E*<sup>l</sup> (TO) mode, which is suppressed in the

**Figure 6.** Room temperature Raman spectra of ZnSe. S1, S2, and S3 stand for ZB, coexist of ZB and WZ, WZ ZnSe nanostructure.

ZB phase. This indicates the existence of ZB phase in S1. Thus, structure of the sample can be shown through RS, and we got S1‐ZB phase, S3‐WZ, S2 the coexist of ZB and WZ [7] (cm‐1).

**Figure 7** shows the room temperature RS of CdSe/Ge‐based nanowires. The LO mode of Ge in CdSe‐Ge (or CdSe‐Ge‐CdSe), ‐CdSe‐Ge core/polycrystalline Ge sheath, and ‐Ge‐GeSe heterostructural nanowires has a downshift by 8, 5, and 2 cm‐1 in comparison with that of the bulk counterpart Ge (299 cm‐1), respectively. With regard to the microstructure of heterostruc‐ tural nanowires, the downshift of the LO mode may be caused by tensile stress, which affects the Raman line by a downshift. And the different shift scales are attracted by the different sizes of the Ge subnanowires and Ge nanocrystalline [8].

**Figure 7.** Raman spectrum of (a) CdSe‐Ge biaxial nanowires and CdSe‐Ge‐CdSe triaxial nanowires. (b) CdSe‐Ge biaxial nanowire core/polycrystalline Ge sheath heterostructures. (c) Ge‐GeSe biaxial heterostructure nanowires.

The individual layer in SnS2 is known as an S‐Sn‐S sandwich bonded unit. Each Sn atom is octahedrally coordinated with six nearest neighbor sulfur atoms, while each S atom is nest‐ ed at the top of a triangle of Sn atoms. The sandwich layers in the elementary cell occur along the *c* axis and bonded together by Vander Waals forces. The normal modes of vibra‐ tion in SnS2 are given by the irreducible representations of the *D*3d point group at the center of the Brillouin zone: Γ = *A*lg + *E*g + 2*A*2u + 2*E*2u. Two Raman‐active modes (*A*1g and *E*g) and two IR‐active modes (*A*2u and *E*u) are found. In view of the existence of an inversion center, the IR‐ and Raman‐active modes are mutually exclusive. On the other hand, six atoms in the unit cell of SnS2 extend over two sandwich layers. Eighteen normal vibration modes can be represented by the following irreducible form: Γ = 3*A*1 + 3*B*1 + 3*E*1 + 3*E*2. Based on the analysis above, there are six modes, which are both IR‐ and Raman‐active, belonging to *A*1 and *E*<sup>l</sup> , and three Raman‐active modes belonging to *E*2. The *B*1 modes are silent, while the three acoustic modes belong to *A*1 and *E*1 [9].

The RS of β‐SnS2 nanocrystal is illustrated in our former work [10]. The spectra show one first‐ order peak at 312 cm‐1 that corresponding to *A*1g mode. The RS of as‐prepared SnS2 shows a slight redshift in comparison with that of bulk materials (peak at 317 cm‐1). The redshift of phonon peaks is due to spatial confinement of phonon modes. The first‐order *E*g mode (peak at 208 cm‐1) cannot be observed, which likely results from a nanosize effect. A wide peak between 450 and 750 cm‐1, which only observed in the bulk materials at lower temperature, may be attributed to second‐order effects.

ZB phase. This indicates the existence of ZB phase in S1. Thus, structure of the sample can be shown through RS, and we got S1‐ZB phase, S3‐WZ, S2 the coexist of ZB and WZ [7] (cm‐1).

36 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 7** shows the room temperature RS of CdSe/Ge‐based nanowires. The LO mode of Ge in CdSe‐Ge (or CdSe‐Ge‐CdSe), ‐CdSe‐Ge core/polycrystalline Ge sheath, and ‐Ge‐GeSe heterostructural nanowires has a downshift by 8, 5, and 2 cm‐1 in comparison with that of the bulk counterpart Ge (299 cm‐1), respectively. With regard to the microstructure of heterostruc‐ tural nanowires, the downshift of the LO mode may be caused by tensile stress, which affects the Raman line by a downshift. And the different shift scales are attracted by the different sizes

**Figure 7.** Raman spectrum of (a) CdSe‐Ge biaxial nanowires and CdSe‐Ge‐CdSe triaxial nanowires. (b) CdSe‐Ge biaxial

The individual layer in SnS2 is known as an S‐Sn‐S sandwich bonded unit. Each Sn atom is octahedrally coordinated with six nearest neighbor sulfur atoms, while each S atom is nest‐ ed at the top of a triangle of Sn atoms. The sandwich layers in the elementary cell occur along the *c* axis and bonded together by Vander Waals forces. The normal modes of vibra‐ tion in SnS2 are given by the irreducible representations of the *D*3d point group at the center of the Brillouin zone: Γ = *A*lg + *E*g + 2*A*2u + 2*E*2u. Two Raman‐active modes (*A*1g and *E*g) and two IR‐active modes (*A*2u and *E*u) are found. In view of the existence of an inversion center, the IR‐ and Raman‐active modes are mutually exclusive. On the other hand, six atoms in the unit cell of SnS2 extend over two sandwich layers. Eighteen normal vibration modes can be represented by the following irreducible form: Γ = 3*A*1 + 3*B*1 + 3*E*1 + 3*E*2. Based on the analysis above, there are six modes, which are both IR‐ and Raman‐active, belonging to *A*1 and *E*<sup>l</sup>

and three Raman‐active modes belonging to *E*2. The *B*1 modes are silent, while the three

The RS of β‐SnS2 nanocrystal is illustrated in our former work [10]. The spectra show one first‐ order peak at 312 cm‐1 that corresponding to *A*1g mode. The RS of as‐prepared SnS2 shows a slight redshift in comparison with that of bulk materials (peak at 317 cm‐1). The redshift of phonon peaks is due to spatial confinement of phonon modes. The first‐order *E*g mode (peak

,

nanowire core/polycrystalline Ge sheath heterostructures. (c) Ge‐GeSe biaxial heterostructure nanowires.

of the Ge subnanowires and Ge nanocrystalline [8].

acoustic modes belong to *A*1 and *E*1 [9].

The phonon dispersion of single‐layer MoS2 has three acoustic and six optical branches derivatized from the nine vibrational modes at the Γ point. The three acoustic branches are the in‐plane longitudinal acoustic (LA), the transverse acoustic (TA), and the out‐of‐plane acoustic (ZA) modes. The six optical branches are two in‐plane longitudinal optical (LO1 and LO2), two in‐plane transverse optical (TO1 and TO2), and two out‐of‐plane optical (ZO1 and ZO2) branches.

For 2L and bulk MoS2, there are 18 phonon branches, which are split from nine phonon branches in 1LMoS2. The phonon dispersions of 1L and bulk MoS2 are very similar, except for the three new branches below 100 cm‐1 in bulk because of interlayer vibrations. There are similar optical phonon dispersion curves for 1L, 2L, and bulk MoS2 because of the weak Vander Waals interlayer interactions in 2L and bulk MoS2 [11].

Raman spectroscopy is also used to accurately identify the layer number of MoS2. The frequency difference between out‐of‐plane *A*1g and in‐plane *E*2g<sup>1</sup> mode of MoS2 is denoted as . . From monolayer to bulk MoS2, monotonically increases from 19.57 cm‐1 to 25.5 cm‐1. In our work [12], two strong peak at ∼379 cm‐1 and ∼402 cm‐1 can be assigned as in‐plane *E*2g<sup>1</sup> mode and out‐of‐plane *A*1g mode of MoS2, respectively, which has a redshift in comparison with that of the bulk MoS2. The is about 23 cm‐1, indicating that the as‐grown MoS2 contains tri‐layer MoS2.

The phonon dispersion and density‐of‐states curves along the principal symmetry directions of kesterite CZTS were calculated using a density functional theory by Khare et al. [13]. The phonon states around 50–160 cm‐1 are mainly composed of vibrations of the three metal cations with some contribution from the sulfur anions. The phonon states around 250–300 cm‐1 are mainly composed of vibrations of the Zn cations and S anions with some contribution from the Cu cations. The phonon states from 310 to 340 cm‐1 are mainly a result of vibrations of S anions, whereas those from 340 to 370 cm‐1 are composed of the vibrations of Sn cations and S anions.

To more exactly confirm secondary phases in Cu2‐II‐IV‐VI4 semiconductors, Raman scattering studies have been extensively performed. From the vibrational point of view, the zone‐center phonon representation of the kesterite structure space group *I*4 is constituted of 21 optical modes: Γ = 3*A* + 6*B* + 6*E*1 + 6*E*2, where 12*B*, *E*1, and *E*2 modes are infrared active, whereas 15*A*, *B*, *E*1, and *E*2 modes are Raman active. According to our work [14], the single peak at about 328 cm‐1 of Raman spectrum of the as‐prepared CZTS nanocrystals can be assigned to breathing mode of sulfur atoms around metal ions in CZTS. Moreover, Raman spectrum of CZTS has about 8 cm‐1 redshifts compared with that of the responding bulk counterpart which may be due to a smaller size effect.

In our work of fabrication of Cu2ZnSnSxSe4‐x solid solution nanocrystallines [15], RS revealed that vibrating modes were modulated by *x*‐values. The peak position of 170, 189, and 229 cm‐1 shifted to higher frequency with increasing *x*‐value in CZTSSe, respectively. Those peaks completely disappeared when *x* = 4. Moreover, a wide peak located at about 330 cm‐1 appeared when *x* > 0 and the relative intensity increased with increasing *x*‐value. Such results indicate that Se elements were gradually replaced by S elements in CZTSSe solid solution system.

## **Acknowledgements**

This work was supported by the National Natural Science Foundation of China under Grant Nos. 11174049 and 61376017.

## **Author details**

Lin Sun, Lingcong Shi and Chunrui Wang\*

\*Address all correspondence to: crwang@dhu.edu.cn

Department of Applied Physics, Donghua University, Shanghai, China

## **References**


[8] Cai, J. Controllable synthesis and vibrating properties of CdSe based heterostructure nanowires. Master's thesis. Donghua University. 2011.

completely disappeared when *x* = 4. Moreover, a wide peak located at about 330 cm‐1 appeared when *x* > 0 and the relative intensity increased with increasing *x*‐value. Such results indicate that Se elements were gradually replaced by S elements in CZTSSe solid solution system.

38 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

This work was supported by the National Natural Science Foundation of China under Grant

[1] Xu, J., Wang, C., Wu, B., Xu, X., Chen, X., Oh, H., Baek, H., & Yi, G. C. Twinning effect on photoluminescence spectra of ZnSe nanowires. Journal of Applied Physics.

[2] Xu, J., Wang, C., Lu, A., Wu, B., Chen, X., Oh, H., Baek, H., Yi, G., & Ouyang, L. Photoluminescence of excitons and defects in ZnSe‐based longitudinal twinning nanowires. Journal of Physics D: Applied Physics. 2014;47(48):485302. doi:

[3] Xu, J., Lu, A., Wang, C., Zou, R., Liu, X., Wu, X., Wang, Y., Li, S., Sun, L., Chen, X., Oh, H., Baek, H., Yi, G., & Chu, J. ZnSe‐based longitudinal twinning nanowires. Advanced

[4] Zhang, G. et al. Lattice Vibration Spectroscopy. Beijing: Higher Education Press; 2001

[6] Stroscio, M. A., & Dutta, M. Phonons in Nanostructures. Cambridge: Cambridge

[7] Wang, H. Luminescence and vibrating properties of Zn‐based group II‐VI nanostruc‐

[5] Huang, K., & Han, R. Solid‐State Physics. Beijing: Higher Education Press; 1988.

Engineering Materials. 2014;16(4):459–465. doi:10.1002/adem.201300405.

**Acknowledgements**

Nos. 11174049 and 61376017.

Lin Sun, Lingcong Shi and Chunrui Wang\*

\*Address all correspondence to: crwang@dhu.edu.cn

2014;116(17):174303. doi:10.1063/1.4900850.

tures. Master's thesis. Donghua University. 2012.

10.1088/0022‐3727/47/48/485302.

University Press; 2005.

Department of Applied Physics, Donghua University, Shanghai, China

**Author details**

**References**


Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Structural Characterization of Lithium Niobate Nanoparticles Prepared by the Sol-Gel Process, Using X-Ray and Raman Spectroscopy and Scanning Electron Microscopy Structural Characterization of Lithium Niobate Nanoparticles Prepared by the Sol-Gel Process, Using X-Ray and Raman Spectroscopy and Scanning Electron Microscopy**

Pedro R.S. Prezas and Manuel P.F. Graça

Pedro R.S. Prezas and Manuel P.F. Graça

Additional information is available at the end of the chapter Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/64395

#### **Abstract**

40 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

The widespread use of lithium niobate (LN) in several technological applications, notably in optical and electrooptical systems, is a consequence of its remarkable piezoelectric, electrooptical, photoelastic, acousto-optic, and nonlinear optical coefficients. In this chapter, the structural and electrical characterization of LN nanosized particles synthesized by the Pechini route is discussed. Compared to solidstate reaction processes, wet chemistry processes can be advantageous alternatives for the synthesis of polycrystalline LN, because they require lower processing temperatures, and thus the loss of stoichiometry and formation of secondary phases can be minimized. The powders obtained by drying the gel (base powder) were heat-treated for 4 h at temperatures between 400 and 1000°C, according to the differential thermal analysis (DTA) results. It was found that the powders sintered at 450°C contain only the LN phase, while those heat-treated at 500°C already contain the secondary LiNb3O8 phase. The structural and electrical characterization of the samples sintered at 450°C, for different times, was performed using X-ray diffraction (XRD) in conjunction with Rietveld refinement, Raman spectroscopy, scanning electron microscopy (SEM), and impedance spectroscopy in the temperature range between 200 and 360 K and in the frequency range between 100 Hz and 1 MHz and by measuring the ac and dc conductivities.

**Keywords:** lithium niobate, structural properties, X-ray spectroscopy, Raman spectroscopy, electrical properties, lithium triniobate, sol-gel process

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

## **1. Introduction**

Lithium niobate (LiNbO3, LN) is a well-known artificially synthesized ferroelectric material with considerable technological importance, being in competition with barium titanate (BaTiO3, BTO) in several high-tech applications. In fact, an inspection of the number of publications related with LN and BTO will show that since the mid-1990s, the number of reports on both materials has been following the same increasing trend, with similar number of publications, reinforcing the importance of LN among the scientific communities. **Table 1** displays some of the main physical properties of single-crystalline LN [1].


**Table 1.** Main physical properties of single-crystalline stoichiometric LN. RT stands for room temperature (generally 300 K) [1–3].

LN single crystals display several excellent properties, such as high piezoelectric, electrooptical, photoelastic, acousto-optic, and nonlinear optical coefficients. They are known to have very low acoustic losses, offering a great versatility as a substrate for integrated optic systems: a considerable number of optical devices have been developed based on LN, such as wave guides, surface acoustic wave (SAW) devices, electrooptical wavelength filters and polarization modulators, nonlinear frequency converters (frequency doubling and second harmonic generation), nonvolatile memories, and ultrafast optical processing systems. Its combination of electrooptical and photogalvanic effects makes it photorefractive without the need of applying an external electrical field, thus being able to be applied in holographic data storage. It offers also the possibility of being easily doped, in a controllable way, with optical-active ionic species, using standard techniques such as ion implantation or thermal diffusion.

**1. Introduction**

Density at RT (g/cm3

300 K) [1–3].

Lithium niobate (LiNbO3, LN) is a well-known artificially synthesized ferroelectric material with considerable technological importance, being in competition with barium titanate (BaTiO3, BTO) in several high-tech applications. In fact, an inspection of the number of publications related with LN and BTO will show that since the mid-1990s, the number of reports on both materials has been following the same increasing trend, with similar number of publications, reinforcing the importance of LN among the scientific communities. **Table 1**

displays some of the main physical properties of single-crystalline LN [1].

42 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

) 4.64

Resistivity, *ρ* (c-axis) (Ω cm) log *ρ* = (7150/T) − 2.823 (at RT) = 1021

**Table 1.** Main physical properties of single-crystalline stoichiometric LN. RT stands for room temperature (generally

LN single crystals display several excellent properties, such as high piezoelectric, electrooptical, photoelastic, acousto-optic, and nonlinear optical coefficients. They are known to have very low acoustic losses, offering a great versatility as a substrate for integrated optic systems: a considerable number of optical devices have been developed based on LN, such as wave guides, surface acoustic wave (SAW) devices, electrooptical wavelength filters and polarization modulators, nonlinear frequency converters (frequency doubling and second harmonic generation), nonvolatile memories, and ultrafast optical processing systems. Its combination of electrooptical and photogalvanic effects makes it photorefractive without the need of applying an external electrical field, thus being able to be applied in holographic data storage. It offers also the possibility of being easily doped, in a controllable way, with optical-active ionic species, using standard techniques such as ion implantation or thermal diffusion.

>1000 (1 kHz)

Melting temperature (°C) 1260 Curie temperature (°C) 1210

Refractive index (ordinary), *n*<sup>0</sup> 2.296 Electrooptical coefficient, r33 (m/V) 30 × 10−12 Transparency window (μm) 0.4–5

Dielectric constant at RT (*ε*′)—c-axis 80 (100 kHz)

Dielectric loss at RT (tan *δ*)—c-axis ≈0 (100 kHz)

Coercive field (at 1210°C) (V/m) 20 Spontaneous polarization at RT (*Ps* [×10−2 C m−2]) 70 Piezoelectric coefficient (d33 [pC/N]) 6 Thermal conductivity at RT (W m−1 K−1) 3.92 The physical properties aforementioned are optimized for the case where LN is grown as a single crystal and with stoichiometric composition. Regarding the stoichiometry, LN has a relatively broad composition range, and therefore, it can be labeled as congruent lithium niobate (cLN, 48.35–48.6 mol% Li2O) and stoichiometric (sLN, ~50 mol% Li2O). **Figure 1** displays the phase diagram of the Li2O-Nb2O5 binary system, showing the possibility of growing pure LN crystals by using 50% up to ~52% of Nb2O5. It also shows the transition of ferroelectric phase to paraelectric by increasing the synthesis temperature and Nb2O5 content. The large majority of LN single crystals are grown by the conventional Czochralski method, which yields cLN single crystals. Some competitor methods have been developed for growing stoichiometric crystals, including the vapor transport equilibration (VTE) method, which is a post-grown procedure [4]. The former is more suitable for thin and small samples, because for larger and thicker crystals, very large solid-state diffusion times are required for the Li/Nb ratio equilibration. To attain larger stoichiometric single crystals, more direct growth methods can be applied, such as the double crucible Czochralski method with an automatic power supply [5, 6] or the high-temperature top-seeded solution growth (HTTSSG) method from the K2O-Li2O-Nb2O5 ternary mixture, which is the one capable of yielding compositions closest to 50 mol% Li2O [5, 7].

The nonlinear and photorefractive properties will generally degrade with the loss of stoichiometry and consequent increase of defects and impurity density. As a matter of fact, the congruent composition range is regarded as having an intrinsic defect structure which is dominated by lithium vacancies, known as the lithium vacancy model, which translates in Eq. (1) [6]:

$$[L\ell\_{L\ell}]\_{1-5\chi}[Nb\_{L\ell}]\_{x}[V\_{L\ell}]\_{4\chi}Nb\_{Nb}O\_3\tag{1}$$

In this model, as depicted in Eq. (1), for every four lithium vacancies created, a niobium ion occupies a lithium network site, assuring electrical charge neutrality. The cLN is not suitable for high-temperature applications, because degradation processes can start to occur for temperatures starting from 300°C [6, 8]. On the other hand, studies show that sLN can be stable

**Figure 1.** Phase diagram of the Li2O-Nb2O5 binary system [3].

up to temperatures of at least 900°C [6, 9], because some properties like the electrical conductivity do not change under thermal cycling up to such temperatures.

As it was aforementioned, the dominant process in the growth of LN single crystals is the Czochralski method. However, this method is known for its technical and economic drawbacks, as well as being time-consuming. Thus, alternative preparation processes have been researched and explored. Solid-state reaction processes generally require high processing temperatures (>1000°C), which lead to the loss of lithium by evaporation [10]. As a consequence, secondary crystalline phases such as Li3NbO4 and LiNb3O8 can be formed, changing the stoichiometry and deteriorating the properties. Wet chemistry methods, such as sol-gel methodologies and hydrothermal methods, can be good alternatives because they require lower processing temperatures, such as calcination and thermal-sintering treatments, and thus the formation of secondary phases can be minimized [10, 11]. Single crystals in the nanometer and micrometer size ranges can be synthesized at low temperatures, such as 240°C, by these methods [11]. When such methods are applied, typically polycrystalline LN samples are produced, i.e., a material composed by small single crystals in the micrometric or nanometric range randomly distributed with no evident preferential orientation. Polycrystalline LN finds a lot of applications, especially as thin films for integrated optic applications, although generally the properties of polycrystalline materials are not as good as their single-crystalline counterpart. For example, the piezoelectric properties of polycrystalline LN are inferior to the single crystal, and in the best case, they might approach them if all of its domains are perfectly orientated. Further, relative to single-crystalline thin films, the grain boundaries in polycrystalline films may lead to increased light scattering and larger optical losses in wave guides, which may reduce their utility and potentiality in some applications [12]. However, their production is cheaper and easier compared with the growth processes for single crystals, and all these cons and drawbacks have to be considered and well balanced for potential applications.

Amorphous LN is also important for some applications. In an amorphous material, there is no long-range order, and the network can be described as distorted unitary cells randomly oriented. LN single crystals and polycrystals have low electrical conductivity (~10−12 S/cm at 500 K for single crystals [13]), and ionic diffusion or mobility is reduced in these materials. However, the amorphous structure is always a more open structure compared with the crystalline composition or, in other words, has a smaller density, which promotes and facilitates the ionic diffusivity, making them suitable for technical application such as solid-state electrolytes for Li-ion batteries. In fact, the reported activation energies for the ionic diffusivity are considerably smaller (half in the 25–150°C temperature range [13]) in amorphous LN.

In this chapter, the structural and electrical characterization of LiNbO3 nanosized particles prepared by the Pechini route, also known in the sol-gel methodologies as the polymeric precursor route, is discussed. The powders obtained by drying the gel (base powder) were heat-treated for 4 h at temperatures between 400 and 1000°C, according to the differential thermal analysis (DTA) results. The sintering temperature revealed to be, as expected, an important parameter in controlling the development of secondary crystalline phases, and it was found that the powders sintered at 450°C contain only the LN phase, while those heattreated at 500°C already contain the secondary LiNb3O8 phase. Their structural characterization was performed using X-ray diffraction (XRD) in conjunction with Rietveld refinement, Raman spectroscopy, and scanning electron microscopy (SEM). The grains observed have sizes lower than 100 nm and an approximately spherical geometry. The electrical characterization of pellets made from the base powder heat-treated at 450°C was made by measuring the dc and ac conductivities and measuring the complex impedance (*Z*\*) in the temperature range between 200 and 360 K and in the frequency range between 100 Hz and 1 MHz. From the measured complex impedance values, the complex permittivity (*ε*\*) was calculated, since the geometrical characteristics of the pellets legitimate the use of the parallel plate capacitor model. The correlation between the structure and morphology with the electrical and dielectric properties is one of the main topics of the present chapter.

## **2. Structural, morphologic, and electrical properties**

## **2.1. Structural properties**

up to temperatures of at least 900°C [6, 9], because some properties like the electrical conduc-

As it was aforementioned, the dominant process in the growth of LN single crystals is the Czochralski method. However, this method is known for its technical and economic drawbacks, as well as being time-consuming. Thus, alternative preparation processes have been researched and explored. Solid-state reaction processes generally require high processing temperatures (>1000°C), which lead to the loss of lithium by evaporation [10]. As a consequence, secondary crystalline phases such as Li3NbO4 and LiNb3O8 can be formed, changing the stoichiometry and deteriorating the properties. Wet chemistry methods, such as sol-gel methodologies and hydrothermal methods, can be good alternatives because they require lower processing temperatures, such as calcination and thermal-sintering treatments, and thus the formation of secondary phases can be minimized [10, 11]. Single crystals in the nanometer and micrometer size ranges can be synthesized at low temperatures, such as 240°C, by these methods [11]. When such methods are applied, typically polycrystalline LN samples are produced, i.e., a material composed by small single crystals in the micrometric or nanometric range randomly distributed with no evident preferential orientation. Polycrystalline LN finds a lot of applications, especially as thin films for integrated optic applications, although generally the properties of polycrystalline materials are not as good as their single-crystalline counterpart. For example, the piezoelectric properties of polycrystalline LN are inferior to the single crystal, and in the best case, they might approach them if all of its domains are perfectly orientated. Further, relative to single-crystalline thin films, the grain boundaries in polycrystalline films may lead to increased light scattering and larger optical losses in wave guides, which may reduce their utility and potentiality in some applications [12]. However, their production is cheaper and easier compared with the growth processes for single crystals, and all these cons and drawbacks have to be considered and well balanced for potential applica-

Amorphous LN is also important for some applications. In an amorphous material, there is no long-range order, and the network can be described as distorted unitary cells randomly oriented. LN single crystals and polycrystals have low electrical conductivity (~10−12 S/cm at 500 K for single crystals [13]), and ionic diffusion or mobility is reduced in these materials. However, the amorphous structure is always a more open structure compared with the crystalline composition or, in other words, has a smaller density, which promotes and facilitates the ionic diffusivity, making them suitable for technical application such as solid-state electrolytes for Li-ion batteries. In fact, the reported activation energies for the ionic diffusivity are considerably smaller (half in the 25–150°C temperature range [13]) in amorphous LN.

In this chapter, the structural and electrical characterization of LiNbO3 nanosized particles prepared by the Pechini route, also known in the sol-gel methodologies as the polymeric precursor route, is discussed. The powders obtained by drying the gel (base powder) were heat-treated for 4 h at temperatures between 400 and 1000°C, according to the differential thermal analysis (DTA) results. The sintering temperature revealed to be, as expected, an important parameter in controlling the development of secondary crystalline phases, and it was found that the powders sintered at 450°C contain only the LN phase, while those heat-

tivity do not change under thermal cycling up to such temperatures.

44 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

tions.

LN belongs to a group of materials whose crystalline structure is a perovskite. This structure has the typical chemical formula ABO3, where the cation A usually is too large for an effective complete packaging, causing a distortion in the unit cell and leading to a displacement of the O2− anions from their expected sites. However, in the case of LN, the distortion is related with the small radius of the lithium ion. For temperatures lower than 1415 K, which is the Curie temperature (*Tc*) of sLN, this material is in its ferroelectric state, and consequently, it exhibits a spontaneous polarization, due to a nonuniform charge distribution of the lithium and niobium ions. In this ferroelectric phase, this material has a trigonal crystalline structure, with threefold rotation symmetry around its c-axis. **Figure 2(a)** and **(c)** shows the atomic model of LN in its ferroelectric crystalline phase. In this configuration, the crystalline structure consists in layers of oxygen atoms parallel to each other with the Li+ and Nb5+ cations lying along the

**Figure 2.** (a) and (c) Atomic model of the LN ferroelectric phase. (b) Atomic model of the LN paraelectric phase. ∆Li indicates the displacement along the c-axis of the Li+ cations, represented as black spheres, while ∆Nb indicates the displacement along the c-axis of the Nb5+ cations. Both displacements are represented relatively to the center of the oxygen (red spheres) planes [14].

c-axis, surrounded by oxygen octahedra: in the unitary cell, one-third of the octahedral interstices are occupied by Li+ cations; another one-third by Nb5+ cations and the remaining (one-third) interstices are structural voids [2, 14].

As depicted in **Figure 2**, in the ferroelectric state, the displacement of the Li+ and Nb5+ cations relatively to the center of the oxygen planes originates a spontaneous polarization along the c-axis with a magnitude of 0.7 C/m2 at 300 K (see **Table 1**). The displacement can be up or down with respect to the oxygen sublattice, and both cations are displaced in the same direction because of the Coulomb repulsion. Above the Curie temperature, due to the thermal expansion of the crystalline lattice axes, the structure is no longer distorted, because the Li+ and Nb5+ cations move to lattice sites lying in the planes of the oxygen layers, as **Figure 2(b)** displays. Thus, the transition to the paraelectric state occurs, and LN ceases to exhibit a permanent spontaneous polarization [2, 14].

As it was stated in Section 1, polycrystalline LN is also of great technological importance. In this form, the structure can be described as composed by small single crystals in the micrometric or nanometric range randomly distributed with no evident preferential orientation. Relatively to the ferroelectricity, it is composed by several ferroelectric domains, which are regions with different orientations of the spontaneous polarization *Ps*. In this case, the thermodynamic potential for describing the ferroelectric phase transition has to account with a nonuniform *Ps* distribution, organized in domains, and therefore the domain depolarization energy *WE* and the energy of the domain walls *WW* are introduced in the potential [3].

The thermodynamic model for the single-crystal case, an "ideal" ferroelectric, does not need to include the former energy terms *WE* and *WW* and can be described by Eq. (2) [3]:

$$G\{P,T\} = G\_0 + \frac{a(T)}{2}P^2 + \frac{\beta(T)}{4}P^4 \tag{2}$$

This model is based on the second-order phase transition as described by Landau-Ginsburg; with at least a fourth-order polynomial in *P*, the polarization. *G*(*P*,*T*) is the Gibbs function, and *α* and *β* are second- and fourth-order expansion temperature-dependent terms. As it was said, this rather simple form applies for the case when *Ps* is uniform for all the material, as in the case of a single crystal. In the ferroelectric/paraelectric phase transition, the behavior of the plots of the type *G*(*P*,*T*) versus *P*, for different temperatures, is shown in **Figure 3** [3]. As it can be seen, for *T*2 and *T*0,, there is only one minimum, while for *T*1, in the ferroelectric phase, two minimum values exist, which correspond to the values of the spontaneous polarization *Ps* (can be positive or negative, according to the direction—**Figure 2**). These values can be determined by solving the differential (∂*G*/∂*P*)*Ps* = 0, resulting in = ± − for temperatures lower than *Tc* and *Ps* = 0 for temperatures higher than *Tc* [3]. The parameters *α* and *β* are related with the dielectric constants of LN, and more specifically, *α* can be expressed above *Tc*, in the paraelectric phase, according to the Curie-Weiss law shown in Eq. (3) [3, 15]:

Raman Spectroscopy and Scanning Electron Microscopy Structural Characterization of Lithium Niobate Nanoparticles Prepared by the Sol-Gel Process, Using X-Ray and Raman Spectroscopy and Scanning Electron Microscopy http://dx.doi.org/10.5772/64395 47

c-axis, surrounded by oxygen octahedra: in the unitary cell, one-third of the octahedral

relatively to the center of the oxygen planes originates a spontaneous polarization along the

with respect to the oxygen sublattice, and both cations are displaced in the same direction because of the Coulomb repulsion. Above the Curie temperature, due to the thermal expansion

cations move to lattice sites lying in the planes of the oxygen layers, as **Figure 2(b)** displays. Thus, the transition to the paraelectric state occurs, and LN ceases to exhibit a permanent

As it was stated in Section 1, polycrystalline LN is also of great technological importance. In this form, the structure can be described as composed by small single crystals in the micrometric or nanometric range randomly distributed with no evident preferential orientation. Relatively to the ferroelectricity, it is composed by several ferroelectric domains, which are regions with different orientations of the spontaneous polarization *Ps*. In this case, the thermodynamic potential for describing the ferroelectric phase transition has to account with a nonuniform *Ps* distribution, organized in domains, and therefore the domain depolarization

energy *WE* and the energy of the domain walls *WW* are introduced in the potential [3].

to include the former energy terms *WE* and *WW* and can be described by Eq. (2) [3]:

The thermodynamic model for the single-crystal case, an "ideal" ferroelectric, does not need

This model is based on the second-order phase transition as described by Landau-Ginsburg; with at least a fourth-order polynomial in *P*, the polarization. *G*(*P*,*T*) is the Gibbs function, and *α* and *β* are second- and fourth-order expansion temperature-dependent terms. As it was said, this rather simple form applies for the case when *Ps* is uniform for all the material, as in the case of a single crystal. In the ferroelectric/paraelectric phase transition, the behavior of the plots of the type *G*(*P*,*T*) versus *P*, for different temperatures, is shown in **Figure 3** [3]. As it can

minimum values exist, which correspond to the values of the spontaneous polarization *Ps* (can be positive or negative, according to the direction—**Figure 2**). These values can be determined

*Tc* and *Ps* = 0 for temperatures higher than *Tc* [3]. The parameters *α* and *β* are related with the dielectric constants of LN, and more specifically, *α* can be expressed above *Tc*, in the paraelectric

by solving the differential (∂*G*/∂*P*)*Ps* = 0, resulting in = ± −

phase, according to the Curie-Weiss law shown in Eq. (3) [3, 15]:

there is only one minimum, while for *T*1, in the ferroelectric phase, two

of the crystalline lattice axes, the structure is no longer distorted, because the Li+

As depicted in **Figure 2**, in the ferroelectric state, the displacement of the Li+

46 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

cations; another one-third by Nb5+ cations and the remaining

at 300 K (see **Table 1**). The displacement can be up or down

and Nb5+ cations

and Nb5+

(2)

for temperatures lower than

interstices are occupied by Li+

c-axis with a magnitude of 0.7 C/m2

spontaneous polarization [2, 14].

be seen, for *T*2 and *T*0,,

(one-third) interstices are structural voids [2, 14].

$$\chi = \frac{1}{a} = \frac{c}{r - \tau\_c} \tag{3}$$

**Figure 3.** The Gibbs free energy in function of the polarization *P. T*0 is equal to *Tc*, and the quantitative relation between the temperatures is *T*1 < *T*0 < *T*2 [3].

where *χ* is the dielectric susceptibility and *C* is a material-dependent constant.

The above-considered model fails when predicting quantities such as the coercive field, both for congruent and stoichiometric LN, because the inversion mechanisms of *Ps* occur through the formation of ferroelectric domains and the model does not account with *Ps* discontinuities. However, this thermodynamic model can be improved to better characterize a ferroelectric material containing domains, according to Eq. (4) [3]:

$$G\{P,T\} = G\_0 + \int\_V \left[\frac{a}{2}P^2 + \frac{\beta}{4}P^4 + \frac{1}{2}\delta\{\nabla P\}^2\right]dV + W\_E + W\_W \tag{4}$$

As it was stated, the terms depolarization energy *WE* and the energy of the domain walls *WW* are here introduced. The integration volume, *WE* and *WW* depend on the domain structure and geometry. In [3] the *WE* and *WW* expressions are described for a simple periodic domain structure model. The manipulation of the structure and geometry of the domain walls in a ferroelectric such as LN was, and still is, an important subject of study, because depending on the technological application, some geometries/shapes may be preferred over others: for example, acoustic and optical frequency conversion devices will benefit with periodic gratings of antiparallel domains [15]. The domain shape will depend on the temperature at which they are created, through the application of external electric fields and also on the crystal stoichiometry/composition. When created at room temperature, they can show different shapes due to small variation of stoichiometric composition [15]. **Figure 4** shows the preferred shapes of domains created at 25 and 125°C, for a congruent LN. It is visible that the domains have a polygonal shape with six sides, known as *y* walls. Curiously, the domain shape as depicted in **Figure 4(a)** is the same for stoichiometric LN, while in other ferroelectric materials such as LiTaO3, the same does not happen [15].

**Figure 4.** Piezoelectric force microscopy phase contrast images obtained in a congruent LN. The domains were created at 25 and 125°C [15].

**Figure 5.** XRD spectra revealing the effect of heat treatments on amorphous LN prepared by complete hydrolysis of the LN double alkoxide [16].

As for the structure of amorphous LN, it was said that the network can be described as distorted unitary cells randomly oriented. **Figure 5** reveals the effect of heat treatments (HTs) on amorphous LN prepared by complete hydrolysis of the LN double alkoxide [16]. The XRD spectra of amorphous LN have the typical form of the spectrum for 473 K displayed in **Figure 5**, with two broad bands around 30 and 50–60°. These broad bands are a trademark of amorphous materials, and they are typically visible for diffraction angles where the crystalline phase has the most intense diffraction peaks, revealing at least a short-range-order preservation. The heat treatments promote the reconfiguration of the amorphous phase to a more thermodynamically stable crystalline phase; although for low treatment temperatures and times, the material may be composed by a heterogeneous mixture of an amorphous and a crystalline phase: for the heat treatment at 573 K for 0.5 h, it is still noticeable the coexistence of a broad band with the diffraction peaks of the LN crystalline phase [16]. The structure of amorphous LN was also described by Kitabatake et al. to be constructed from the network of NbO6 octahedra which contains a micronetwork similar to crystalline LN [17]. The high dielectric constant and a relaxation mechanism were attributed to the high mobility of the Li+ ion in the LN structure [17].

Going further on the structural properties, the Raman spectroscopy is a useful nondestructive technique to access about the structure and composition of materials. The Raman spectrum of LN will generally depend on its stoichiometry, i.e., the shape, width, and position of some Raman shifts may change according to the Li/Nb ratio [18]. Furthermore, the Li/Nb ratio of a given LN sample may be determined by analyzing the width of some Raman lines, for a given temperature [18, 19].

**Figure 4.** Piezoelectric force microscopy phase contrast images obtained in a congruent LN. The domains were created

48 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 5.** XRD spectra revealing the effect of heat treatments on amorphous LN prepared by complete hydrolysis of

As for the structure of amorphous LN, it was said that the network can be described as distorted unitary cells randomly oriented. **Figure 5** reveals the effect of heat treatments (HTs) on amorphous LN prepared by complete hydrolysis of the LN double alkoxide [16]. The XRD spectra of amorphous LN have the typical form of the spectrum for 473 K displayed in **Figure 5**, with two broad bands around 30 and 50–60°. These broad bands are a trademark of amorphous materials, and they are typically visible for diffraction angles where the crystalline phase has the most intense diffraction peaks, revealing at least a short-range-order preservation. The heat treatments promote the reconfiguration of the amorphous phase to a more thermodynamically stable crystalline phase; although for low treatment temperatures and times, the material may be composed by a heterogeneous mixture of an amorphous and a crystalline phase: for the heat treatment at 573 K for 0.5 h, it is still noticeable the coexistence

at 25 and 125°C [15].

the LN double alkoxide [16].

**Figure 6** exhibits experimental full width at half maximum (FWHM) values of the Raman lines detected at about 153 and 876 cm−1, for samples with different lithium contents (mol%) [19]. The measurements were carried out at room temperature (note that the Raman lines' width also depends on the temperature). The FWHM dependency with the Li content is approximately linear, and hence a calibration line can be obtained. The uncertainty related with the Li content determination by this method was calculated to be 0.05 mol%, with an estimated uncertainty of 0.2 cm−1 in the 876 cm−1 line FWHM and 0.1 cm−1 in the 153 cm−1 line [19]. Therefore, this technique can be a simple nondestructive method to estimate the Li/Nb ratio in LN crystals, with an excellent accuracy.

**Figure 6.** Full width at half maximum of the Raman lines at the wavenumbers 153 and 876 cm−1. The dots are experimental values obtained for samples with different lithium contents (mol%), at room temperature, and the lines are the linear least-squares fits [19].

**Figure 7** displays the Raman spectra of a nearly stoichiometric LN crystal, with *xc* = 49.7 %, and a congruent LN crystal with *xc* = 48.5 %, where *xc* is given by <sup>=</sup> <sup>+</sup> × 100 % [18]. According to the group theory, when belonging to the *R3c* spatial group, eighteen vibrational modes are to be expected, which can be reduced in the representation 4A1 + 9E + 5A2 [18]. The A2 vibrational modes are not active in Raman and FTIR (silent modes), while both A1 and E modes are active in Raman and FTIR. The A1 modes are polarized along the Z-axis, while the E modes represent vibrations along the X- and Y-axes (see **Figure 4**). Therefore, in the XYZ coordinate system, as indicated in **Figure 7**, Z-axis lies in the c-axis direction while the X-axis in the *a*-axis crystallographic direction. The Y-axis is perpendicular to Z and X. The notation represented in the same figure is a universally used notation first described by Damen et al. For example, in X(YZ)Y, the symbols inside the parenthesis are, from left to right, the polarization of the incident and scattered light, while the ones outside the parenthesis, from left to right, represent the directions of the incident and scattered light, respectively [20]. As depicted in **Figure 7**, the E(TO) transversal modes can be detected in the X(ZY)Z configuration, while E(TO) and E(LO) can be detected in both X(ZY)Z and X(YZ)Y configurations [18]. The A1(TO) phonons, represented in **Figure 7**, at right, can be detected in the X(ZZ)Y configuration. The spectra clearly show that there is a broadening of the lines in the congruent composition, relatively to the nearly stoichiometric, i.e., the nearly stoichiometric spectrum lines are more resolved. Furthermore, there are lines that are only clearly visible in the nearly stoichiometric LN, and thus vibrational mode attribution in congruent LN can be an incomplete task [18]. As a final remark, when dealing with polycrystalline LN, the discussion about the different possible configurations to detect different vibrational modes is not applicable, since in the polycrystalline sample, we have nano- or micrometric single crystals randomly oriented, and thus interaction volume of the laser beam with the sample will include all these different orientations. In Section 2.4, the case study, we include the Raman spectra of polycrystalline LN, where a typical overlapping of vibrational modes is visible. The overlapping is due to the fact that, as **Figure 7** shows, some of the E(TO + LO) and A1(TO) vibration modes are in the same wavenumber range, and consequently, they will overlap in the polycrystalline LN samples.

**Figure 7.** At left: Raman spectra of two LN crystals with composition *xc* = 49.7 % (nearly stoichiometric) and *xc* = 48.5 % (congruent), exhibiting the E(TO) and E(LO) vibrational modes. The arrows highlight lines that are more clearly visible in the nearly stoichiometric composition. At right: the configuration X(ZZ)Y allows the detection of the A1(TO) phonons [18].

## **2.2. Morphological characteristics**

modes are to be expected, which can be reduced in the representation 4A1 + 9E + 5A2 [18]. The A2 vibrational modes are not active in Raman and FTIR (silent modes), while both A1 and E modes are active in Raman and FTIR. The A1 modes are polarized along the Z-axis, while the E modes represent vibrations along the X- and Y-axes (see **Figure 4**). Therefore, in the XYZ coordinate system, as indicated in **Figure 7**, Z-axis lies in the c-axis direction while the X-axis in the *a*-axis crystallographic direction. The Y-axis is perpendicular to Z and X. The notation represented in the same figure is a universally used notation first described by Damen et al. For example, in X(YZ)Y, the symbols inside the parenthesis are, from left to right, the polarization of the incident and scattered light, while the ones outside the parenthesis, from left to right, represent the directions of the incident and scattered light, respectively [20]. As depicted in **Figure 7**, the E(TO) transversal modes can be detected in the X(ZY)Z configuration, while E(TO) and E(LO) can be detected in both X(ZY)Z and X(YZ)Y configurations [18]. The A1(TO) phonons, represented in **Figure 7**, at right, can be detected in the X(ZZ)Y configuration. The spectra clearly show that there is a broadening of the lines in the congruent composition, relatively to the nearly stoichiometric, i.e., the nearly stoichiometric spectrum lines are more resolved. Furthermore, there are lines that are only clearly visible in the nearly stoichiometric LN, and thus vibrational mode attribution in congruent LN can be an incomplete task [18]. As a final remark, when dealing with polycrystalline LN, the discussion about the different possible configurations to detect different vibrational modes is not applicable, since in the polycrystalline sample, we have nano- or micrometric single crystals randomly oriented, and thus interaction volume of the laser beam with the sample will include all these different orientations. In Section 2.4, the case study, we include the Raman spectra of polycrystalline LN, where a typical overlapping of vibrational modes is visible. The overlapping is due to the fact that, as **Figure 7** shows, some of the E(TO + LO) and A1(TO) vibration modes are in the same wavenumber range, and consequently, they will overlap in the polycrystalline LN

50 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 7.** At left: Raman spectra of two LN crystals with composition *xc* = 49.7 % (nearly stoichiometric) and *xc* = 48.5 % (congruent), exhibiting the E(TO) and E(LO) vibrational modes. The arrows highlight lines that are more clearly visible in the nearly stoichiometric composition. At right: the configuration X(ZZ)Y allows the detection of the A1(TO) pho-

samples.

nons [18].

Morphology means "the study of form or pattern," and morphological characterization techniques, such as scanning electron microscopy (SEM) or transmission electron microscopy (TEM), allow to characterize the morphology of a given material. The morphological characteristics of LN will obviously rely upon the synthesis process, stoichiometry, and concentration of intrinsic defects. Depending on the synthesis process and crystal growth conditions, the grains observed for polycrystalline LN can display well-defined symmetries and a different range of sizes.

**Figure 8.** At left: SEM micrograph of polycrystalline LN prepared by a low-temperature hydrothermal route [21]. At right: SEM micrograph of polycrystalline LN prepared by the reactive molten salt synthesis (RMSS) process [10].

Zhan et al. [21] report in their work a low-temperature hydrothermal route to prepare polycrystalline LN. The XRD characterization revealed the formation of a pure hexagonal single phase of stoichiometric LN. The SEM micrograph of the LN powder, presented in **Figure 8**, shows a regular rhombohedral grain morphology, in agreement with the XRD results, although some imperfections, such as bended surfaces, are visible. The grain size ranges from 300 nm to approximately 1 μm. Kamali et al. [10] prepared polycrystalline LN using a modification of the molten salt synthesis (MSS): in conventional MSS, the mixed powders are heated above the liquids' temperature of the salt mixture, and this molten salt acts as the reaction medium, remaining inert during the synthesis. Salt mixtures such as KCl-NaCl are typically used. In the MSS modification approached by [10], the salt can react with other reagents during the synthesis process, being labeled as reactive molten salt synthesis (RMSS). They heat-treated at 973 K Nb2Cl5 powder in a LiCl molten salt, in a water-containing atmosphere, whereby the molten salt is one of the precursors for LN synthesis [10]. Using this RMSS approach, they produced single-phased LN, i.e., the loss by evaporation of Li2O was avoided. A SEM micrograph of the obtained LN particles is shown in **Figure 8**, on the right side [10]. The revealed morphology shows grains with dimensions ranging from several hundreds of nanometers to a few micrometers. The rhombohedral symmetry is also visible, although cleavages and bends are visible.

In **Figure 9**, it is visible a TEM bright-field micrograph of the polycrystalline LN prepared by the RMSS process. The inset on the right top shows a selected area electron diffraction pattern, being the area marked by the black arrow. The diffraction pattern is consistent with singlecrystalline rhombohedral LN. The inset on the left bottom shows a high-resolution micrograph of the area marked by the white arrow. The rhombohedral LN (104) atomic plane patterns are visible, with an interplanar spacing of 0.27 nm [10].

**Figure 9.** TEM bright-field micrograph of the LN particles prepared by the reactive molten salt synthesis (RMSS). Inset on the top right: selected area electron diffraction pattern of the area marked by the black arrow. Inset on the left bottom: high-resolution micrograph of the area marked by the white arrow [10].

The grain morphology will be determined by the growth conditions in such a way that the final morphology reflects the configuration with the minimum surface energy. In crystalline solid materials, the surface tension will depend on the crystallographic planes and direction, because to create a new surface, it is necessary to break bonds. At a constant pressure and temperature, the work required to create a new portion of surface *dAs* in a one-component system is given by Eq. (5) [22]:

$$dW\_{T,p} = \chi dA\_s \tag{5}$$

where *γ* is the surface energy (J/m2 ). This represents an excess of energy relatively to the bulk and will depend on the number of bonds of the surface (crystallographic plane) and their bond energy. The change of the Gibbs free energy can be written according to Eq. (6) [22]:

$$dG = -SdT + Vdp + \chi dA\_s \tag{6}$$

where *γ* is defined as in Eq. (7) [22]:

$$\boldsymbol{\chi} = \begin{pmatrix} \frac{\partial G}{\partial A\_{\boldsymbol{\beta}}} \end{pmatrix}\_{\boldsymbol{T}, \boldsymbol{P}} \tag{7}$$

The formation of new surfaces leads to a positive Gibbs energy contribution, whereby smaller particles will be unstable when compared with larger particles. The equilibrium morphology of the crystal will be determined by the surfaces with lower Gibbs energy, while surfaces of higher energy are sacrificed. Different crystallographic planes will have a different number of bonds per unit of area, and the bond strengths can also change according to the composition. Actually, very often when a surface energy value of a given crystalline material is indicated, it is in fact an average of the surface energy of the different crystalline faces. Taking as example a face-centered cubic lattice, when increasing the Miller indices, typically the atomic density of the planes decreases. The exception is that in the plane family [1 1 1], which contains six nearest neighbors, three bonds for each surface atom have to be broken when cutting the crystal along such direction, while for [1 0 0] and [1 1 0] planes, with lower atomic density, four and six bonds have to be broken, respectively [22]. Therefore, the surface energy of the former planes is larger relatively to the [1 1 1] plane family. Planes with the highest density have a lower surface energy and rate of growth, and therefore the final morphology of the crystal growth will be defined by the high-density atomic planes [21, 22]. However, several studies have indicated that a spherical morphology, which is the configuration that minimizes the surface area, is energetically more favorable for solids at high temperatures, and the difference of surface energy between different crystallographic planes becomes a less important factor [22].

#### **2.3. Electrical and dielectric properties**

crystalline rhombohedral LN. The inset on the left bottom shows a high-resolution micrograph of the area marked by the white arrow. The rhombohedral LN (104) atomic plane patterns are

52 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 9.** TEM bright-field micrograph of the LN particles prepared by the reactive molten salt synthesis (RMSS). Inset on the top right: selected area electron diffraction pattern of the area marked by the black arrow. Inset on the left bot-

The grain morphology will be determined by the growth conditions in such a way that the final morphology reflects the configuration with the minimum surface energy. In crystalline solid materials, the surface tension will depend on the crystallographic planes and direction, because to create a new surface, it is necessary to break bonds. At a constant pressure and temperature, the work required to create a new portion of surface *dAs* in a one-component

and will depend on the number of bonds of the surface (crystallographic plane) and their bond

The formation of new surfaces leads to a positive Gibbs energy contribution, whereby smaller particles will be unstable when compared with larger particles. The equilibrium morphology

energy. The change of the Gibbs free energy can be written according to Eq. (6) [22]:

). This represents an excess of energy relatively to the bulk

(5)

(6)

(7)

visible, with an interplanar spacing of 0.27 nm [10].

tom: high-resolution micrograph of the area marked by the white arrow [10].

system is given by Eq. (5) [22]:

where *γ* is the surface energy (J/m2

where *γ* is defined as in Eq. (7) [22]:

In this section, we will start to address the electrical properties of LN single crystalline and polycrystalline. Afterward, we will address polycrystalline LN. However, for both cases, it is important to analyze the properties for different temperature ranges and different stoichiometries, since both parameters have influence on the mechanisms of electrical conduction.

**Figure 10.** Dependence of a LN stoichiometric sample (sample 3 of **Figure 12**) total electrical conductivity with the oxygen partial pressure *p*0, at 1173 K (900°C). The solid line is the linear fit of the experimental values, while the dotted line is the extrapolation [6].

It is well known that the electrical conductivity of LN single crystals, as well as some optical properties, is strongly dependent on the surrounding environmental characteristics, in particular the partial oxygen pressure *p*0, as well as the Li/Nb ratio (stoichiometry). It was demonstrated that the electrical conductivity in high temperature ranges, between 600 and 1300 K, has a dependency of the type *p*<sup>0</sup> −1/4 for low *p*<sup>0</sup> ≲1 torr (1 torr ≈ 1/760 of a standard atmosphere). **Figure 10** presents the dependence of a sample with [Li]/[Nb] = 1 (sample 3; see inset table of **Figure 12**) total electrical conductivity with *p*0, at 1173 K (900°C) [6]. The solid line, which represents the linear fit of the experimental values, has a slope of approximately ¼ [6].

**Figure 11.** Dependence of *σ*dc and *E*A at room temperature with reduction temperature for different reduced congruent LN single crystals [23].

**Figure 12.** Arrhenius representation of the electrical conductivity of single-crystalline LN samples with different lithium contents, in the temperature range between 500 and 900°C. [VLi] represents the mol% of lithium vacancies, calculated through the lithium vacancy model (Eq. (1)). The activation energies (*E*A) for the different samples are also indicated (adapted with permission from [6]).

The electrical properties of LN are conditioned by the oxidation or reduction atmosphere, during thermal annealing: in a low *p*0 (≲1 torr) environment, it will consist of a reducing atmosphere. The effects of a reducing atmosphere on LN crystals are typically referred in the literature to originate the following modifications: the first is loss of oxygens from the structure, which leads to the release of electrons which are trapped by Nb5+ cations, consequently originating Nb4+ cations; the second is that the reducing atmosphere leads to the diffusion and loss of lithium cations, creating more lithium vacancies and an excess of niobium cations relatively to lithium, thus leading to the occupation of Li+ lattice sites by the Nb5+ species (the so-called anti-site niobium defects NbLi), according to the lithium vacancy model, presented in Eq. (1) [6, 23]. Dhar et al. studied the low temperature (77–373 K) dependency of dc electrical conduction in reduced congruent LN single crystals [23]. The samples had different levels of oxygen reduction according to the temperature of reduction, in a vacuum of approximately 10−5 mbar. **Figure 11** shows the dependence of the dc conductivity (*σ*dc) and activation energy (*E*A) at room temperature with the reduction temperature for different samples [23].

The presence of a maximum in *σ*dc and a minimum in *E*A can be explained by the Mott's variable range hopping (VRH) mechanism: the oxygens released during reduction can produce free electrons according to Eqs. (8) and (9) [23]:

$$2Nb^{5+} + O^{2-} \leftrightarrow 2Nb^{4+} + O\_v^{2-} + 1/2O\_2 \tag{8}$$

and

particular the partial oxygen pressure *p*0, as well as the Li/Nb ratio (stoichiometry). It was demonstrated that the electrical conductivity in high temperature ranges, between 600 and

54 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

atmosphere). **Figure 10** presents the dependence of a sample with [Li]/[Nb] = 1 (sample 3; see inset table of **Figure 12**) total electrical conductivity with *p*0, at 1173 K (900°C) [6]. The solid line, which represents the linear fit of the experimental values, has a slope of approximately

**Figure 11.** Dependence of *σ*dc and *E*A at room temperature with reduction temperature for different reduced congruent

**Figure 12.** Arrhenius representation of the electrical conductivity of single-crystalline LN samples with different lithium contents, in the temperature range between 500 and 900°C. [VLi] represents the mol% of lithium vacancies, calculated through the lithium vacancy model (Eq. (1)). The activation energies (*E*A) for the different samples are also indicated

−1/4 for low *p*<sup>0</sup> ≲1 torr (1 torr ≈ 1/760 of a standard

1300 K, has a dependency of the type *p*<sup>0</sup>

¼ [6].

LN single crystals [23].

(adapted with permission from [6]).

$$Nb^{4+} \leftrightarrow Nb^{5+} + e^- \tag{9}$$

and therefore the release of oxygen during reduction originates free electrons that can get trapped in niobium ions, and the conduction mechanism is assigned to polaronic hopping between Nb5+ and Nb4+ cations [23]. The maximum and minimum observed in **Figure 11** can be explained according to the ratio of Nb4+/Nb5+ states: for low reduction temperatures, few Nb4+ states will be created, while for high reduction temperatures, Nb4+ will predominate. However, for intermediate reduction temperature, there will be a case where we will get Nb4+/Nb5+ = 0.5. In that case, a maximum in the conductivity and a minimum in *E*A are to be expected, because the different oxidation states through which the polaronic hopping occurs are closer to each other [23]. They also concluded that actually the reduction annealing in low *p*0 does not lead to a significant loss of lithium ions, as it was aforementioned (and is frequently mentioned in the literature), because they have shown that when reheating the reduced samples in an oxygen-rich atmosphere, without any content of lithium vapor, the conductivity decreases and regains practically the same value as unreduced samples, which imply that annealing at low *p*0 does not have an important role in lithium loss [23]. For a polaronic VRH, the conductivity has a dependency as expressed in Eq. (10):

$$
\sigma\_{dc} = \sigma\_0 \exp\left[-\left(\frac{T\_0}{T}\right)^S\right] \tag{10}
$$

where *σ*0 is the pre-exponential factor, *T*0 is Mott's characteristic temperature, and *s* is the exponent for the VRH model. For reduced LN single crystals, the exponent *s* = ¼ is the one which better describes the temperature dependency of *σ*dc (check on [23] to see a log(*σ*dc) vs *T* − 1/4 plot).

For higher temperature ranges, in reduced LN single crystals, the VRH of polarons continues to be one of the mechanisms for the electrical conduction. However, and especially for congruent samples, lithium diffusion starts to be thermally activated, and when increasing the temperature, the main contribution for the total electrical conductivity may become ionic, assigned to lithium diffusion through lithium vacancies in the network (once again, we recall the lithium vacancy model) [6]. **Figure 12** shows the Arrhenius representation of the total electrical conductivity of LN single-crystalline samples with different lithium oxide molar percentages, in the temperature range between 773 and 1173 K [6]. The conductivity increases with the decrease of the Li2O content, indicating the influence of lithium diffusion through lithium vacancies. The ionic conductivity will be larger for congruent LN, because the density of lithium vacancies is larger.

With respect to the frequency dependency of the electrical properties, typically studied by means of impedance spectroscopy (IS), some results of the work done by Mansingh and Dhar will be addressed, namely, those related with the ac electrical conductivity (*σ*ac) and the dielectric constant (*ε*′) of congruent LN single crystals [24]. This work was published in 1985; however, more recent papers reporting dielectric studies as a function of frequency and temperature for LN single crystals are surprisingly not that easy to find, because most of them deal with polycrystalline LN or with LN doped with other elements.

**Figure 13.** Dependence of σac and σdc with the temperature (77–700 K) for different fixed frequencies (kHz): (•) DC, (○) 0.1, (x) 1, (Δ) 10, (□) 100 [24].

**Figure 13** shows for a congruent LN single crystal the dependence of *σ*ac and also *σ*dc (although in a more limited temperature range relatively to *σ*ac) with the temperature (77–700 K) for different frequencies, between 100 Hz and 100 kHz. It is visible that for lower temperatures *σ*ac presents high-frequency dispersion, and it is considerably higher than *σ*dc, while for higher temperatures it becomes practically frequency-independent and strongly temperaturedependent. Moreover, the temperature at which *σ*ac starts to have the same value as *σ*dc increases with the increase of the frequency. The mechanism for lower temperatures was found to be well described by a hopping-over-the-barrier (HOB) mechanism, and it was correlated with electron hopping between different valence states of the niobium, because of the reduction of Nb5+ due to oxygen deficiencies (as it was referred before) [24].

where *σ*0 is the pre-exponential factor, *T*0 is Mott's characteristic temperature, and *s* is the exponent for the VRH model. For reduced LN single crystals, the exponent *s* = ¼ is the one which better describes the temperature dependency of *σ*dc (check on [23] to see a log(*σ*dc) vs *T*

56 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

For higher temperature ranges, in reduced LN single crystals, the VRH of polarons continues to be one of the mechanisms for the electrical conduction. However, and especially for congruent samples, lithium diffusion starts to be thermally activated, and when increasing the temperature, the main contribution for the total electrical conductivity may become ionic, assigned to lithium diffusion through lithium vacancies in the network (once again, we recall the lithium vacancy model) [6]. **Figure 12** shows the Arrhenius representation of the total electrical conductivity of LN single-crystalline samples with different lithium oxide molar percentages, in the temperature range between 773 and 1173 K [6]. The conductivity increases with the decrease of the Li2O content, indicating the influence of lithium diffusion through lithium vacancies. The ionic conductivity will be larger for congruent LN, because the density

With respect to the frequency dependency of the electrical properties, typically studied by means of impedance spectroscopy (IS), some results of the work done by Mansingh and Dhar will be addressed, namely, those related with the ac electrical conductivity (*σ*ac) and the dielectric constant (*ε*′) of congruent LN single crystals [24]. This work was published in 1985; however, more recent papers reporting dielectric studies as a function of frequency and temperature for LN single crystals are surprisingly not that easy to find, because most of them

**Figure 13.** Dependence of σac and σdc with the temperature (77–700 K) for different fixed frequencies (kHz): (•) DC, (○)

deal with polycrystalline LN or with LN doped with other elements.

− 1/4 plot).

of lithium vacancies is larger.

0.1, (x) 1, (Δ) 10, (□) 100 [24].

**Figure 14.** Frequency dependence of σac for some fixed temperatures (K): (◑) 77, (▼) 220, (▽) 320, (■) 415, (□) 475, (▲) 530, (∆) 580, (●) 625, (○) 650, (x) 680 [24].

**Figure 14** shows the frequency dependence of *σ*ac for some fixed temperatures. For lower temperatures, up to 530 K, the dependency of *σ*ac with the frequency can be expressed by the relation presented in Eq. (11) [24]:

(11)

**Figure 15.** Frequency dependency of the dielectric constant (ε') for different fixed temperatures (K): (◑) 77, (▲) 530, (∆) 580, (●) 625, (○) 650, (x) 680 [24].

This is the well-known relation found by Mott and Davis which describes the frequency dependency of *σ*ac for many amorphous and crystalline materials. The HOB mechanism presents a frequency dependency which can be described by Eq. (11). Furthermore, the HOB mechanism predicts a decrease of the frequency exponent *s* with the increase of temperature, and the values of *s* calculated by Mansingh and Dhar (~1 for 77 K and ~0.6 for 530 K) agree satisfactorily with the HOB model [24]. For higher temperatures, as it was aforementioned, *σ*ac becomes practically frequency-independent and with a magnitude close to *σ*dc. At the same time, for the same high temperature range (relatively to *σ*ac, see **Figure 14**), *ε*′ is characterized by a strong frequency dispersion, as shown in **Figure 15**.

The temperature dependence of *ε*′ for different fixed frequencies, between 100 Hz and 100 kHz, is also shown in **Figure 16**.

It can be noted in **Figure 16** that the temperature from which *ε*′ shows a sharp increase increases with the increase of frequency. So, from the presented plots of *σ*ac and *ε*′, it is evident that the temperature dependences show evidence of two distinct mechanisms for the conductivity. At low temperatures, the mechanism was already identified, the HOB mechanism with a high distribution of relaxation times. For higher temperatures, the strong *ε*′ dispersion is probably associated with the dc conduction mechanisms, while both ac and dc conductivities are determined by the same mechanism, long-range hopping of charge carriers [24]. A sample with thickness reduced to half, keeping the electrode surface area constant, was included in **Figure 16** to demonstrate that the sharp increase of *ε*′ is not related with the electrode barriers and spatial charge accumulation at the electrode/sample interface [24].

Raman Spectroscopy and Scanning Electron Microscopy Structural Characterization of Lithium Niobate Nanoparticles Prepared by the Sol-Gel Process, Using X-Ray and Raman Spectroscopy and Scanning Electron Microscopy http://dx.doi.org/10.5772/64395 59

(11)

**Figure 15.** Frequency dependency of the dielectric constant (ε') for different fixed temperatures (K): (◑) 77, (▲) 530, (∆)

58 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

This is the well-known relation found by Mott and Davis which describes the frequency dependency of *σ*ac for many amorphous and crystalline materials. The HOB mechanism presents a frequency dependency which can be described by Eq. (11). Furthermore, the HOB mechanism predicts a decrease of the frequency exponent *s* with the increase of temperature, and the values of *s* calculated by Mansingh and Dhar (~1 for 77 K and ~0.6 for 530 K) agree satisfactorily with the HOB model [24]. For higher temperatures, as it was aforementioned, *σ*ac becomes practically frequency-independent and with a magnitude close to *σ*dc. At the same time, for the same high temperature range (relatively to *σ*ac, see **Figure 14**), *ε*′ is characterized

The temperature dependence of *ε*′ for different fixed frequencies, between 100 Hz and 100 kHz,

It can be noted in **Figure 16** that the temperature from which *ε*′ shows a sharp increase increases with the increase of frequency. So, from the presented plots of *σ*ac and *ε*′, it is evident that the temperature dependences show evidence of two distinct mechanisms for the conductivity. At low temperatures, the mechanism was already identified, the HOB mechanism with a high distribution of relaxation times. For higher temperatures, the strong *ε*′ dispersion is probably associated with the dc conduction mechanisms, while both ac and dc conductivities are determined by the same mechanism, long-range hopping of charge carriers [24]. A sample with thickness reduced to half, keeping the electrode surface area constant, was included in **Figure 16** to demonstrate that the sharp increase of *ε*′ is not related with the electrode barriers

580, (●) 625, (○) 650, (x) 680 [24].

is also shown in **Figure 16**.

by a strong frequency dispersion, as shown in **Figure 15**.

and spatial charge accumulation at the electrode/sample interface [24].

**Figure 16.** Temperature dependency of the dielectric constant (ε') for different fixed frequencies (kHz): (○) 0.1, (x) 1, (Δ) 10, (■) 100, (●) Sample with half of the thickness, keeping the same area [24].

We will end this section by briefly addressing the electrical and dielectric properties of polycrystalline LN. In such case, the behavior of the referred properties can reflect the presence of grain boundaries in the material. This effect of grain boundaries can be more clearly seen in IS measurements, because the characteristic frequencies (or times) at which grain boundary processes occur are different from those that occur in the bulk of the grains, and therefore Nyquist diagrams [plot of the negative of the imaginary part of the impedance, −Im(Z), in the y-axis over the real part of the impedance, Re(Z), in the x-axis] originate successive semicircles, where each point of the semicircle corresponds to a different frequency value which increases counterclockwise. Lanfredi and Rodrigues report in their work IS studies of the electrical conductivity and dielectric constant of polycrystalline LN [25]. **Figure 17** presents Nyquist diagrams for different temperatures of two polycrystalline LN samples *a* and *b*. Sample *b* has approximately half of the thickness to electrode surface area ratio (*l*/A) relatively to sample *a*.

**Figure 17.** At left: Nyquist diagram for different temperatures for a polycrystalline LN sample with a thickness to electrode surface area ratio *l*/A = 0.200 cm−1 (sample *a*). At right: Nyquist diagram for different temperatures for sample *a* polycrystalline LN sample with a thickness to surface area ratio l/A = 0.105 cm−1 (sample *b*), approximately half of sample *a*. For both samples, the smallest semicircle corresponds to a measurement performed at 700°C [25].

Comparing both diagrams, it is visible that for the same temperature, the real part of the complex impedance Re(Z) of sample *b* is approximately half of sample *a*, thus confirming that the high-frequency semicircle is the bulk response of the samples, since the resistance is directly proportional to the path length [25]. Furthermore, the frequency value distribution in the bulkresponse semicircle is the same for both samples, indicating the homogeneity of the bulk response, and that the relaxation frequency, given by the peak of the bulk semicircle (in the peak, the relation 2π*f*0*R*b*C*b = 1 is fulfilled, where *R*b and *C*b are bulk resistance and capacitance, respectively), is an intrinsic property of the material and does not depend on geometrical factors [25]. As expected, the bulk resistance decreases with the increase of the temperature. The low-frequency semicircle is assigned to the response of grain boundaries, and its depressed shape is an indicator of a nonhomogeneous electrical behavior of grain boundaries [25]. This nonhomogeneous behavior can be related with an existence of a distribution of relaxation times.

The complex impedance semicircle for the bulk response can be well fitted by simple *R*b*C*<sup>b</sup> equivalent circuit. A bulk electrical conductivity *σ*b can be defined according to Eq. (12):

$$
\sigma\_{\rm b} = \frac{1}{\kappa\_{\rm b}} \frac{\iota}{A} \tag{12}
$$

**Figure 18.** Arrhenius representation of the bulk electrical conductivity *σ*b of the polycrystalline LN samples *a* and *b*, in the temperature range between 450 and 800°C [25].

Raman Spectroscopy and Scanning Electron Microscopy Structural Characterization of Lithium Niobate Nanoparticles Prepared by the Sol-Gel Process, Using X-Ray and Raman Spectroscopy and Scanning Electron Microscopy http://dx.doi.org/10.5772/64395 61

**Figure 19.** Frequency dependency, in the range of 5–107 Hz, of *ε*′ for some fixed high temperatures, for sample *b* [25].

*R* b can be determined through the Nyquist plots by the second interception (just before the grain boundary response) of the bulk semicircle with the real axis. **Figure 18** displays for both samples *a* and *b* the Arrhenius representation of *σ*b in the temperature range between 450 and 800°C [25]. The activation energies are very similar.

To conclude this section, it is included in **Figure 19** the frequency dependency, between 5 and 107 Hz, of *ε*′ for some fixed high temperatures, for sample *b*.

For lower frequencies, a strong dispersion of *ε*′ is observed. This is due to spatial charge accumulation at the grain boundaries, and the charge accumulation at interface electrode/ sample may also contribute to the sharp increase of *ε*′ for lower frequencies. This behavior is often observed for polycrystalline materials.

## **2.4. Case study: preparation and characterization of polycrystalline LN by the Pechini method**

## *2.4.1. Preparation process: the Pechini route*

Comparing both diagrams, it is visible that for the same temperature, the real part of the complex impedance Re(Z) of sample *b* is approximately half of sample *a*, thus confirming that the high-frequency semicircle is the bulk response of the samples, since the resistance is directly proportional to the path length [25]. Furthermore, the frequency value distribution in the bulkresponse semicircle is the same for both samples, indicating the homogeneity of the bulk response, and that the relaxation frequency, given by the peak of the bulk semicircle (in the peak, the relation 2π*f*0*R*b*C*b = 1 is fulfilled, where *R*b and *C*b are bulk resistance and capacitance, respectively), is an intrinsic property of the material and does not depend on geometrical factors [25]. As expected, the bulk resistance decreases with the increase of the temperature. The low-frequency semicircle is assigned to the response of grain boundaries, and its depressed shape is an indicator of a nonhomogeneous electrical behavior of grain boundaries [25]. This nonhomogeneous behavior can be related with an existence of a distribution of relaxation

60 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

The complex impedance semicircle for the bulk response can be well fitted by simple *R*b*C*<sup>b</sup> equivalent circuit. A bulk electrical conductivity *σ*b can be defined according to Eq. (12):

**Figure 18.** Arrhenius representation of the bulk electrical conductivity *σ*b of the polycrystalline LN samples *a* and *b*, in

the temperature range between 450 and 800°C [25].

(12)

times.

The sol-gel process is a well-known route for the synthesis of different types of materials, and in its basic description, it can be referred as a technique that synthesizes a solid compound through a chemical reaction in solution at low temperatures. There are different sol-gel methodologies according to the type of precursors used and the chemical reactions leading to the formation of the gel: there is the sol-gel methodology based on the hydrolysis-condensation of metal alkoxides, the "chelate-gel" route, involving aqueous solutions containing metal chelates, and the Pechini route. The sol-gel methodologies have general advantages such as the very good control of the stoichiometry and purity of the final material, low processing temperatures, possibility, and good flexibility in developing thin films as well as the possibility to have control over some important characteristics, such as the size and shape of the particles and homogeneity.

The Pechini route takes its name on its developer, Maggio Pechini in 1967 [26]. In particular, it was developed to include metals which are not suitable for traditional sol-gel reactions due to their unfavorable hydrolysis equilibria, and thus this method has the advantage of not requiring that the metallic species involved form stable hydroxo-complexes. This method is known for its use on the synthesis of multicomponent metal oxide materials [26], and basically this method uses an R-hydroxycarboxylic acid, such as citric acid (CA), to lead the formation of stable metal complex, i.e., the metallic cations of interest form stable complexes known as chelates. After this step, a polyalcohol, such as ethylene glycol (EG), is used to promote the polyesterification of the chelates, leading to the formation of a polymeric resin, where the metallic cations are trapped in the organic polymeric network. In other words, the polyalcohol is able to create links between the chelates by polyesterification reactions. The formation of the polymeric resin results in the formation of the gel. The subsequent drying process leads to the pyrolysis of the organic compounds, resulting in the formation of multicomponent metal oxide [26].

In this case study, the precursors lithium nitrate (LiNO3) and niobium chloride (NbCl5) (purity > 99%) were chosen. A molar ratio of 1:1 between LiNO3 and NbCl5 was established in order to enhance the formation of the LiNbO3 stoichiometric phase. Firstly, the LiNO3 and NbCl5 were dissolved in deionized water and in a hydrogen peroxide solution (H2O2, 3%, V/V), respectively. For each gram of NbCl5, 3.2 ml of H2O2 was used, originating a yellow transparent and clear solution. Both precursor solutions were mixed with citric acid (CA), fixing a molar ratio of 1:1 between the CA and the metallic cations, in order to form the metal complexes (chelates). The mixing was performed using a magnetic stirrer for 30 min at room temperature. After the mixing process, ethylene glycol (EG) was added to promote the polyesterification of the chelates. A mass ratio of 2:3 was established between the CA and EG to determine the quantity of EG to use. The final solution was mixed again with a magnetic stirrer for about 3 h, and the final gel was yellow and transparent, maintaining its macroscopic appearance for a long time period (>1 month). **Figure 20** outlines the entire preparation process.

The base powder was obtained after drying the gel at 300°C for 1 h, with a heating ramp of 5°C/min, yielding a black/grayish powder.

#### *2.4.2. Thermal, structural, and morphological properties*

The base powder was subjected to several heat treatments (HTs) at temperatures between 400 and 1000°C. These temperatures were chosen according to the differential thermal analysis (DTA) results, presented in **Figure 21**. This thermal technique was performed between room temperature and 1200 °C using a Linseis 63A apparatus. The heating rate was 20 °C/min and Al2O3 powder as used as reference. In **Figure 21**, the thermogram shows the presence of three exothermic thermal processes at the temperatures of 490, 790, and 1050°C, approximately. Consequently, HTs were performed at 450, 500, 800, and 1000°C, for 4 h.

Raman Spectroscopy and Scanning Electron Microscopy Structural Characterization of Lithium Niobate Nanoparticles Prepared by the Sol-Gel Process, Using X-Ray and Raman Spectroscopy and Scanning Electron Microscopyhttp://dx.doi.org/10.5772/64395 63

to have control over some important characteristics, such as the size and shape of the particles

62 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

The Pechini route takes its name on its developer, Maggio Pechini in 1967 [26]. In particular, it was developed to include metals which are not suitable for traditional sol-gel reactions due to their unfavorable hydrolysis equilibria, and thus this method has the advantage of not requiring that the metallic species involved form stable hydroxo-complexes. This method is known for its use on the synthesis of multicomponent metal oxide materials [26], and basically this method uses an R-hydroxycarboxylic acid, such as citric acid (CA), to lead the formation of stable metal complex, i.e., the metallic cations of interest form stable complexes known as chelates. After this step, a polyalcohol, such as ethylene glycol (EG), is used to promote the polyesterification of the chelates, leading to the formation of a polymeric resin, where the metallic cations are trapped in the organic polymeric network. In other words, the polyalcohol is able to create links between the chelates by polyesterification reactions. The formation of the polymeric resin results in the formation of the gel. The subsequent drying process leads to the pyrolysis of the organic compounds, resulting in the formation of multicomponent metal

In this case study, the precursors lithium nitrate (LiNO3) and niobium chloride (NbCl5) (purity > 99%) were chosen. A molar ratio of 1:1 between LiNO3 and NbCl5 was established in order to enhance the formation of the LiNbO3 stoichiometric phase. Firstly, the LiNO3 and NbCl5 were dissolved in deionized water and in a hydrogen peroxide solution (H2O2, 3%, V/V), respectively. For each gram of NbCl5, 3.2 ml of H2O2 was used, originating a yellow transparent and clear solution. Both precursor solutions were mixed with citric acid (CA), fixing a molar ratio of 1:1 between the CA and the metallic cations, in order to form the metal complexes (chelates). The mixing was performed using a magnetic stirrer for 30 min at room temperature. After the mixing process, ethylene glycol (EG) was added to promote the polyesterification of the chelates. A mass ratio of 2:3 was established between the CA and EG to determine the quantity of EG to use. The final solution was mixed again with a magnetic stirrer for about 3 h, and the final gel was yellow and transparent, maintaining its macroscopic appearance for a long time period (>1 month). **Figure 20** outlines the entire preparation process.

The base powder was obtained after drying the gel at 300°C for 1 h, with a heating ramp of

The base powder was subjected to several heat treatments (HTs) at temperatures between 400 and 1000°C. These temperatures were chosen according to the differential thermal analysis (DTA) results, presented in **Figure 21**. This thermal technique was performed between room temperature and 1200 °C using a Linseis 63A apparatus. The heating rate was 20 °C/min and Al2O3 powder as used as reference. In **Figure 21**, the thermogram shows the presence of three exothermic thermal processes at the temperatures of 490, 790, and 1050°C, approximately.

Consequently, HTs were performed at 450, 500, 800, and 1000°C, for 4 h.

5°C/min, yielding a black/grayish powder.

*2.4.2. Thermal, structural, and morphological properties*

and homogeneity.

oxide [26].

**Figure 20.** Diagram of the Pechini method used for the synthesis of the LN base powder. CA, citric acid; EG, ethylene glycol.

**Figure 21.** DTA thermogram of the base powder synthesized by the Pechini method. This thermal analysis was performed between room temperature and 1200 °C, with a heating rate of 20 °C/min.

The XRD measurements performed on these powders (not shown here) revealed that for the HT at 500°C, the LN and LiNb3O8 crystalline phases are present and that the increase of the HT temperature promotes the development of the LiNb3O8 phase. However, the powder HT at 450°C only contained the LiNbO3 phase, whereby this powder was used to prepare pellets which were then sintered at 450°C for 4, 12, 24, 48, and 96 h. Thirty milligrams of powder was used for the preparation of the 10-mm diameter pellets, resulting in a thickness of about 1 mm when applying a uniaxial pressure of 1.5 tons. Hereafter, we will refer to these pellets as samples.

**Figure 22.** XRD patterns of the base powder HT at 450°C and of the samples sintered for 4, 12, 24, 48, and 96 h (× LiNbO3; O LiNb3O8).

**Figure 22** depicts the XRD patterns of the samples sintered during the aforementioned time intervals. The patterns show that the sintering process activated the formation of the LiNb3O8 phase. The XRD technique was performed on a Philips X'Pert MPD (CuKα radiation, *λ* = 1.54056 Å), with a step 0.02° in 1 s, in the 2*θ* angle range of 10–60°. The identification of the crystalline phases was made using the database of the Joint Committee on Powder Diffraction Standards–International Center for Diffraction Data. To get a further insight about the contents of each phase in the samples as well as to calculate the crystallite sizes associated with each phase, a Rietveld refinement was performed for all the diffraction patterns shown in **Figure 22**, using the PowderCell software. In **Figure 23**, the Rietveld fits of the samples 4 h and 4 h + 96 h are presented.

**Figure 23.** The Rietveld fits of the XRD patterns for the powder HT at 450°C, containing only the LN crystalline phase and the sample sintered for 96 h, containing both LN and LiNb3O8.

The Rietveld fit parameters indicate a good fit of the structural models to the experimental data (**Table 2**). Although the XRD patterns shown in **Figure 22** may suggest that the LiNb3O8 phase is present in small amounts, the mass percentages shown in **Table 2** show that the presence of this phase is relevant, reaching the maximum value for the sample 4 h + 96 h. In fact, both LN and LiNb3O8 have reflections lying in close diffraction angles, and some of the observed peaks contain a contribution of the LiNb3O8 phase, besides the LN phase, explaining the relatively high mass percentages. The crystallite size of both phases stands approximately constant for the different samples, especially for the LiNb3O8 phase, which has larger sizes relatively to the LN phase.

at 450°C only contained the LiNbO3 phase, whereby this powder was used to prepare pellets which were then sintered at 450°C for 4, 12, 24, 48, and 96 h. Thirty milligrams of powder was used for the preparation of the 10-mm diameter pellets, resulting in a thickness of about 1 mm when applying a uniaxial pressure of 1.5 tons. Hereafter, we will refer to these pellets as

64 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 22.** XRD patterns of the base powder HT at 450°C and of the samples sintered for 4, 12, 24, 48, and 96 h (× LiN-

**Figure 22** depicts the XRD patterns of the samples sintered during the aforementioned time intervals. The patterns show that the sintering process activated the formation of the LiNb3O8 phase. The XRD technique was performed on a Philips X'Pert MPD (CuKα radiation, *λ* = 1.54056 Å), with a step 0.02° in 1 s, in the 2*θ* angle range of 10–60°. The identification of the crystalline phases was made using the database of the Joint Committee on Powder Diffraction Standards–International Center for Diffraction Data. To get a further insight about the contents of each phase in the samples as well as to calculate the crystallite sizes associated with each phase, a Rietveld refinement was performed for all the diffraction patterns shown in **Figure 22**, using the PowderCell software. In **Figure 23**, the Rietveld fits

**Figure 23.** The Rietveld fits of the XRD patterns for the powder HT at 450°C, containing only the LN crystalline phase

samples.

bO3; O LiNb3O8).

of the samples 4 h and 4 h + 96 h are presented.

and the sample sintered for 96 h, containing both LN and LiNb3O8.


**Table 2.** The initial three parameters are the weighted profile *R*-factor (*R*wp), the expected *R*-factor (*R*exp), and the "chi squared" *χ*<sup>2</sup> . The crystallite size and mass percentage of each crystalline phase in all the samples are also indicated. The last two columns show the dielectric constant (*ε*′) and loss tangent (tan *δ*) at 10 kHz and room temperature (300 K).

**Figure 24.** The Raman spectra of the samples sintered for different times between the time range 4 and 96 h, performed at room temperature.

In **Figure 24**, the Raman spectra of the sintered samples are presented. The spectra show the presence of vibrational bands which are the result of an overlapping of vibrational models of LN and also of the LiNb3O8 crystalline phase, as a consequence of the polycrystalline structure of the prepared samples. For a further analysis of the LN and LiNb3O8 vibrational modes, the authors suggest the reading of Bartasyte et al. report [27]. The room-temperature Raman spectroscopy was performed in backscattering geometry using a T64000 Jobin-Yvon spectrometer. A microscope objective (50×) focused the exciting light (Ar+ laser, *λ* = 532 nm) onto the sample (spot diameter <0.8 μm).

**Figure 25.** SEM micrographs of the LN polycrystalline samples prepared by the Pechini method, sintered at 450°C for 4, 12, 24, 48, and 96 h.

In **Figure 25**, SEM micrographs of the samples are shown, as well as the variation of the grain size with the sintering time. The grain size increases significantly with the sintering time from 4 to 12 h and then decreases slightly up to 96 h. As for the morphology, the grains show an approximate spherical geometry. The SEM was executed on a HITACHI S4100-1. All samples were sputtered with carbon before the analysis.

#### *2.4.3. Electrical and dielectric properties*

The electrical analysis of these types of samples is not evident. **Figure 26** shows the temperature dependence of the dc conductivity (*σ*dc) for all samples, revealing a decrease of the conductivity with the increase of the sintering time. This suggests a probable decrease in the number of charge carriers.

However, **Figure 27** shows that the activation energy, calculated in the high-temperature region (marked by the Arrhenius regression line in **Figure 26**), decreases substantially from sample sintered at 4 h to the sample sintered at 96 h. This profile indicates that the height of the potential barriers, from which the charge carriers must pass through, decreases, which should promote an increase in their mobility. Therefore, this analysis indicates a decrease in the number of charge carriers and also an increase in their mobility.

Raman Spectroscopy and Scanning Electron Microscopy Structural Characterization of Lithium Niobate Nanoparticles Prepared by the Sol-Gel Process, Using X-Ray and Raman Spectroscopy and Scanning Electron Microscopy http://dx.doi.org/10.5772/64395 67

of the prepared samples. For a further analysis of the LN and LiNb3O8 vibrational modes, the authors suggest the reading of Bartasyte et al. report [27]. The room-temperature Raman spectroscopy was performed in backscattering geometry using a T64000 Jobin-Yvon spec-

**Figure 25.** SEM micrographs of the LN polycrystalline samples prepared by the Pechini method, sintered at 450°C for

In **Figure 25**, SEM micrographs of the samples are shown, as well as the variation of the grain size with the sintering time. The grain size increases significantly with the sintering time from 4 to 12 h and then decreases slightly up to 96 h. As for the morphology, the grains show an approximate spherical geometry. The SEM was executed on a HITACHI S4100-1. All samples

The electrical analysis of these types of samples is not evident. **Figure 26** shows the temperature dependence of the dc conductivity (*σ*dc) for all samples, revealing a decrease of the conductivity with the increase of the sintering time. This suggests a probable decrease in the number of

However, **Figure 27** shows that the activation energy, calculated in the high-temperature region (marked by the Arrhenius regression line in **Figure 26**), decreases substantially from sample sintered at 4 h to the sample sintered at 96 h. This profile indicates that the height of the potential barriers, from which the charge carriers must pass through, decreases, which should promote an increase in their mobility. Therefore, this analysis indicates a decrease in the

laser, *λ* = 532 nm) onto

trometer. A microscope objective (50×) focused the exciting light (Ar+

66 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

the sample (spot diameter <0.8 μm).

4, 12, 24, 48, and 96 h.

charge carriers.

were sputtered with carbon before the analysis.

number of charge carriers and also an increase in their mobility.

*2.4.3. Electrical and dielectric properties*

**Figure 26.** Arrhenius representation of the dc conductivity (*σ*dc) for the samples sintered at 450°C for 4, 12, 24, 48, and 96 h.

**Figure 27.** Dc conductivity (*σ*dc) and activation energy (*E*a(dc)) of the samples sintered at 450°C for 4, 12, 24, 48, and 96 h, at room temperature (300 K).

As discussed in Section 2.3, the electrical conduction in crystalline LN can be due to oxygen vacancies, in low-pressure and/or high-temperature conditions (polaron-hopping mechanism), and due to lithium ions in high-pressure conditions (ionic conduction). In this case, the conduction will depend on the ratio between Li/Nb both for high and low pressures. Therefore, in this case context, the conduction related with the lithium-ion (Li+ ) hypothesis seems to be more relevant. The existence of the LiNb3O8 secondary phase, which is a reach niobium LN phase, implies an increase of the number of Li+ ions not connected to a crystalline structure, which allied to the decrease of the activation energy should improve the *σ*dc, which is not observed. This fact indicates that the number of Li+ ions inserted in the crystalline structure increases and is explained by two hypotheses: there is a possible existence of an amorphous phase in all samples and thus the number of lithium ions inserted in this amorphous phase should decrease with the increase of the sintering time, stimulating an increase of the crystalline amount. The second hypothesis is associated with the low-melting point of lithium (~454 K). The increase of the sintering time must raise the possibility of some Li+ ions to be released during sintering. Density measurements revealed that all samples have a density between 3.53 and 3.69 g/cm3 , which are values lower than the characteristic ones for LN (4.65 g/cm3 ) and LiNb3O8 (3.87 g/cm3 ). This fact increases the probabilities of the first hypothesis.

Both dc and ac conductivities (**Figures 26**–**29**) increase with the rise of the measurement temperature, showing that both mechanisms are thermally activated. However, with the increase in the sintering time, the *σ*ac shows the opposite trend of *σ*dc (it increases). This indicates that the conduction mechanism and dominant charge carriers are not the same in both processes. In our opinion, the *σ*ac increase should be related with the decrease of the grain size (**Figure 25**) observed from sample sintered at 12 h up to the sample sintered at 96 h.

**Figure 28.** Arrhenius representation of the ac conductivity (*σ*ac) for the samples sintered at 450°C for 4, 12, 24, 48, and 96 h.

**Figure 29.** Ac conductivity (*σ*dc) and activation energy (*E*a(ac)) of the samples sintered at 450°C for 4, 12, 24, 48, and 96 h, at 10 kHz and room temperature (300 K).

The dielectric constant is maximum for the sample sintered at 24 h (**Table 2**), measured at room temperature and 10 kHz, which is in accordance with the Rietveld refinement results (**Table 2**), by presenting the highest crystallite size. The sample sintered at 48 h shows a dielectric constant value very near the maximum, which should be related with the amount of LN phase present in the sample and not the size of their grains (**Table 2**). It must be noted that the values presented in **Table 2** were obtained without assuming the existence of the hypothetical amorphous phase. These two samples present a dielectric loss below 0.15 at room temperature and 10 kHz (**Table 2**), being almost constant for temperatures between 200 and 300 K.

should decrease with the increase of the sintering time, stimulating an increase of the crystalline amount. The second hypothesis is associated with the low-melting point of lithium

released during sintering. Density measurements revealed that all samples have a density

Both dc and ac conductivities (**Figures 26**–**29**) increase with the rise of the measurement temperature, showing that both mechanisms are thermally activated. However, with the increase in the sintering time, the *σ*ac shows the opposite trend of *σ*dc (it increases). This indicates that the conduction mechanism and dominant charge carriers are not the same in both processes. In our opinion, the *σ*ac increase should be related with the decrease of the grain size

**Figure 28.** Arrhenius representation of the ac conductivity (*σ*ac) for the samples sintered at 450°C for 4, 12, 24, 48, and

**Figure 29.** Ac conductivity (*σ*dc) and activation energy (*E*a(ac)) of the samples sintered at 450°C for 4, 12, 24, 48, and

, which are values lower than the characteristic ones for LN

). This fact increases the probabilities of the first hypoth-

ions to be

(~454 K). The increase of the sintering time must raise the possibility of some Li+

68 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

(**Figure 25**) observed from sample sintered at 12 h up to the sample sintered at 96 h.

between 3.53 and 3.69 g/cm3

) and LiNb3O8 (3.87 g/cm3

(4.65 g/cm3

esis.

96 h.

96 h, at 10 kHz and room temperature (300 K).

The 3D plots (**Figures 30** and **31**) show the presence of a dielectric relaxation phenomenon practically independent on the measurement temperature. However, the frequency of the maximum observed in the loss tangent diagram decreases with the increase of the sintering time, which can be related to the suggested decrease of the amorphous phase content and consequent increase of the LN in crystalline form which is a material where the dielectric depolarization is very difficult, i.e., high-relaxation time characteristic.

**Figure 30.** At left: dependency of the dielectric constant with the temperature and frequency for the sample sintered at 450°C for 24 h. At right: dependency of the dielectric constant with the temperature and frequency for the sample sintered at 450°C for 96 h.

**Figure 31.** At left: dependency of the loss tangent with the temperature and frequency for the sample sintered at 450°C for 24 h. At right: dependency of the loss tangent with the temperature and frequency for the sample sintered at 450°C for 96 h.

## **Author details**

Pedro R.S. Prezas\* and Manuel P.F. Graça

\*Address all correspondence to: pedro.rafael@ua.pt

University of Aveiro/I3N—Physics Department, Aveiro, Portugal

## **References**


[11] Graça M.P.F., Prezas P.R., Costa M.M., Valente M.A., *Structural and dielectric characterization of LiNbO3 nano-size powders obtained by Pechini method*, J. Sol-Gel Sci. Technol., 2012, 64:78-85

**Author details**

Pedro R.S. Prezas\*

**References**

1989, 72(8):1311-1321

Croatia, ISBN: 978-953-307-350-7.

J. Cryst. Growth, 1992, 116:327-332

State Mater. Sci., 1998, 3(5):469-473

*synthesis method*, Ceram. Int., 2014, 40:1835-1841

Ionics, 2012, 225:26-29

360:181-184

8:6.1-6.7

and Manuel P.F. Graça

University of Aveiro/I3N—Physics Department, Aveiro, Portugal

70 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

[1] Abouelleil M.M. and Leonberger F.J., *Waveguides in lithium niobate*, J. Am. Ceram. Soc.,

[2] Graça M.P.F. and Valente M.A. *Glass ceramics with para, anti or ferroelectric active phases*, Advances in Ceramics – Electric and Magnetic Ceramics, Bioceramics, Ceramics and Environment, Prof. Sikalidis C. (Ed.), InTech (2011). Janeza Trdine 9, 51000 Rijeka,

[3] Volk T. and Wohlecke (2008), Lithium Niobate: Defects, Photorefraction and Ferroelectric Switching*,* Springer-Verlag, Berlin, Heidelberg, ISBN: 978-3-540-70765-3.

[4] Bordui P.F., Norwood R.G., Jundt D.H., Fejer M.M., *Preparation and characterization of*

[5] Kitamura K., Yamamoto J.K., Iyi N., Kimura S., Hayashi T., *Stoichiometric LiNbO3 single crystal growth by double crucible Czochralski method using automatic powder supply system*,

[6] Weidenfelder A., Shi J., Fielitz P., Borchardt G., Becker K.D., Fritze H., *Electrical and electromechanical properties of stoichiometric lithium niobate at high-temperatures*, Solid State

[7] Szaller Zs., Péter Á., Polgár K., Szabó Gy., *High temperature top seeded solution growth of stoichiometric lithium niobate LiNbO3 (sLN) with planar interface*, J. Cryst. Growth, 2012,

[8] Damjanovic D., *Materials for high temperature piezoelectric transducers*, Curr. Opin. Solid

[9] Ohlendorf G., Richter D., Sauerwald J., Fritze H., *High-temperature electrical conductivity and electromechanical properties of stoichiometric lithium niobate*, Diff. Fundam., 2008,

[10] Kamali A.R. and Fray D.J., *Preparation of lithium niobate particles via reactive molten salt*

*off-congruent lithium niobate crystals*, J. Appl. Phys., 1992, 71(2):875-879

\*Address all correspondence to: pedro.rafael@ua.pt


## **Raman Spectroscopy, a Useful Tool to Study Nuclear Materials Raman Spectroscopy, a Useful Tool to Study Nuclear Materials**

Laura J. Bonales, Jone M. Elorrieta, Álvaro Lobato and Joaquin Cobos Joaquin Cobos Additional information is available at the end of the chapter

Additional information is available at the end of the chapter

Laura J. Bonales, Jone M. Elorrieta, Álvaro Lobato and

http://dx.doi.org/10.5772/64436

#### **Abstract**

[26] Roque-Malherbe R.M.A. (2009), *The Physical Chemistry of Materials: Energy and Environmental Applications*, CRC Press, 6000 Broken Sound Parkway, NW Suite 300 Boca Raton,

72 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

[27] Bartasyte A., Plausinaitiene V., Abrutis A., Stanionyte S., Margueron S., Boulet P., et al.*, Identification of LiNbO3, LiNb3O8 and Li3NbO4 phases in thin films synthesized with different deposition techniques by means of XRD and Raman spectroscopy*, J. Phys.: Condens.

FL 33487, United States, ISBN: 9781420082722.

Matter., 2013, 25(20):205901.

The use of the Raman technique is nowadays being widely spread in many scientific and industrial disciplines. The rise of this spectroscopy is due to the technology developed in some of its main components (the laser, charge-coupled device (CCD) sensors, gratings, filters, etc.), what reduces the cost of the equipment. Characterization by Raman spectroscopy has long and well-established tradition in fields such as condensed matter physics and chemistry. In nuclear sciences, by contrast, it is far from being extensively applied, even though this technique can be especially useful. It is a fact that only a scarce number of Raman laboratories dealing with nuclear materials exist, and therefore a limited database related to these materials. In such a context, this chapter is devoted to the practical use of Raman spectroscopy for nuclear materials characterization.

**Keywords:** Raman, nuclear, uranium oxides, U-secondary phase

## **1. Introduction**

Nuclear power is a controversial subject that generates a debate in today's society; nevertheless, the existing 438 nuclear reactors [1] produce approximately 15% of the world's electricity [2], making it a major world energy source.

Proponents of nuclear energy describe nuclear power production as a low running costs and a nature friend since it can be considered a low carbon technology compared with fossil fuels such as coal, gas, and oil [3]. Opponents of nuclear power argue that this energy has very high initial costs, complex nuclear waste management, and high plant decommissioning costs, and

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

highlight the environmental and public risks and dangers associated with it [4, 5]. This debate has been mirrored by the number of nuclear power plant (NPP) constructions. For example [6], before the accident in Fukushima Daiichi in 2011, the number of NPPs was increasing due to the concerns over greenhouse gas emissions to avoid further global warming. Then, the accident impacted public acceptance of nuclear power and had an effect of decreasing the number of nuclear reactors [7]. In recent years, the number of constructions commencing are on the rise again [8], and the main concern is related to the nuclear waste management, mainly spent nuclear fuel (SNF).

The most common nuclear fuel consists of uranium dioxide, UO2, enriched from 0.7 to 3–5% of 235U depending on which reactor it will be loaded into [9]. After its irradiation in the reactor core, the fuel is composed of a matrix of UO2 (>95%) doped with fission products and transuranium elements [10], which are found as bubbles (Xe, Kr), metallic precipitates (Mo, Tc, Ru, Rh, and Pd), oxide precipitates (Rb, Cs, Ba, and Zr), solid solutions, and transuranium elements dissolved by U substitution in the UO2 matrix [11]. These elements are not distributed homogeneously as a consequence of the thermal gradient within the UO2 pellet (temperature as high as 1700°C at the center of the pellet and decreasing to 400°C outwards) [12, 13]. Besides, the spent nuclear fuel suffers substantial microstructural modifications from the initial fresh fuel such as coarsening of the grains and extensive microcracking. Thus, SNF can be described as a complex, hot, and radioactive waste and therefore extremely dangerous. Bruno et al. [14] provide a particularly suitable example to demonstrate how hazardous the SNF is, that is, …"*One year after discharge from a reactor…a person exposed to this level of radioactivity at a distance of one meter would receive a lethal dose in less than one minute…."*

After several thousands of years, the total radioactivity of the SNF equals the radioactivity of natural uranium [15]. Therefore, within the management of spent nuclear fuel, the safe storage of this radioactive waste from the discharge of the reactor until the decay reaches natural uranium radioactivity is considered. Countries adopt different stages of these nuclear storages according to their internal policies [16], but usually the following steps are suitable: (i) spent fuel pools [17], (ii) intermediate storage or reprocessing [18], and (iii) final storage [19].

After SNF is removed from the reactor, it is stored for the first few years on-side in water containers or pools, located close to the reactor in order to allow the spent fuel to decay, both radioactively and thermally. Then, it can be transported to a reprocessing facility or to a definitive storage facility. However, since final repositories for spent fuel do not exist for the moment, interim storage is required. NPPs use the spent fuel dry-cask storages, which are steel and concrete containers filled with an inert gas as a first step for interim storage. Although no ultimate storage in operation exists, the deep geological repository is internationally accepted as the best solution [20].

The performance of the mentioned repositories requires knowledge of the SNF stability at different storage conditions. Thereby, the studies of the spent fuel behavior can be mainly divided into dry and wet conditions, given the different evolution observed in each case. The studies of spent nuclear fuel under dry conditions are mainly focused on the oxidation of both the UO2 matrix and the AnO2 [21] present in the SNF.1 In case of shielding failure, the oxidation of AnO2 and UO2 takes place owing to its contact with the atmospheric oxygen and the high temperatures present (up to 400°C) [15]. This oxidation occurs via oxygen incorporation into the fluorite structure (fcc) of the stoichiometric oxide, for example, some actinides as plutonium and uranium can oxidize to AnO2+*x* (*x* < 0.25) maintaining the fcc structure [22]. Further oxidation to higher-oxidation states (V and VI) leads to different structures. For example, the transformation of UO2 into U3O8 via the two-step reaction [23] UO2→ U4O9/U3O7→ U3O8 entails an increase in the volume of around 36% and, consequently, it might cause the loss of the UO2 matrix integrity.

On the other hand, the studies of spent nuclear fuel under wet conditions are focused on the corrosion process of this waste. This might happen in case the SNF shielding fails while stored in pools or in the deep geological repository at timescales of the order of some thousands of years [24] when it is assumed that the barriers that protect the waste will be breached and SNF will be in contact with water [25]. The UO2 matrix of the spent nuclear fuel might dissolve with water and then the release to the biosphere of the SNF radioactive contents might occur [26–28].

This corrosion process is primarily described by the oxidation of uranium, U(IV) → U(VI), and then the alteration products formation, usually containing UO2 2+ in their crystal structures [29] U(VI) → UO2 2+ (s).

Great effort has been performed to analyze the reaction mechanism and to establish the key parameter that controls the corrosion of the SNF such as leaching/dissolution experiments [30–32] and studies of the uraninite, a natural analog of the spent nuclear fuel matrix [33, 34]. These stability studies require the characterization of the SNF and its reaction products, with O2 and/or water, which is a great challenge not only because these materials are very complicated (containing almost the entire periodic table) [11] but also because intense radiation field inherently associated to these materials makes it difficult to examine them in safe conditions.

In order to minimize radiation doses and the release of radioactive material, the working procedure employed to study these materials must fulfill the ALARA principle (acronym for "as low as reasonably achievable") [35]. Such a reliable procedure must, hence, minimize the time that radioactive materials are handled and maximize the distance to them. Raman spectroscopy is an analyzing technique that has been established in recent years as a useful tool since it fulfills the mentioned safe principles, as shown by the increase in the number of publications dealing with the characterization of nuclear materials by this technique [36–44]. This is due to some of its features as (1) that it does not require any special preparation of the sample, (2) it allows the analysis of a very small amount of sample, and (3) it is a nondestructive technique.

Besides these safety principles, the confinement of the whole apparatus in a glove box or a hot cell is also very common, which obviously complicates the measurements [45]. Despite the advantages mentioned above, the characterization of these SNF and related nuclear materials is far from being well established. Existing databases must be improved and new methods

highlight the environmental and public risks and dangers associated with it [4, 5]. This debate has been mirrored by the number of nuclear power plant (NPP) constructions. For example [6], before the accident in Fukushima Daiichi in 2011, the number of NPPs was increasing due to the concerns over greenhouse gas emissions to avoid further global warming. Then, the accident impacted public acceptance of nuclear power and had an effect of decreasing the number of nuclear reactors [7]. In recent years, the number of constructions commencing are on the rise again [8], and the main concern is related to the nuclear waste management, mainly

74 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

The most common nuclear fuel consists of uranium dioxide, UO2, enriched from 0.7 to 3–5% of 235U depending on which reactor it will be loaded into [9]. After its irradiation in the reactor core, the fuel is composed of a matrix of UO2 (>95%) doped with fission products and transuranium elements [10], which are found as bubbles (Xe, Kr), metallic precipitates (Mo, Tc, Ru, Rh, and Pd), oxide precipitates (Rb, Cs, Ba, and Zr), solid solutions, and transuranium elements dissolved by U substitution in the UO2 matrix [11]. These elements are not distributed homogeneously as a consequence of the thermal gradient within the UO2 pellet (temperature as high as 1700°C at the center of the pellet and decreasing to 400°C outwards) [12, 13]. Besides, the spent nuclear fuel suffers substantial microstructural modifications from the initial fresh fuel such as coarsening of the grains and extensive microcracking. Thus, SNF can be described as a complex, hot, and radioactive waste and therefore extremely dangerous. Bruno et al. [14] provide a particularly suitable example to demonstrate how hazardous the SNF is, that is, …"*One year after discharge from a reactor…a person exposed to this level of radioactivity at a distance*

After several thousands of years, the total radioactivity of the SNF equals the radioactivity of natural uranium [15]. Therefore, within the management of spent nuclear fuel, the safe storage of this radioactive waste from the discharge of the reactor until the decay reaches natural uranium radioactivity is considered. Countries adopt different stages of these nuclear storages according to their internal policies [16], but usually the following steps are suitable: (i) spent fuel pools [17], (ii) intermediate storage or reprocessing [18], and (iii) final storage [19].

After SNF is removed from the reactor, it is stored for the first few years on-side in water containers or pools, located close to the reactor in order to allow the spent fuel to decay, both radioactively and thermally. Then, it can be transported to a reprocessing facility or to a definitive storage facility. However, since final repositories for spent fuel do not exist for the moment, interim storage is required. NPPs use the spent fuel dry-cask storages, which are steel and concrete containers filled with an inert gas as a first step for interim storage. Although no ultimate storage in operation exists, the deep geological repository is internationally accepted

The performance of the mentioned repositories requires knowledge of the SNF stability at different storage conditions. Thereby, the studies of the spent fuel behavior can be mainly divided into dry and wet conditions, given the different evolution observed in each case. The studies of spent nuclear fuel under dry conditions are mainly focused on the oxidation of both

of AnO2 and UO2 takes place owing to its contact with the atmospheric oxygen and the high

In case of shielding failure, the oxidation

*of one meter would receive a lethal dose in less than one minute…."*

the UO2 matrix and the AnO2 [21] present in the SNF.1

spent nuclear fuel (SNF).

as the best solution [20].

<sup>1</sup> A meaning minor actinides such as Np, Pu, and Am.

must be developed. Due to the hazardous feature of nuclear materials, both the development of new protocols and Raman spectra acquisition (for the purpose of extending the databases) are usually performed first by analyzing the behavior of different SNF analogs and, once the method is feasible, by applying it to the real SNF. Such analogs can be divided into two kinds: synthetic analogs such as uranium dioxide (UO2) [46, 47] or SIMFUEL (simulated fuel) [48, 49], and natural analogs such as uraninite.

In this context, this chapter is structured as follows: In the first part, Raman spectroscopy is described. First, the theoretical aspects on an introductory level are explained. Second, the main components of the Raman spectrometers are presented and, as an example, the *LabRam HR Evolution* spectrometer is described in more detail. The "Results" section has been divided into two, corresponding to dry and wet conditions; in each part, the developed method and the results found for analogs of the SNF are shown. Namely, the materials studied in this section are the different uranium oxides, UO2+*x* (0 < *x* < 0.25), U4O9/U3O7, and U3O8, and several secondary phases such as rutherfordine, soddyite, uranophane alpha, or kasolite.

## **2. Raman spectroscopy technique**

#### **2.1. Description of the Raman phenomena**

Raman effect owes its name to the Indian physicist Chandrasekhara Venkata Raman [50] who won the Nobel Prize for its discovery. In his Nobel lecture, given on December 11, 1930, Sir C.V. Raman said…"*The frequency differences determined from the spectra, the width and character of the lines appearing in them, and the intensity and state of polarization of the scattered radiations enable us to obtain an insight into the ultimate structure of the scattering substance […]. It follows that the new field of spectroscopy has practically unrestricted scope in the study of problems related to the structure of matter*" [51].

As other molecular spectroscopy techniques, Raman scattering is based on the analysis of lightmatter interaction [52], that is, absorption, emission, or scattering of a photon. Two interpretations of this phenomenon can be considered: the quantum mechanical method and the classical interpretation. In the purely classical interpretation, the radiation is considered as an electromagnetic wave, and the matter as an assembly of independent classical rotors and vibrators. This model can explain satisfactorily the main features of the light scattering such as the frequency dependence and some key aspect related to their selection rules.

Raman effect is described as an inelastical scattering of light. From a macroscopic point of view, light scattering consists in a deviation of light from its straight trajectory (original direction of incident light). Molecules scatter light because the electric field of the incident light wave forces the electrons within the molecule to oscillate (see **Figure 1**), producing oscillating electric moments leading to the reemission of radiation in all directions [53].

must be developed. Due to the hazardous feature of nuclear materials, both the development of new protocols and Raman spectra acquisition (for the purpose of extending the databases) are usually performed first by analyzing the behavior of different SNF analogs and, once the method is feasible, by applying it to the real SNF. Such analogs can be divided into two kinds: synthetic analogs such as uranium dioxide (UO2) [46, 47] or SIMFUEL (simulated fuel) [48,

76 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

In this context, this chapter is structured as follows: In the first part, Raman spectroscopy is described. First, the theoretical aspects on an introductory level are explained. Second, the main components of the Raman spectrometers are presented and, as an example, the *LabRam HR Evolution* spectrometer is described in more detail. The "Results" section has been divided into two, corresponding to dry and wet conditions; in each part, the developed method and the results found for analogs of the SNF are shown. Namely, the materials studied in this section are the different uranium oxides, UO2+*x* (0 < *x* < 0.25), U4O9/U3O7, and U3O8, and several

Raman effect owes its name to the Indian physicist Chandrasekhara Venkata Raman [50] who won the Nobel Prize for its discovery. In his Nobel lecture, given on December 11, 1930, Sir C.V. Raman said…"*The frequency differences determined from the spectra, the width and character of the lines appearing in them, and the intensity and state of polarization of the scattered radiations enable us to obtain an insight into the ultimate structure of the scattering substance […]. It follows that the new field of spectroscopy has practically unrestricted scope in the study of problems related to the*

As other molecular spectroscopy techniques, Raman scattering is based on the analysis of lightmatter interaction [52], that is, absorption, emission, or scattering of a photon. Two interpretations of this phenomenon can be considered: the quantum mechanical method and the classical interpretation. In the purely classical interpretation, the radiation is considered as an electromagnetic wave, and the matter as an assembly of independent classical rotors and vibrators. This model can explain satisfactorily the main features of the light scattering such

Raman effect is described as an inelastical scattering of light. From a macroscopic point of view, light scattering consists in a deviation of light from its straight trajectory (original direction of incident light). Molecules scatter light because the electric field of the incident light wave forces the electrons within the molecule to oscillate (see **Figure 1**), producing oscillating electric

as the frequency dependence and some key aspect related to their selection rules.

moments leading to the reemission of radiation in all directions [53].

secondary phases such as rutherfordine, soddyite, uranophane alpha, or kasolite.

49], and natural analogs such as uraninite.

**2. Raman spectroscopy technique**

**2.1. Description of the Raman phenomena**

*structure of matter*" [51].

**Figure 1.** Light scattering produced by the interaction of the incident light's electric field and the molecule electrons.

Such process produces two types of radiation, Rayleigh radiation, which has the same frequency that the incident light (*ν*0), and Raman radiation, which consists in a new set of frequencies with more or less energy than the incident radiation (*ν*0 ± *ν*1), where *ν*1 is typically related to the rotational, vibrational, and electronic levels of the molecule. In **Figure 2**, a general scheme of the scattering process and its difference with the absorption process from the point of view of the photons and the energy levels of the molecule are represented.

**Figure 2.** Energy level diagrams describing the physical phenomenon of (1) IR absorption, (2) Rayleigh scattering, and (3) Raman scattering.

Before the interaction of the radiation with the system, there are N photons of energy *hcν*0. In the case of the absorption process, the interaction of the radiation with the system leads to the excitation of the molecule to a higher energy state resulting in a radiation which consists in N − 1 photons of energy *hcν*0. This process can occur, if and only if the incoming photon has the same energy as the difference between the initial and final state of the molecule, *E*f − *E*<sup>i</sup> = *hcν*fi = *hcν*0, fulfilling the condition of energy conservation.

Let us now consider the scattering process, the interaction between the incident radiation and the system produces the annihilation of a photon of energy *hcν*0, and simultaneously the creation of a new photon with energy *E*s. Now the radiation consists in N − 1 photons of energy *hcν*0, a new photon of energy *hcν*s, and the transition to the molecule to a final state with energy *E*f . In the overall process, the energy must be conserved so, *hcν*0 = *hcν*s + *E*<sup>f</sup> .

This two-photon process can be visualized as two simultaneous stages. First, the annihilation stage which leads the molecule to a virtual high-energy state. Virtual states are created when the laser interacts with the molecule and causes polarization; hence, their energy is determined by the frequency of the incident light source used (*ν*0). At this stage, there is no energy conservation implying that the role of the incident radiation in the scattering is to perturb the molecule given the possibility to allow different spectroscopic transitions rather than the absorption process. Second, the creation stage, where the molecule reaches its final state with energy *E*<sup>f</sup> producing the new photon. At this point, we can consider two types of scattered light: (1) the Rayleigh scattering, or elastic scattering, where the final state of the molecule is its own initial state, *E*<sup>f</sup> = *E*<sup>i</sup> *,* and, correspondingly, the energy of the scattered light corresponds to the initial frequency value, *ν*s = *ν*0. (2) The Raman scattering, or inelastic scattering, in which the molecule reaches a final state different from its initial state; hence, the energy of the scattered light has a different frequency value from the incident radiation, *ν*s = *ν*0 ± *ν*fi. This process is much less probable than Rayleigh scattering (only 10−5 − 10−8 of the incident beam intensity). If the final state has a higher energy than the initial state, *E*<sup>f</sup> > *E*<sup>i</sup> , the scattered photon loses energy, *ν*s = *ν*0 − *ν*fi. This radiation is known as Stokes Raman scattering. By contrast, if the final state has a lower energy than the initial state, *E*<sup>f</sup> < *E*<sup>i</sup> , the scattered photon increases its energy, *ν*s = *ν*0 + *ν*fi, giving the anti-Stokes Raman scattering. Relative probabilities of Stokes and anti-Stokes radiation depend on the population of the molecule states, *f* and *i*, and therefore on temperature according to the Maxwell-Boltzmann distribution. As both give the same information, it is customary to measure only the "Stokes" side of the spectrum.

Even though this general scheme describes scattering phenomena in a qualitative way, it highlights some key aspect of the Raman spectroscopy and its differences with the absorption process. Nevertheless, it is worth to describe the classical treatment of the Raman scattering in order to provide a deeper insight in the frequency dependence and the microscopic origin of the scattered light. Classical wave interpretation [54, 55] of the Raman effect is based on the time-dependent polarizability of the molecules. Consider one of the simplest scattering systems, a vibrating diatomic AB molecule.

Such a system can be modeled, at first approximation, as two balls attached by a spring (**Figure 3**). According to Hook´s law, its relative movement can be described by the second Newton law as follows:

**Figure 3.** Simplified model of a diatomic AB molecule.

$$
\mu \left( \frac{d^2 \mathbf{x}\_1}{dt^2} + \frac{d^2 \mathbf{x}\_2}{dt^2} \right) = K \left( \mathbf{x}\_1 + \mathbf{x}\_2 \right) \tag{1}
$$

where *μ* represents the reduced mass of the molecule, *x* represents the displacement, and *K* represents the bond strength. For small vibrations, the harmonic approximation holds, and then the normal coordinates *q*(*t*) of the vibrating molecule can be expressed as

$$q = q\_0 \cos\left(2\pi\nu\_m t\right) \tag{2}$$

where *q0* is the amplitude and *ν*m is the natural vibration frequency which is defined in terms of its bond strength as

$$\nu\_m = \frac{1}{2\pi} \sqrt{\frac{K}{\mu}} \tag{3}$$

When incident light interacts with a molecule, induces a dipole moment, *P*, equal to the product of the polarizability of the molecule, *α*, and the electric field of the incident light source *E*

$$P = \text{ or } E\_0 \cos(2\pi\nu\_o t),\tag{4}$$

where *E*0 and *ν*o are the electric field amplitude and frequency, respectively. As far as the molecule is vibrating, its polarizability varies according to the relative displacement of these atoms and therefore we can express *α* as a power series *q*

$$\alpha = \left. \alpha\_0 + q \left( \frac{\partial \alpha}{\partial q} \right)\_0 + \dots \right. \tag{5}$$

which when combined with Eqs. (3) and (5) results in,

the laser interacts with the molecule and causes polarization; hence, their energy is determined by the frequency of the incident light source used (*ν*0). At this stage, there is no energy conservation implying that the role of the incident radiation in the scattering is to perturb the molecule given the possibility to allow different spectroscopic transitions rather than the absorption process. Second, the creation stage, where the molecule reaches its final state with

78 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

light: (1) the Rayleigh scattering, or elastic scattering, where the final state of the molecule is

to the initial frequency value, *ν*s = *ν*0. (2) The Raman scattering, or inelastic scattering, in which the molecule reaches a final state different from its initial state; hence, the energy of the scattered light has a different frequency value from the incident radiation, *ν*s = *ν*0 ± *ν*fi. This process is much less probable than Rayleigh scattering (only 10−5 − 10−8 of the incident beam

loses energy, *ν*s = *ν*0 − *ν*fi. This radiation is known as Stokes Raman scattering. By contrast, if the

energy, *ν*s = *ν*0 + *ν*fi, giving the anti-Stokes Raman scattering. Relative probabilities of Stokes and anti-Stokes radiation depend on the population of the molecule states, *f* and *i*, and therefore on temperature according to the Maxwell-Boltzmann distribution. As both give the same

Even though this general scheme describes scattering phenomena in a qualitative way, it highlights some key aspect of the Raman spectroscopy and its differences with the absorption process. Nevertheless, it is worth to describe the classical treatment of the Raman scattering in order to provide a deeper insight in the frequency dependence and the microscopic origin of the scattered light. Classical wave interpretation [54, 55] of the Raman effect is based on the time-dependent polarizability of the molecules. Consider one of the simplest scattering

Such a system can be modeled, at first approximation, as two balls attached by a spring (**Figure 3**). According to Hook´s law, its relative movement can be described by the second

( ) 2 2

2 2 1 2 *dx dx Kx x*

è ø (1)

1 2

*dt dt*

æ ö ç ÷ + =+

m

information, it is customary to measure only the "Stokes" side of the spectrum.

producing the new photon. At this point, we can consider two types of scattered

*,* and, correspondingly, the energy of the scattered light corresponds

< *E*<sup>i</sup>

> *E*<sup>i</sup>

, the scattered photon increases its

, the scattered photon

energy *E*<sup>f</sup>

its own initial state, *E*<sup>f</sup>

= *E*<sup>i</sup>

final state has a lower energy than the initial state, *E*<sup>f</sup>

systems, a vibrating diatomic AB molecule.

**Figure 3.** Simplified model of a diatomic AB molecule.

Newton law as follows:

intensity). If the final state has a higher energy than the initial state, *E*<sup>f</sup>

$$P = \alpha\_0 E\_0 \cos\left(2\pi\nu\_0 t\right) + q\_0 \cos\left(2\pi\nu\_n t\right) E\_0 \cos\left(2\pi\nu\_0 t\right) \left(\frac{\partial a}{\partial q}\right)\_0 \tag{6}$$

$$P = \alpha\_o E\_o \cos(2\pi \mathbf{v}\_o t) + \left(\frac{\partial \alpha}{\partial q}\right)\_0 q\_o E\_o \left[\cos\left(2\pi \left\{\mathbf{v}\_o - \mathbf{v}\_m\right\} t\right) + \cos\left(2\pi \left\{\mathbf{v}\_o + \mathbf{v}\_m\right\} t\right)\right] \tag{7}$$

From Eq. (7), it is evident that the induced electric dipole is formed by three different terms. The first one gives rise to an oscillating moment at the same frequency of the incident light, the Rayleigh scattering, and two additional terms which accounts for the Stokes and anti-stokes Raman scattering. Therefore, Rayleigh scattering arises from an electric dipole which oscillates at the same frequency induced in the molecule by the electric field of the incident radiation, whereas Raman scattering arises from the modulation of the electric dipole with the natural frequency of the vibrating molecule. This modulation is produced by the electrons of the molecule, whose rearrangement produces a coupling between the nuclear motion and the electric field of the radiation.

#### **2.2. Dispersive Raman spectrometer**

From the basis of the Raman effect described above, it is easy to deduce that in a conventional (or dispersive) Raman spectrometer,2 the main difficulty lies in separating the intense stray light of the Rayleigh scattering from the much weaker Raman-scattered light. Besides, as Raman scattering has low efficiency, the optimization of each of the instrumental components becomes critically important.

The main components of a Raman setup are as follows:


*1. Excitation source:* Traditionally, mercury arc lamps were used as light sources until being replaced by laser sources. Laser beams are highly monochromatic, present small diameter and, with the help of different optic devices, can be focused on small samples. Different lasers can be used as the light source in Raman spectrometry, as the ones shown in **Table 1** [56].


**Table 1.** Lasers used as light source in Raman spectroscopy.

In addition, in order to enhance the laser quality it is possible to employ a pass-band filter, designed to pass only a certain band of frequencies while attenuating all signals outside this band. This component is commonly known as interferometric filter.

*2. Sample illumination system and collection optics*: The collimation and focusing optics of the exciting radiation onto the sample depends on the experimental setup. In principle, excitation

<sup>2</sup> Raman systems are subdivided into two principals according to the spectral analysis of the Raman light, namely Fouriertransform (FT) systems using an interferometer, and dispersive systems.

and collection from the sample can be accomplished in any geometry, although 90 and 180°C (backscattering) are more frequently employed. The use of fiber optics helps to make the spectrometers more versatile.

whereas Raman scattering arises from the modulation of the electric dipole with the natural frequency of the vibrating molecule. This modulation is produced by the electrons of the molecule, whose rearrangement produces a coupling between the nuclear motion and the

80 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

From the basis of the Raman effect described above, it is easy to deduce that in a conventional

light of the Rayleigh scattering from the much weaker Raman-scattered light. Besides, as Raman scattering has low efficiency, the optimization of each of the instrumental components

*1. Excitation source:* Traditionally, mercury arc lamps were used as light sources until being replaced by laser sources. Laser beams are highly monochromatic, present small diameter and, with the help of different optic devices, can be focused on small samples. Different lasers can

In addition, in order to enhance the laser quality it is possible to employ a pass-band filter, designed to pass only a certain band of frequencies while attenuating all signals outside this

*2. Sample illumination system and collection optics*: The collimation and focusing optics of the exciting radiation onto the sample depends on the experimental setup. In principle, excitation

2 Raman systems are subdivided into two principals according to the spectral analysis of the Raman light, namely Fourier-

be used as the light source in Raman spectrometry, as the ones shown in **Table 1** [56].

**Laser Wavelength (nm)** Ar ion 530.9/647.1 He-Ne 632.8 Near IR diode 785/830 Nd-YAG 1064 Frequency-doubled Nd:YAG 532 Nd:YVO4 diode 532

band. This component is commonly known as interferometric filter.

transform (FT) systems using an interferometer, and dispersive systems.

the main difficulty lies in separating the intense stray

electric field of the radiation.

becomes critically important.

(1) Excitation source

(5) Recording device

(4) Detector

**2.2. Dispersive Raman spectrometer**

(or dispersive) Raman spectrometer,2

(3) Wavelength selectors and separators

**Table 1.** Lasers used as light source in Raman spectroscopy.

The main components of a Raman setup are as follows:

(2) Sample illumination systems and collection optics

*3. Wavelength selectors and/or separators:* The separation or removal of the intense Rayleigh scattering can be achieved by using two different types of filters: notch and edge filters. Notch filters allow the acquisition of the anti-Stokes and Stokes Raman spectra down to ~30 cm−1, but their use is expensive since they must be replaced very frequently (~2 years). For this reason, the use of edge filters is widespread. These are wide pass-band filters, which imply that the anti- Stokes Raman spectrum cannot be obtained and typical minimum wavenumbers are ~50 cm−1. After the removal or suppression of the Rayleigh radiation, the separation of the different Raman radiations scattered by the sample should be performed. The first Raman spectrometers used prisms, but nowadays these are replaced by gratings that are typically holographically produced. It is worth noting that filters can be neglected if coupling of two or three monochromators is set in a series. This configuration allows not only to separate the Raman lines but also to remove the Rayleigh scatter.

*4. Detectors:* Just like in other spectrometers, the former detectors, that is, photographic films, were substituted first by photodiode array detectors and then by charge transfer devices (CTDs) such as charge-coupled devices (CCDs). CCDs are silicon-based semiconductors arranged as an array of photosensitive elements, each one generating photoelectrons and storing them as an electrical charge. Charges are stored on each individual pixel as a function of the number of photons striking that pixel and then read by an analog-to-digital converter [54].

A schematic representation of a modern micro-Raman spectrometer is shown in **Figure 4**.

**Figure 4.** Descriptive scheme of the main components of a Raman microspectrometer.

In the micro-Raman technique, a microscope is integrated in a conventional Raman spectrometer, enabling both visual and spectroscopic measurements. As can be seen in **Figure 4**, in these types of equipment the focusing and collection optics of the scattered radiation are identical. In addition to the analysis of a single point, these spectrometers allow mapping and imaging measurements.

## **3. Results**

As explained before, this section has been divided into two parts corresponding to dry and wet conditions; into the corresponding part the developed methods and the results obtained for analogs of the spent nuclear fuel matrix and its alteration products are shown. Namely, the materials studied in this section are the different uranium oxides, UO2+*x* (0 < *x* < 0.25), U4O9/ U3O7, and U3O8, and several secondary phases such as rutherfordine, soddyite, uranophane alpha, and kasolite.

The results shown in this section have been obtained by using the LabRaman HR Evolution (Horiba Jobin Yvon Technology, i.e., a dispersive spectrometer equipped with a microscope that enables the unification of both focusing and collection optics. It is possible to couple any laser to the spectrometer optical system as the excitation source. We specifically use the internal HeNe laser of 20-mW nominal power and an excitation wavelength of 632.8 nm (red). The laser beam is focused on the sample through a confocal microscope with different magnifications (5×, 20×, 50×, and 100×). Scattered radiation is then collected by the microscope on its way back (180° scattering) and the Rayleigh contribution removed by an edge filter that cuts at <50 cm−1. Thereafter, the Raman-scattered radiation is registered in a Peltier-cooled CCD of 1024 × 256 pixels after crossing a diffraction grating which disperses the signal into its constituent parts. Three gratings of 600, 1800, and 2400 grooves/mm can be selected. The spectral resolution of each grating is ~1, 0.5, and 0.25 cm−1/pixel, respectively. The microscope holds a motorized platen in order to carry out both point-to-point and image-scanning spectra, with a 0.1-μm resolution.

In addition to the abovementioned components, different lenses and mirrors can be found throughout the whole optical path, whose function is to correctly direct the beam within the optical system. Due to the amount of components that the laser beam encounters along its way before reaching the sample, a consequent power reduction of around 50% takes place. Nevertheless, the power attained at the sample surface is still sufficient to properly carry out the experiments.

The sample optical image and the spectra acquisition/visualization are performed by means of specific software designed by Horiba. The acquisition parameters and data processing of each spectrum depend on the sample and, above all, on the aim of the study.

#### **3.1. Characterization of different uranium oxides**

Here, a methodology to characterize uranium oxide powder with different oxidation degrees is described, and the spectra of stoichiometric UO2, hyperstoichiometric UO2+*x*, (0 < *x* < 0.25), U4O9/U3O7, and finally U3O8 have been shown. The sample preparation for obtaining these uranium oxides with different stoichiometry is based on the TGA technique and described in detail elsewhere.

In the micro-Raman technique, a microscope is integrated in a conventional Raman spectrometer, enabling both visual and spectroscopic measurements. As can be seen in **Figure 4**, in these types of equipment the focusing and collection optics of the scattered radiation are identical. In addition to the analysis of a single point, these spectrometers allow mapping and imaging

82 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

As explained before, this section has been divided into two parts corresponding to dry and wet conditions; into the corresponding part the developed methods and the results obtained for analogs of the spent nuclear fuel matrix and its alteration products are shown. Namely, the materials studied in this section are the different uranium oxides, UO2+*x* (0 < *x* < 0.25), U4O9/ U3O7, and U3O8, and several secondary phases such as rutherfordine, soddyite, uranophane

The results shown in this section have been obtained by using the LabRaman HR Evolution (Horiba Jobin Yvon Technology, i.e., a dispersive spectrometer equipped with a microscope that enables the unification of both focusing and collection optics. It is possible to couple any laser to the spectrometer optical system as the excitation source. We specifically use the internal HeNe laser of 20-mW nominal power and an excitation wavelength of 632.8 nm (red). The laser beam is focused on the sample through a confocal microscope with different magnifications (5×, 20×, 50×, and 100×). Scattered radiation is then collected by the microscope on its way back (180° scattering) and the Rayleigh contribution removed by an edge filter that cuts at <50 cm−1. Thereafter, the Raman-scattered radiation is registered in a Peltier-cooled CCD of 1024 × 256 pixels after crossing a diffraction grating which disperses the signal into its constituent parts. Three gratings of 600, 1800, and 2400 grooves/mm can be selected. The spectral resolution of each grating is ~1, 0.5, and 0.25 cm−1/pixel, respectively. The microscope holds a motorized platen in order to carry out both point-to-point and image-scanning spectra,

In addition to the abovementioned components, different lenses and mirrors can be found throughout the whole optical path, whose function is to correctly direct the beam within the optical system. Due to the amount of components that the laser beam encounters along its way before reaching the sample, a consequent power reduction of around 50% takes place. Nevertheless, the power attained at the sample surface is still sufficient to properly carry out

The sample optical image and the spectra acquisition/visualization are performed by means of specific software designed by Horiba. The acquisition parameters and data processing of

Here, a methodology to characterize uranium oxide powder with different oxidation degrees is described, and the spectra of stoichiometric UO2, hyperstoichiometric UO2+*x*, (0 < *x* < 0.25),

each spectrum depend on the sample and, above all, on the aim of the study.

**3.1. Characterization of different uranium oxides**

measurements.

**3. Results**

alpha, and kasolite.

with a 0.1-μm resolution.

the experiments.

The protocol used to analyze any uranium oxide powder can be summarized in the following steps:

*1. Sample visualization*: A small amount of uranium oxide is spread over the surface of a microscope slice, which is housed in the stage of the microscope. By using different objectives, we visualize the particles that compound the uranium oxide powder. The microscope digital camera allows us to get optical image of the sample, such as the images shown in **Figure 5**. As can be seen, the powder is finely divided in particles of a size of ~10–20 μm.

**Figure 5.** Optical image of UO2 powder, acquired with the 5×, 20×, and 100× microscope objectives (from left to right).

**Figure 6.** Raman spectra acquired as laser power is increased (for the same acquisition times).

*2. Setting the acquisition conditions*: All spectra are acquired using the laser with an excitation wavelength of 632.8 nm and the 600-grooves/mm grating, thus obtaining a spectral resolution of ~1 cm−1/pixel (see *Micro-Raman spectrometer set-up* section). The laser beam is focused on the sample through the 100× magnification objective. Due to the fact that lasers can induce a local temperature increase by up to several hundred degrees if they are focused on a small spot, it is crucial to check the stability of the sample at high temperature; otherwise, the laser can damage it. In order to do that, a previous study of the sample behavior at different laser powers needs to be done. In this way, **Figure 6** shows the spectra obtained as increasing the laser power, for an acquisition time of 10 min. As can be observed, the sample is stable up to 2 mW for such acquisition time, and then it is burnt from that power on. Therefore, when carrying out the uranium oxide powder characterization experiments, the laser power is minimized to 1 mW in order to ensure that there is no sample alteration during the measurements.

**Figure 7.** Raman spectra acquired by the multipoint sampling method, in order to check homogeneity of the sample.

*3. Checking the sample homogeneity*: Since the Raman laser excites only a very small portion of the sample (few microns), its homogeneity becomes a critical issue. Therefore, in order to check the sample homogeneity several spectra of different particles are acquired and compared. For obtaining these spectra, the multipoint sampling method is employed. This method uses sequential sample movement and spectrum acquisition, repeated as many times as desired, that is, the motorized *XY* microscope stage is moved to the position in which each spectrum is acquired. **Figure 7** shows the Raman spectra of different particles of a uranium dioxide sample. It can be appreciated that all spectra are similar, indicating that the sample is very homogeneous.

*4. Spectra acquisition*: Once the sample homogeneity is checked, and in order to enhance the intensity/noise ratio all spectra are added. In **Figure 8**, the sum spectrum is shown.

*5. Spectra analysis*: The aim of the Raman spectra analysis is to obtain information about the frequency, intensity, width, and area of their bands; for this purpose, it is necessary to previously know the number of bands or contributions in the spectrum. One way to detect such contributions is to calculate the spectrum second derivative. This method allows us, first, to determine the number of contributions, since each will lead to a minimum, and, second, to accurately approximate the Raman frequency band center from the position of this minimum. As an example, the second derivative of the uranium oxide sum spectrum is shown in **Figure 10**. Once the number of contributions of each band is estimated, a Lorentzian fit is conducted using the obtained frequency values as fixed parameters. **Figure 8** also shows the profile analysis of the sum spectrum, where four bands are detected at ~445, 560, 630, and 1150 cm−1.

is crucial to check the stability of the sample at high temperature; otherwise, the laser can damage it. In order to do that, a previous study of the sample behavior at different laser powers needs to be done. In this way, **Figure 6** shows the spectra obtained as increasing the laser power, for an acquisition time of 10 min. As can be observed, the sample is stable up to 2 mW for such acquisition time, and then it is burnt from that power on. Therefore, when carrying out the uranium oxide powder characterization experiments, the laser power is minimized to 1 mW

**Figure 7.** Raman spectra acquired by the multipoint sampling method, in order to check homogeneity of the sample.

homogeneous.

*3. Checking the sample homogeneity*: Since the Raman laser excites only a very small portion of the sample (few microns), its homogeneity becomes a critical issue. Therefore, in order to check the sample homogeneity several spectra of different particles are acquired and compared. For obtaining these spectra, the multipoint sampling method is employed. This method uses sequential sample movement and spectrum acquisition, repeated as many times as desired, that is, the motorized *XY* microscope stage is moved to the position in which each spectrum is acquired. **Figure 7** shows the Raman spectra of different particles of a uranium dioxide sample. It can be appreciated that all spectra are similar, indicating that the sample is very

*4. Spectra acquisition*: Once the sample homogeneity is checked, and in order to enhance the

*5. Spectra analysis*: The aim of the Raman spectra analysis is to obtain information about the frequency, intensity, width, and area of their bands; for this purpose, it is necessary to previously know the number of bands or contributions in the spectrum. One way to detect such contributions is to calculate the spectrum second derivative. This method allows us, first, to determine the number of contributions, since each will lead to a minimum, and, second, to accurately approximate the Raman frequency band center from the position of this minimum.

intensity/noise ratio all spectra are added. In **Figure 8**, the sum spectrum is shown.

in order to ensure that there is no sample alteration during the measurements.

84 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

UO2 presents a fluorite-type structure (fcc), where uranium cations are located at the cubiccoordinated sites and oxygen anions at the tetrahedral-coordinated ones. As oxidation takes place, excess oxygen occupies interstitial positions thus leading to hyperstoichiometric UO2+*<sup>x</sup>* [57]. The crystal system remains cubic up to *x* = 0.25, known as U4O9 [58]. Further oxidation causes the transformation from cubic to tetragonal structure (U3O7) [59] and finally to orthorhombic (U3O8).

**Figure 8.** Raman spectrum of uranium oxide powder, corresponding to the sum of several spectra acquired at distinct points of the sample, and its profile analysis (up), and second derivative of such sum Raman spectrum (down).

Since the space group corresponding to uranium dioxide is *Fm3m* [60], group theory predicts two vibrational modes for UO2: a Raman active mode (*T*2g) and an infrared active mode (*T*1u). In such a way, the Raman spectrum of stoichiometric UO2 presents a band at ~445 cm−1 assigned to the mentioned *T*2g vibrational mode [61]. Likewise, another band at ~1150 cm−1 is observed, which has been attributed to the 2LO phonon [62]. With regard to the characteristic spectrum of UO2+*x*, it features the same two bands as the stoichiometric oxide, but also an additional broad band located at 500–700 cm−1 [63]. The same broad band is detected for U4O9 and U3O7, with a much greater contribution; besides, the 1150 cm−1 band completely disappears in these oxide spectra [64]. Since U4O9 and U3O7 spectra are similar, it is difficult to distinguish one from each other. Moreover, due to the change to the orthorhombic structure, a widely different spectroscopic profile is obtained for U3O8 [65].

By following the protocol described above, spectra corresponding to uranium oxide powder samples with different sequential oxidation degrees have been obtained: UO2+*x* (0 < *x* < 0.25), U4O9/U3O7, and U3O8. Some of these spectra are shown in **Figure 9**. Therefore, the behavior of the uranium dioxide Raman spectrum as the oxidation degree increases can be described by the next features: (1) the apparition of different contribution bands at ~500–700 cm−1, typical of the hyperstoichiometric oxides UO2+*x* (0 < *x* < 0.25), which are due to the incorporation of oxygen into the cubic structure of UO2 [66]; (2) the disappearance of the 1150 cm−1 band, characteristic of U4O9/U3O7 [67]; and (3) the typical three bands at ~375, 450, and 515 cm−1 and a band at ~812 cm−1 corresponding to the structure of U3O8 [68, 69].

**Figure 9.** Raman spectra of different uranium oxides, where the bottom spectrum corresponds to the hyperstoichiometric UO2+*x*, the middle one to U4O9/U3O7, and the top one corresponds to the final U3O8.

#### **3.2. Characterization of secondary phases in natural samples**

In this section, we present a method based on Raman spectroscopy that allows us an easy and fast identification of secondary phases formed at nature. Secondary phases are present in nature as rims of corrosion products (typically of one or two centimeters wide) found on weathered uraninite3 crystals. These structures are known as *gummites* because of the difficulties in distinguishing individual phases. The typical alteration rim around an oxidized uraninite crystal, as was described by Frondel [70, 71], is schematically shown in **Figure 10**.

The ore is composed by the uraninite, usually brown to dark brown depending on its oxidation state. Zone 1 contains domains of uranyl oxide hydrates: fourmarierite vandendriesscheite, wölsendorfite, calciouranoite, clarkeite, becquerelite, curite, and schoepite, whereas zone 2

<sup>3</sup> Mineral composed by uranium dioxide, UO2, sometimes with small amounts of thorium, therefore with variable formula (U,Th)O2 (http://www.minerals.net/mineral/uraninite.aspx#sthash.aTasdt1U.dpuf).

consists most commonly of uranyl silicates: uranophane, kasolite, sklodowskite, and soddyite. Anyhow, as expected, the specific alteration products depend on local conditions [72].

By following the protocol described above, spectra corresponding to uranium oxide powder samples with different sequential oxidation degrees have been obtained: UO2+*x* (0 < *x* < 0.25), U4O9/U3O7, and U3O8. Some of these spectra are shown in **Figure 9**. Therefore, the behavior of the uranium dioxide Raman spectrum as the oxidation degree increases can be described by the next features: (1) the apparition of different contribution bands at ~500–700 cm−1, typical of the hyperstoichiometric oxides UO2+*x* (0 < *x* < 0.25), which are due to the incorporation of oxygen into the cubic structure of UO2 [66]; (2) the disappearance of the 1150 cm−1 band, characteristic of U4O9/U3O7 [67]; and (3) the typical three bands at ~375, 450, and 515 cm−1 and a band at

86 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 9.** Raman spectra of different uranium oxides, where the bottom spectrum corresponds to the hyperstoichio-

In this section, we present a method based on Raman spectroscopy that allows us an easy and fast identification of secondary phases formed at nature. Secondary phases are present in nature as rims of corrosion products (typically of one or two centimeters wide) found on

ties in distinguishing individual phases. The typical alteration rim around an oxidized uraninite crystal, as was described by Frondel [70, 71], is schematically shown in **Figure 10**.

The ore is composed by the uraninite, usually brown to dark brown depending on its oxidation state. Zone 1 contains domains of uranyl oxide hydrates: fourmarierite vandendriesscheite, wölsendorfite, calciouranoite, clarkeite, becquerelite, curite, and schoepite, whereas zone 2

3 Mineral composed by uranium dioxide, UO2, sometimes with small amounts of thorium, therefore with variable formula

crystals. These structures are known as *gummites* because of the difficul-

metric UO2+*x*, the middle one to U4O9/U3O7, and the top one corresponds to the final U3O8.

**3.2. Characterization of secondary phases in natural samples**

(U,Th)O2 (http://www.minerals.net/mineral/uraninite.aspx#sthash.aTasdt1U.dpuf).

weathered uraninite3

~812 cm−1 corresponding to the structure of U3O8 [68, 69].

**Figure 10.** Scheme corresponding to the alteration rim of an oxidized uraninite crystal, as described by Frondel.

As an example of how to use Raman spectroscopy to analyze this kind of samples, we show below the characterization of a gummite sample collected in 1960 from Sierra Albarrana (Córdoba, Spain). More details of this study can be found in Ref. [73]. The surface of a polished section of the sample was analyzed by acquiring different spectra along a 10-mm line from the center outwards, in order to know the alteration products sequence (see **Figure 11**).

**Figure 11.** Scheme of the 10-mm line along which different spectra were acquired from the center of the oxidized uraninite crystal outwards.

A combination of the line-mapping and step-by-step procedures can be used to acquire the spectra in this kind of samples. Specifically, in this study a line mapping is performed using the automatized line-scanning tool. This tool allows Raman spectra acquisition of different sample points along a line by automatically moving the stage in one or two directions (*X*-*Y*). The microscope objective used with a magnification of 20× allows the visualization of a maximum 500 × 70-μm area. Therefore, in order to analyze the whole sample (10 mm), 20 lines with five equidistant points each have been measured, thus acquiring 100 spectra. This was performed with the step-by-step procedure, in which the motorized stage is moved 500 μm (the line-mapping length) in the *x*-direction to allow the analysis of the next part of the sample. The acquisition time for each spectrum was 100 s on an extended shift of 100–1200 cm−1. A typical spectrum acquired in this way is shown in **Figure 12**. This spectrum is the characteristic of a mixture of U-minerals that contain uranyl groups in their structure.

**Figure 12.** Typical Raman spectrum acquired during the step-by-step and line-mapping combination procedure. The inset shows the frequency range corresponding to the *ν*1 symmetric stretch.

It has been demonstrated that the symmetrical-stretching vibration of UO2 2+ can be used as a fingerprint to identify each U-mineral phase [74]. UO2 2+ presents a linear symmetry which corresponds to the punctual group D∞h. It has four normal modes (3 *N* − 5, *N* = number of atoms) and three fundamental vibrations: the symmetric-stretching vibration *ν*1, the doubly degenerate bending vibration *ν*2(*δ*), and the anti-symmetric-stretching vibration *ν*3 (see **Table 2**).


**Table 2.** Normal modes of UO2 2+. Although the perfect linear structure has only a *ν*1 Raman active vibration mode, symmetry lowering (C∞h → C∞v → C2v → Cs) leads to Raman activation of the two IR bands, as well as their overtones and combination vibrations. Moreover, the frequency of each active band is sensible to the environment in which the uranyl group is housed; therefore, each U-mineral has a characteristic *ν*1 symmetric-stretching vibration frequency, which can be used as a fingerprint.


**Table 3.** Characteristic frequencies of the found U-minerals.

A combination of the line-mapping and step-by-step procedures can be used to acquire the spectra in this kind of samples. Specifically, in this study a line mapping is performed using the automatized line-scanning tool. This tool allows Raman spectra acquisition of different sample points along a line by automatically moving the stage in one or two directions (*X*-*Y*). The microscope objective used with a magnification of 20× allows the visualization of a maximum 500 × 70-μm area. Therefore, in order to analyze the whole sample (10 mm), 20 lines with five equidistant points each have been measured, thus acquiring 100 spectra. This was performed with the step-by-step procedure, in which the motorized stage is moved 500 μm (the line-mapping length) in the *x*-direction to allow the analysis of the next part of the sample. The acquisition time for each spectrum was 100 s on an extended shift of 100–1200 cm−1. A typical spectrum acquired in this way is shown in **Figure 12**. This spectrum is the characteristic

**Figure 12.** Typical Raman spectrum acquired during the step-by-step and line-mapping combination procedure. The

corresponds to the punctual group D∞h. It has four normal modes (3 *N* − 5, *N* = number of atoms) and three fundamental vibrations: the symmetric-stretching vibration *ν*1, the doubly degenerate bending vibration *ν*2(*δ*), and the anti-symmetric-stretching vibration *ν*3 (see

2+ can be used as a

2+ presents a linear symmetry which

of a mixture of U-minerals that contain uranyl groups in their structure.

88 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

inset shows the frequency range corresponding to the *ν*1 symmetric stretch.

fingerprint to identify each U-mineral phase [74]. UO2

2+.

**Table 2**).

**Table 2.** Normal modes of UO2

It has been demonstrated that the symmetrical-stretching vibration of UO2

**Fundamental mode Vibration Activity Infrared frequency (cm −1 )**

*ν* <sup>1</sup> Symmetric stretch R 700–900 *ν* 2(*δ*) Bending IR 200–300 *ν* <sup>3</sup> Anti-symmetric stretch IR 850–1000 In the inset of **Figure 12**, we show the frequency range corresponding to the *ν*1 symmetric stretch, from 700 to 900 cm−1. As can be seen, there are four bands in this region. This must be due to a mixture of four different phases, if we understand the Raman spectra for mixtures as the direct sum of the individual spectrum of each component in the mixture (as long as these components do not interact with each other). Therefore, in this kind of mixtures the vibration bands do not undergo any displacement, and the band profile of the mixture spectrum results in the spectra of the different components or vice versa.

Taking this into account, the characteristic frequency bands observed in **Figure 12** correspond to the following U-minerals: rutherfordine, UO2(CO3), uranophane alpha, Ca(UO2)2(SiO3OH)2 5H2O, soddyite, (UO2)2SiO2 2H2O, and kasolite, PbUO2SiO4H2O (see **Table 3**). See Refs. [75– 78] for the assignments.


**Table 4.** Result data matrix.

In order to perform a semi-quantitative analysis of the sample with the aim of detection of different phases along the sample, next spectra processing has been carried out:

(i) Second-derivative calculation in the *ν*1 region (700–900 cm−1).

(ii) Verification of the existence of a minimum at each characteristic frequency.

(iii) Construction of a data matrix of 0 and 1, where 0 means there is no minimum at the characteristic frequency of the mineral and 1 means there is such a minimum (see **Table 4**).

This data matrix enables constructing different diagrams. As an example, in **Figure 13** we present a scheme where the existence or absence of each phase at each position can be appreciated only by looking at the minimum of the second-derivative spectrum.

**Figure 13.** Sequence of the urananite alteration products.

As can be seen, the sequence of alteration products obtained was as follows: (1) uraninite constitutes the unaltered core of the sample, 0–0.4 mm. (2) Rutherfordine appears in the inner part, 0.4–3.3 mm, in contact with the uraninite core. (3) Then, a mixture of uranyl silicates, soddyite, uranophane alpha, and kasolite is found. Soddyite prevails in the inner part, 0.4– 7.1 mm; uranophane alpha predominates in the outer part of the sample, 7.1–10 mm, and kasolite appears intermittently (1.0–3.3, 4.6–7.1, and 8.8–10 mm).

## **Author details**

Laura J. Bonales\* , Jone M. Elorrieta1 , Álvaro Lobato2 and Joaquin Cobos1

\*Address all correspondence to: laura.jimenez@ciemat.es

1 High-Level Radioactive Waste Unit CIEMAT, Madrid, Spain

2 Department of Physical Chemistry, School of Chemistry, University Complutense of Madrid, Madrid, Spain

## **References**

(i) Second-derivative calculation in the *ν*1 region (700–900 cm−1).

**Figure 13.** Sequence of the urananite alteration products.

**Author details**

Laura J. Bonales\*

Madrid, Madrid, Spain

kasolite appears intermittently (1.0–3.3, 4.6–7.1, and 8.8–10 mm).

, Jone M. Elorrieta1

\*Address all correspondence to: laura.jimenez@ciemat.es

1 High-Level Radioactive Waste Unit CIEMAT, Madrid, Spain

(ii) Verification of the existence of a minimum at each characteristic frequency.

90 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

appreciated only by looking at the minimum of the second-derivative spectrum.

(iii) Construction of a data matrix of 0 and 1, where 0 means there is no minimum at the characteristic frequency of the mineral and 1 means there is such a minimum (see **Table 4**).

This data matrix enables constructing different diagrams. As an example, in **Figure 13** we present a scheme where the existence or absence of each phase at each position can be

As can be seen, the sequence of alteration products obtained was as follows: (1) uraninite constitutes the unaltered core of the sample, 0–0.4 mm. (2) Rutherfordine appears in the inner part, 0.4–3.3 mm, in contact with the uraninite core. (3) Then, a mixture of uranyl silicates, soddyite, uranophane alpha, and kasolite is found. Soddyite prevails in the inner part, 0.4– 7.1 mm; uranophane alpha predominates in the outer part of the sample, 7.1–10 mm, and

, Álvaro Lobato2

2 Department of Physical Chemistry, School of Chemistry, University Complutense of

and Joaquin Cobos1


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#### **Infrared Spectra and Density Functional Theoretical Calculation of Transition Metal Oxide Reaction with Monochloromethane Infrared Spectra and Density Functional Theoretical Calculation of Transition Metal Oxide Reaction with Monochloromethane**

Yanying Zhao, Xin Liu and Shuang Meng Yanying Zhao, Xin Liu and Shuang Meng

Additional information is available at the end of the chapter Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/64437

#### **Abstract**

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In this chapter, we presented a short review of past and present experimental and theoretical work on the reactions of the transition metal monoxide and dioxide molecules with monochloromethane in excess argon matrices. A series of infrared absorption spectra combining with density functional theoretical (DFT) calculation characterized that the transition metal monoxide molecules produced by laser-ablated higher oxides activated C─H and C─Cl bonds of CH3Cl to first form the weakly bound MO(CH3Cl) (M = Sc, Y, Nb, Ta, Ti, Zr, Mn, Fe) complexes, which further photoisomerized to the more stable chlorine-transfer (Cl-transfer) CH3OMCl (M = Sc, Y), CH3M(O)Cl (M = Ti, Zr), CH3MOCl (M = Mn, Fe), and agostic hydrogen-transfer (H-transfer) CH2ClMOH (M = Sc, Y, Nb, Ta) products upon limited light excitation. Transition metal dioxides reaction with CH3Cl also formed MO2(CH3Cl) (M = Ti, Zr, Nb, Ta) complexes, which were further rearranged to the more stable Cl-transfer CH3OM(O)Cl (M = Ti, Zr) and agostic H-transfer CH2ClM(O)OH (M = Nb, Ta) molecules between the metal center atom and the chlorine atom upon ultraviolet light irradiation. Their different reactivity was interpreted according to the different valence electrons of metal center.

**Keywords:** monochloromethane, chlorine transfer, hydrogen transfer, transition metal oxides, agostic interaction

## **1. Introduction**

Monochloromethane, as the one of the simplest halohydrocarbons, also called methyl chloride, plays an important role in the industrial, synthetic, materials chemistry. It is always regarded

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

that monochloromethane is the largest natural source of ozone-depleting chlorine compounds and accounts for about 15% of the present atmospheric chlorine content as one kind of chlorinated volatile organic compounds (CVOCs). At present, monochloromethane is observed in the dry leaf with the content of 0.1–0.3 μg/g/h, and large emissions of monochloromethane are observed from some common certain types of ferns and dipterocarpaceae [1, 2]. Monochloromethane is also industrially produced by the oxidation and chlorination reaction of methane in the presence of metal chloride catalyst, and drying monochloromethane conversed to gasoline and olefins on the methanol to gasoline (MTG) and the methanol to olefins (MTO) catalysts [3, 4]. The conversion of methyl chloride to hydrocarbons has been investigated since the mid-1980s [5]. The product distribution of methyl chloride to hydrocarbons is strikingly similar to methanol conversion over the same topology [6]. Recently several ZSM-5 zeolites and SAPO sieves catalysts were reported the high performances on the catalytic conversion of monochloromethane to light olefins [7–9]. Modified SAPO-34 catalysts were also chosen to enhance its catalytic performance for the conversion of chloromethane to light olefins [10–13]. The oxidation addition of metal into carbon-halogen bonds is a key step in many stoichiometric and catalytic reactions. Activation of compounds containing C─X (X = Cl, Br, I) bonds attracts widespread interest due to the underactive organic functional group and the inherent chemical properties. Predominantly alkyl and aryl halides are extensively applied as electrophiles in the transition metal-catalyzed cross-coupling reactions [14–16]. It has a far-reaching significance on carbon-chlorine (C─Cl) bond catalytic oxidation on the conversion of monochloromethane to gasoline and olefins.

**Scheme 1.** The reactivity of transition metal monoxide and dioxide with monochloromethane in argon from Refs. [27– 30].

The reactions of transition metal centers with chloromethane may serve as the simplest model for understanding the intrinsic mechanism of the organic halides catalytic oxidation processes. The reactions on transition metal atoms with monochloromethane have been intensively studied in solid noble gas matrices. Investigations have reported that C─X bond of CH3X (X = F, Cl, Br, I) are activated by transition metal atoms [17–22]. The higher valence of group 6 metals can form the methylidyne complexes CH = MH2X (M = Mo, W, X = H, F, Cl, Br) [23–26]. In this chapter, the reactions of simple transition-metal oxide molecules with monochloromethane in solid argon were reviewed using matrix infrared absorption spectroscopy and density functional theoretical (DFT) calculations. As shown in **Scheme 1**, the ground-state transition metal monoxide molecules activated carbon-hydrogen (C─H) and C─Cl bond of CH3Cl upon a certain wavelength excitation in argon matrices. The weakly bound MO(CH3Cl) (*x* = 1, 2; M = Sc, Y, Nb, Ta, Ti, Zr, Mn, Fe) complexes were initially formed and then isomerized to the more stable Cl-transfer CH3OMCl (M = Sc, Y) and CH3M(O)Cl (M = Ti, Zr, Nb, Ta, Mn, Fe), and agostic H-transfer CH2ClMOH (M = Sc, Y, Nb, Ta) isomers upon limited visible light excitation. The MO2(CH3Cl) (M = Ti, Zr, Nb, Ta), which were formed from the reactions on MO2 with CH3Cl, were further rearranged to the more stable Cl-transfer CH3OM(O)Cl (M = Ti, Zr) and H-transfer CH2ClM(O)OH (M = Nb, Ta) molecules with agostic interactions between the chlorine and the metal center under ultraviolet light irradiation.

## **2. Experimental and computational methods**

that monochloromethane is the largest natural source of ozone-depleting chlorine compounds and accounts for about 15% of the present atmospheric chlorine content as one kind of chlorinated volatile organic compounds (CVOCs). At present, monochloromethane is observed in the dry leaf with the content of 0.1–0.3 μg/g/h, and large emissions of monochloromethane are observed from some common certain types of ferns and dipterocarpaceae [1, 2]. Monochloromethane is also industrially produced by the oxidation and chlorination reaction of methane in the presence of metal chloride catalyst, and drying monochloromethane conversed to gasoline and olefins on the methanol to gasoline (MTG) and the methanol to olefins (MTO) catalysts [3, 4]. The conversion of methyl chloride to hydrocarbons has been investigated since the mid-1980s [5]. The product distribution of methyl chloride to hydrocarbons is strikingly similar to methanol conversion over the same topology [6]. Recently several ZSM-5 zeolites and SAPO sieves catalysts were reported the high performances on the catalytic conversion of monochloromethane to light olefins [7–9]. Modified SAPO-34 catalysts were also chosen to enhance its catalytic performance for the conversion of chloromethane to light olefins [10–13]. The oxidation addition of metal into carbon-halogen bonds is a key step in many stoichiometric and catalytic reactions. Activation of compounds containing C─X (X = Cl, Br, I) bonds attracts widespread interest due to the underactive organic functional group and the inherent chemical properties. Predominantly alkyl and aryl halides are extensively applied as electrophiles in the transition metal-catalyzed cross-coupling reactions [14–16]. It has a far-reaching significance on carbon-chlorine (C─Cl) bond catalytic oxidation

96 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Scheme 1.** The reactivity of transition metal monoxide and dioxide with monochloromethane in argon from Refs. [27–

The reactions of transition metal centers with chloromethane may serve as the simplest model for understanding the intrinsic mechanism of the organic halides catalytic oxidation processes. The reactions on transition metal atoms with monochloromethane have been intensively studied in solid noble gas matrices. Investigations have reported that C─X bond of CH3X (X = F, Cl, Br, I) are activated by transition metal atoms [17–22]. The higher valence of group 6 metals can form the methylidyne complexes CH = MH2X (M = Mo, W, X = H, F, Cl, Br) [23–26]. In this chapter, the reactions of simple transition-metal oxide molecules with monochloromethane in

on the conversion of monochloromethane to gasoline and olefins.

30].

The experimental setup for pulsed laser-ablated and matrix isolation Fourier transform infrared (FTIR) spectroscopic technique has been previously described in detail [31]. Briefly, the 1064 nm Nd:YAG laser fundamental (Spectra Physics, DCR 150, 20 Hz repetition rate, and 8 ns pulse width) was focused onto the rotating bulk metal oxide targets, which were prepared by sintered metal oxide powders. Laser-evaporation of bulk higher metal oxide targets has been proved to be an extensively available technique to prepare pure metal oxides in noble gas matrices [32–34]. Using standard manometric technique, the CH3Cl/Ar samples were mixed at a proper proportion in a stainless steel vacuum line. The CH3Cl sample was subjected to several freeze-pump-thaw cycles at 77 K before use. The laser-evaporated species were codeposited with chloromethane in excess argon onto a CsI window cooled normally to 6 K by a closed-cycle helium refrigerator (ARS, 202N). The matrix samples were deposited at a rate of approximately 5 mmol/h for 1–2 h. Isotopic-labeled 13CH3Cl and CD3Cl (ISOTEC, 99%) were used without further purification. Infrared spectra between 450 and 4000 cm−1 were recorded on a Bruker IFS 66v/s spectrometer using HgCdTe (MCT) detector cooled by liquid N2 at 0.5 cm−1 resolution. Samples were annealed to different temperatures and cooled back to 6 K to acquire the spectra, and selected samples were subjected to visible or broadband irradiation using a 250 W high-pressure mercury arc lamp with selected wavelength glass filters.

Density functional theoretical calculations were performed by using Gaussian 03 programs [35] to identify the experimental assignments. The three-parameter hybrid functional, according to Becke with additional correlation corrections from Lee, Yang, and Parr (B3LYP), was utilized [36, 37] to optimize ground geometries, calculate frequencies, and derive the zeropoint vibrational energies. Transition-state optimizations were performed with the Berny geometry optimization algorithm at the B3LYP level. The 6-311++G(d, p) basis set was used for the H, C, O, Cl, Sc, Ti, Mn, and Fe atoms [38, 39], DGDZVP basis set for Y, Zr, and Nb atoms [40, 41], and the scalar-relativistic SDD pseudopotential and basis set for Ta atom [42, 43]. In addition, the CCSD(T) method was also applied to accurately calculate the single-point energies of the B3LYP-optimized structures with the same basis sets [44].

## **3. Transition metal monoxides reaction with CH3Cl**

Reaction of transition metal monoxides (ScO, YO, TiO, ZrO, NbO, TaO, MnO, FeO) with monochloromethane was investigated in solid argon by infrared absorption spectroscopy, combining with isotopic substituted experiments and theoretical calculations. The initial reaction step is the formation of the MO(CH3Cl) (M = Sc, Y, Ti, Zr, Nb, Ta, Mn, Fe) complex with metal atom bound with chlorine atom and/or oxygen atom with H atoms on annealing. Upon a certain wavelength photolysis, the MO(CH3Cl) complex was isomerized by the insertion of the M═O to C─H and/or C─Cl/Cl─C bond. Selected region of infrared spectra is illustrated in **Figures 1**–**4**.

**Figure 1.** Difference spectra in the selected regions scandium monoxide with isotopic substituted chloromethane in excess argon. (Spectrum taken after 15 min of broadband irradiation minus spectrum taken after 25 K annealing). (a) 0.5% CH3Cl, (b) 0.5% 13CH3Cl, and (c) 0.5% CD3Cl. (Reprinted with the permission from Ref. [27]. Copyright 2013 American Chemical Society).

**Figure 2.** Difference spectra in the selected regions from co-deposition of a laser-ablated TiO2 target in excess argon. Spectrum taken after 15 min of full-arc broadband photolysis irradiation (*λ* < 300 nm) followed by the 25 K annealing minus spectrum taken after sample annealing at 25 K. (a) 0.5% CH3Cl, (b) 0.5% 13CH3Cl, and (c) 0.5% CD3Cl. (Reprinted with the permission from Ref. [28]. Copyright 2013 American Chemical Society).

Infrared Spectra and Density Functional Theoretical Calculation of Transition Metal Oxide Reaction with Monochloromethane http://dx.doi.org/10.5772/64437 99

**3. Transition metal monoxides reaction with CH3Cl**

98 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

illustrated in **Figures 1**–**4**.

American Chemical Society).

Reaction of transition metal monoxides (ScO, YO, TiO, ZrO, NbO, TaO, MnO, FeO) with monochloromethane was investigated in solid argon by infrared absorption spectroscopy, combining with isotopic substituted experiments and theoretical calculations. The initial reaction step is the formation of the MO(CH3Cl) (M = Sc, Y, Ti, Zr, Nb, Ta, Mn, Fe) complex with metal atom bound with chlorine atom and/or oxygen atom with H atoms on annealing. Upon a certain wavelength photolysis, the MO(CH3Cl) complex was isomerized by the insertion of the M═O to C─H and/or C─Cl/Cl─C bond. Selected region of infrared spectra is

**Figure 1.** Difference spectra in the selected regions scandium monoxide with isotopic substituted chloromethane in excess argon. (Spectrum taken after 15 min of broadband irradiation minus spectrum taken after 25 K annealing). (a) 0.5% CH3Cl, (b) 0.5% 13CH3Cl, and (c) 0.5% CD3Cl. (Reprinted with the permission from Ref. [27]. Copyright 2013

**Figure 2.** Difference spectra in the selected regions from co-deposition of a laser-ablated TiO2 target in excess argon. Spectrum taken after 15 min of full-arc broadband photolysis irradiation (*λ* < 300 nm) followed by the 25 K annealing minus spectrum taken after sample annealing at 25 K. (a) 0.5% CH3Cl, (b) 0.5% 13CH3Cl, and (c) 0.5% CD3Cl. (Reprinted

with the permission from Ref. [28]. Copyright 2013 American Chemical Society).

**Figure 3.** Infrared spectra in the selected region from co-deposition of laser-ablated MnO2 and Fe2O3 target with isotopically substituted CH3Cl in excess argon. Spectra were taken after 1.5 h of sample deposition followed by 25 K annealing and 15 min of irradiation (300 < *λ* < 580 nm) and 25 K annealing. (a) 0.5% CH3Cl, (b) 0.5% 13CH3Cl, and (c) 0.5% CD3Cl. (Reprinted with permission from Ref. [30]. Copyright 2013, with permission from Ref. [28] from Elsevier).

**Figure 4.** Difference spectra in the selected regions from co-deposition of laser-evaporated niobium oxides with isotopic-substituted monochloromethane in excess argon. Spectrum taken after 15 min of full-arc photolysis minus spectrum taken after sample annealing at 25 K. (a) 0.5% CH3Cl, (b) 0.5% 13CH3Cl, and (c) 0.5% CD3Cl. (Reprinted with the permission from Ref. [29]. Copyright 2013 American Chemical Society).

In both the scandium and yttrium experiments, two MO(CH3Cl) (M = Sc, Y) complex isomers were formed spontaneously on annealing [27]. These absorptions of MO(CH3Cl) (M = Sc, Y) complex are observed at 898.4 and 919.1 cm−1 for Sc, and 1050.9, 805.9, and 784.8 cm−1 for Y, as shown in **Table 1**, which are corresponding to the Sc─O and Y─O vibration frequencies. The CH3OMCl and CH2ClMOH (M = Sc, Y) molecules were produced from the weakly bound MO(CH3Cl) complexes through photoinduced isomerization reactions on 250–300 nm wavelength irradiation, as shown in **Figure 1**. The CH3OMCl (M = Sc, Y) isomer observed at 1171.5 and 565.6 cm−1 for Sc and 1149.2 and 490.9 cm−1 for Y can be regarded as being formed through the addition of the C─Cl bond to the O═M bond, whereas the CH2ClMOH (M = Sc, Y) isomer observed at 3775.0 and 738.4 for Sc, and 3774.2 and 627.6 for Y is formed through the addition of the C─H bond to the M═O bond. On the basis of DFT calculations, the MO(CH3Cl) (M = Sc, Y) complex with *C*s structure is more stable than the complex with *C*3v structure by 25.5 (Sc) or 24.0 (Y) kJ/mol. Both CH3OMCl and CH2ClMOH (M = Sc, Y) molecules are more stable than the MO(CH3Cl) complex isomers. The CH3OMCl (M = Sc, Y) molecule was predicted to proceed through a transition state with an energy barrier of 17.7 for Sc and 8.4 kJ/mol for Y from the MO(CH3Cl) complex, whereas the CH2ClMOH isomer also proceeded through a transition state with a much higher energy barrier of 160.1 for Sc and 178.5 kJ/mol for Y from the MO(CH3Cl) complex. The CH3OMCl (M = Sc, Y) structure is about 173.0 for Sc and 180.6 kJ/mol for Y lower in energy than the CH2ClScOH and CH2ClYOH isomer. The CH2ClMOH (M = Sc, Y) molecule was also calculated to involve agostic interaction observed between the metal atom and the chlorine atom due to short bond distances of 2.598 Å for Sc─Cl and 2.821 Å for Y─Cl. Such interaction is quite similar to the agostic interactions generally defined to characterize the distortion of an organometallic moiety, which brings an appended C─H bond into close proximity with the metal center [17, 21, 45].


a Only the values for the most abundant metal isotope are listed.

b The mode assignments of the experimental vibrational frequencies are discussed in the cited literature.

c Relative to the energy sum of ground metal oxide and CH3Cl.

**Table 1.** Ground electronic states, symmetry point groups, vibrational frequencies (cm−1) and binding energies (kJ/mol) for the MO(CH3Cl) species in solid argona .

For IVB metal monoxides, the ground-state MO(CH3Cl) (M = Ti, Zr) complexes correlate to the ground-state TiO (3 Δ) and ZrO (1 Σ− ). The binding energies are predicted to be 20.5 (Ti) and 12.2 kcal/mol (Zr), which are larger than the corresponding values of TiO(CH4) and ZrO(CH4) [45, 46]. The MO(CH3Cl) (M = Ti, Zr) complexes can rearrange to the CH3M(O)Cl isomers by metal terminal insertion to C─Cl bond upon UV light irradiation (*λ* < 300 nm), which are observed at 999.5 and 526.2 cm−1 for Ti, and 915.2 and 488.3 cm−1 for Zr, as shown in **Figure 2**. Theoretical calculations also indicated that the electronic state crossings exist from the MO (M = Ti, Zr) + CH3Cl reaction to the more stable CH3M(O)Cl molecules through the MO(CH3Cl) complexes traverse their corresponding transition states. The CH3M(O)Cl (M = Ti, Zr) molecule was predicted to have a singlet ground state without symmetry. According to CCSD(T) singlepoint calculations on B3LYP optimization geometry, the singlet ground state is 44.3 kcal/mol for CH3Ti(O)Cl and 52.2 kcal/mol for CH3Zr(O)Cl lower in energy than its corresponding triplet state. The triplet MO(CH3Cl) (M = Ti, Zr) isomerized to the singlet CH3M(O)Cl (M = Ti, Zr) molecule through their corresponding transition states, which indicated that these reactions related to the spin crossing under UV light irradiation.


a Only the values for the most abundant metal isotope are listed.

1171.5 and 565.6 cm−1 for Sc and 1149.2 and 490.9 cm−1 for Y can be regarded as being formed through the addition of the C─Cl bond to the O═M bond, whereas the CH2ClMOH (M = Sc, Y) isomer observed at 3775.0 and 738.4 for Sc, and 3774.2 and 627.6 for Y is formed through the addition of the C─H bond to the M═O bond. On the basis of DFT calculations, the MO(CH3Cl) (M = Sc, Y) complex with *C*s structure is more stable than the complex with *C*3v structure by 25.5 (Sc) or 24.0 (Y) kJ/mol. Both CH3OMCl and CH2ClMOH (M = Sc, Y) molecules are more stable than the MO(CH3Cl) complex isomers. The CH3OMCl (M = Sc, Y) molecule was predicted to proceed through a transition state with an energy barrier of 17.7 for Sc and 8.4 kJ/mol for Y from the MO(CH3Cl) complex, whereas the CH2ClMOH isomer also proceeded through a transition state with a much higher energy barrier of 160.1 for Sc and 178.5 kJ/mol for Y from the MO(CH3Cl) complex. The CH3OMCl (M = Sc, Y) structure is about 173.0 for Sc and 180.6 kJ/mol for Y lower in energy than the CH2ClScOH and CH2ClYOH isomer. The CH2ClMOH (M = Sc, Y) molecule was also calculated to involve agostic interaction observed between the metal atom and the chlorine atom due to short bond distances of 2.598 Å for Sc─Cl and 2.821 Å for Y─Cl. Such interaction is quite similar to the agostic interactions generally defined to characterize the distortion of an organometallic moiety, which brings an appended

100 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Molecule Ground state Point group Vibrational frequencyb Binding energyc Ref.**

A1 *C* 3v 919.1 −9.4

A1 *C* 3v 805.9 −13.0

The mode assignments of the experimental vibrational frequencies are discussed in the cited literature.

**Table 1.** Ground electronic states, symmetry point groups, vibrational frequencies (cm−1) and binding energies (kJ/mol)

For IVB metal monoxides, the ground-state MO(CH3Cl) (M = Ti, Zr) complexes correlate to the

12.2 kcal/mol (Zr), which are larger than the corresponding values of TiO(CH4) and ZrO(CH4) [45, 46]. The MO(CH3Cl) (M = Ti, Zr) complexes can rearrange to the CH3M(O)Cl isomers by metal terminal insertion to C─Cl bond upon UV light irradiation (*λ* < 300 nm), which are

A′ *C* <sup>s</sup> 898.4 −34.9 [27]

A′ *C* <sup>s</sup> 1050.9, 783.5 −37.0 [27]

A′ *C* <sup>s</sup> 961.8 −41.4 [28]

A *C* <sup>1</sup> 898.2 −40.5 [28]

A′ *C* <sup>s</sup> 935.6 −29.5 [29]

A *C* <sup>1</sup> 991.5 −5.0 [29]

A′ *C* <sup>s</sup> 843.4 −38.9 [30]

A′ *C*<sup>s</sup> 882.7 −97.4 [30]

). The binding energies are predicted to be 20.5 (Ti) and

C─H bond into close proximity with the metal center [17, 21, 45].

ScO(CH3Cl) <sup>2</sup>

YO(CH3Cl) <sup>2</sup>

TiO(CH3Cl) <sup>3</sup>

ZrO(CH3Cl) <sup>3</sup>

NbO(CH3Cl) <sup>4</sup>

TaO(CH3Cl) <sup>2</sup>

MnO(CH3Cl) <sup>6</sup>

FeO(CH3Cl) <sup>5</sup>

ground-state TiO (3

a

b

c

2

2

for the MO(CH3Cl) species in solid argona

Only the values for the most abundant metal isotope are listed.

Relative to the energy sum of ground metal oxide and CH3Cl.

Δ) and ZrO (1

.

Σ−

b The mode assignments of the experimental vibrational frequencies are discussed in the cited literature.

c Relative to the energy sum of ground metal oxide and CH3Cl.

**Table 2.** Ground electronic states, symmetry point groups, vibrational frequencies (cm−1), and binding energies (kJ/ mol) for the isomers of MO(CH3Cl) in solid argona .

The ground-state NbO(CH3Cl) and TaO(CH3Cl) molecules are related to the ground-state NbO (4 Σ) and TaO (2 ∆). The predicted binding energies of 29.5 (Nb) and 5.0 kJ/mol (Ta) are larger than the corresponding values of NbO(CH4) and TaO(CH4) complexes [46], which were predicted to be very weakly interaction with the metal atom being bound to three hydrogen atoms of CH4. The MO(CH3Cl) (M = Nb, Ta) complexes rearranged to the more stable doublet CH2ClM(O)H isomer upon visible light excitation, as shown in **Table 2**. Thus, some excited states may be involved during the reaction process. The CH2ClM(O)H molecules were predicted to involve agostic interactions between the chlorine atom and the metal center. It is quite interesting to note that the CH2ClM(O)H (M = Nb, Ta) molecules involve agostic interactions between the chlorine atom and the metal atom. It is notable that the group 5 metal methylidene complexes are more agostically distorted than the group 4 metal complexes. Taking CH2ClNb(O)H as an example, the ∠ClCNb was predicted to be only 80.4° with a Cl─Nb distance of 2.624 Å. Agostic distortion interaction is a universal phenomenon in the structures of the early transition metal alkylidene complexes and even more popular in the structures of the small methylidene complexes, in which agostic interactions are also observed between the group 4–6 transition metal atom and one of the R-hydrogen atoms.

The reactions of FeO and MnO with CH3Cl first formed the MO(CH3Cl) (M = Mn, Fe) complexes when annealing, which can isomerize to CH3MOCl (M = Mn, Fe) upon 300 < λ < 580 nm irradiation. The products were characterized by isotopic IR studies with CD3Cl and 13CH3Cl and density functional calculations, as shown in **Figure 3**. Based on theoretical calculations, the MO(CH3Cl) (M = Mn, Fe) complexes have 5 A′ for Fe and 6 A′ ground state for Mn with Cs symmetry, respectively, as listed in **Table 1**. The binding energies of MO(CH3Cl) (M = Mn, Fe) are 9.3 and 23.3 kcal/mol lower than MO + CH3Cl, which are higher in energy than MO(CH4) and MO(Ng) (Ng = Ar, Kr, Xe) at the same calculation level [46–48]. The accurate CCSD(T) single-point calculations illustrate the CH3MOCl isomerism are 13.8 and 3.1 kcal/mol lower in energy than the MO(CH3Cl) (M = Mn, Fe) complexes.

The different reactivity of metal monoxide with CH3Cl can be rationalized in terms of changes in valence electron structures accompanied by electronic spin state crossing. In the scandium and yttrium reactions, the ground ScO and YO molecules reacted with CH3Cl to form two isomeric MO(CH3Cl) (M = Sc, Y) complexes spontaneously on annealing. Broad-band irradiation produced either the addition of the C─Cl bond to the O═M (M = Sc, Y) bond to form the CH3OMCl (M = Sc, Y) molecules with +II oxidation state of center metal or the addition of the C─H bond to the M═O bond to give the CH2ClMOH isomer with the valence of metal remaining in +II oxidation state. The CH2ClMOH (M = Sc, Y) include one α-chlorine atom to form agostic molecules between chlorine atom and metal center atom with less than 90° of ∠ClCM and short Cl---M (M = Sc, Y) distances. No α-H and/or α-Cl atom for the MO(CH3Cl) complex exist, so no agostic interaction is observed. Sc and Y have only three valence electrons, and hence they are not able to form high oxidation state structures. However, Mn and Fe have five and six valence electrons. Because their d orbitals are fully half-filled and hence are not easily lost, upon 300 < k < 580 nm irradiation the MO(CH3Cl) (M = Mn, Fe) complexes triggered the addition of the C─Cl bond to the M═O bond to form the CH3MOCl molecules with +II valence state. The Ti and Zr metals have four valence electrons, and their oxidation states increase from +II to +IV during the addition of MO insertion into the C─Cl bond to the metal to form CH3M(O)Cl molecules. For Nb and Ta, visible light irradiation triggered the H-atom transfer of the MO(CH3Cl) complexes from CH3Cl to the metal center to form the more stable CH2ClM(O)H isomers with the oxidation states of the metal increasing from the +II to +IV. However, the Nb and Ta have five valence electrons, and they cannot form +V oxidation structures, but possessing one valence electron characteristic of the agnostic chlorine effect.

## **4. Transition metal dioxides reaction with CH3Cl**

The ground-state MO2 (M = Ti, Zr, Nb, Ta) molecules react with CH3Cl to first form the weakly bound MO2(CH3Cl) complexes with O···H and M···Cl bonds. For Ti and Zr, the MO2(CH3Cl) complexes can isomerize to the more stable CH3OM(O)Cl molecules with the addition of the C─Cl bond of CH3Cl to one of the O═M bond of MO2 on annealing after broadband light irradiation (*λ* < 300 nm), as shown in **Figures 2** and **4**. And the reaction potential energy profile interpreted the chemical reaction mechanism of C─Cl activation by MO2 (M = Ti, Zr). The photoisomerization reaction of MO2(CH3Cl) (M = Nb, Ta) is quite different from those of MO2(CH3Cl) (M = Ti, Zr). The MO2(CH3Cl) (M = Nb, Ta) complexes were initiated H-transfer under ultraviolet light irradiation to isomerize the more stable CH2ClM(O)OH molecules. The CH2ClM(O)OH (M = Nb, Ta) molecules were predicted to involve agostic interactions between the chlorine atom and the metal center. During the photoisomerization process, no electronic spin state crossings were found, as shown in **Table 3**, different from the reaction of metal monoxides with CH3Cl.


a Only the values for the most abundant metal isotope are listed.

b The mode assignments of the experimental vibrational frequencies are discussed in the cited literature.

c Relative to the energy sum of ground metal oxide and CH3Cl.

**Table 3.** Ground electronic states, symmetry point groups, vibrational frequencies (cm−1), and binding energies (kJ/ mol) for the product from MO2 + CH3Cl in solid argona .

## **5. Conclusion and outlook**

Taking CH2ClNb(O)H as an example, the ∠ClCNb was predicted to be only 80.4° with a Cl─Nb distance of 2.624 Å. Agostic distortion interaction is a universal phenomenon in the structures of the early transition metal alkylidene complexes and even more popular in the structures of the small methylidene complexes, in which agostic interactions are also observed

The reactions of FeO and MnO with CH3Cl first formed the MO(CH3Cl) (M = Mn, Fe) complexes when annealing, which can isomerize to CH3MOCl (M = Mn, Fe) upon 300 < λ < 580 nm irradiation. The products were characterized by isotopic IR studies with CD3Cl and 13CH3Cl and density functional calculations, as shown in **Figure 3**. Based on

state for Mn with Cs symmetry, respectively, as listed in **Table 1**. The binding energies of MO(CH3Cl) (M = Mn, Fe) are 9.3 and 23.3 kcal/mol lower than MO + CH3Cl, which are higher in energy than MO(CH4) and MO(Ng) (Ng = Ar, Kr, Xe) at the same calculation level [46–48]. The accurate CCSD(T) single-point calculations illustrate the CH3MOCl isomerism are 13.8

The different reactivity of metal monoxide with CH3Cl can be rationalized in terms of changes in valence electron structures accompanied by electronic spin state crossing. In the scandium and yttrium reactions, the ground ScO and YO molecules reacted with CH3Cl to form two isomeric MO(CH3Cl) (M = Sc, Y) complexes spontaneously on annealing. Broad-band irradiation produced either the addition of the C─Cl bond to the O═M (M = Sc, Y) bond to form the CH3OMCl (M = Sc, Y) molecules with +II oxidation state of center metal or the addition of the C─H bond to the M═O bond to give the CH2ClMOH isomer with the valence of metal remaining in +II oxidation state. The CH2ClMOH (M = Sc, Y) include one α-chlorine atom to form agostic molecules between chlorine atom and metal center atom with less than 90° of ∠ClCM and short Cl---M (M = Sc, Y) distances. No α-H and/or α-Cl atom for the MO(CH3Cl) complex exist, so no agostic interaction is observed. Sc and Y have only three valence electrons, and hence they are not able to form high oxidation state structures. However, Mn and Fe have five and six valence electrons. Because their d orbitals are fully half-filled and hence are not easily lost, upon 300 < k < 580 nm irradiation the MO(CH3Cl) (M = Mn, Fe) complexes triggered the addition of the C─Cl bond to the M═O bond to form the CH3MOCl molecules with +II valence state. The Ti and Zr metals have four valence electrons, and their oxidation states increase from +II to +IV during the addition of MO insertion into the C─Cl bond to the metal to form CH3M(O)Cl molecules. For Nb and Ta, visible light irradiation triggered the H-atom transfer of the MO(CH3Cl) complexes from CH3Cl to the metal center to form the more stable CH2ClM(O)H isomers with the oxidation states of the metal increasing from the +II to +IV. However, the Nb and Ta have five valence electrons, and they cannot form +V oxidation structures, but possessing one valence electron characteristic of the agnostic chlorine effect.

The ground-state MO2 (M = Ti, Zr, Nb, Ta) molecules react with CH3Cl to first form the weakly bound MO2(CH3Cl) complexes with O···H and M···Cl bonds. For Ti and Zr, the MO2(CH3Cl)

A′ for Fe and 6

A′ ground

between the group 4–6 transition metal atom and one of the R-hydrogen atoms.

102 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

and 3.1 kcal/mol lower in energy than the MO(CH3Cl) (M = Mn, Fe) complexes.

theoretical calculations, the MO(CH3Cl) (M = Mn, Fe) complexes have 5

**4. Transition metal dioxides reaction with CH3Cl**

C─Cl and/or C─H bond of monochloromethane activation by transition metal monoxide and dioxide molecules has been investigated using matrix infrared spectroscopy in excess argon and density functional theoretical calculations. The metal monoxide and dioxide molecules prepared by laser-ablated bulk higher oxide targets reacted with monochloromethane to form the weakly bound MO(CH3Cl) (*x* = 1, 2; M = Sc, Y, Nb, Ta, Ti, Zr, Mn, Fe) complexes, which isomerized to the more stable CH3OMCl (M = Sc, Y), agostic CH2ClMOH (M = Sc, Y, Nb, Ta) and CH3M(O)Cl (M = Ti, Zr, Nb, Ta, Mn, Fe) isomers upon limited visible light excitation. Metal dioxides also reacted with CH3Cl to form MO2(CH3Cl) (M = Ti, Zr, Nb, Ta), which was rearranged to the more stable CH3OM(O)Cl (M = Ti, Zr) and CH2ClM(O)OH (M = Nb, Ta) molecules under ultraviolet light irradiation. Agostic interactions were observed in CH2ClMOH (M = Sc, Y, Nb, Ta) and CH2ClM(O)OH (M = Nb, Ta) between the chlorine atom and the metal center atom.

## **Acknowledgements**

We gratefully acknowledge the financial support from National Natural Science Foundation of China (Grants No. 21273202 and 21473162). Y. Zhao is grateful to the Project Grants 521 Talents Cultivation of Zhejiang Sci-Tech University and China Scholarship Council (CSC) Foundation. This work is also supported by Zhejiang Provincial Top Key Academic Discipline of Chemical Engineering and Technology.

## **Author details**

Yanying Zhao1,2\*, Xin Liu1 and Shuang Meng1


2 State Key Laboratory of Advanced Textiles Materials and Manufacture Technology, MOE, Zhejiang Sci-Tech University, Hangzhou, China

## **References**


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isomerized to the more stable CH3OMCl (M = Sc, Y), agostic CH2ClMOH (M = Sc, Y, Nb, Ta) and CH3M(O)Cl (M = Ti, Zr, Nb, Ta, Mn, Fe) isomers upon limited visible light excitation. Metal dioxides also reacted with CH3Cl to form MO2(CH3Cl) (M = Ti, Zr, Nb, Ta), which was rearranged to the more stable CH3OM(O)Cl (M = Ti, Zr) and CH2ClM(O)OH (M = Nb, Ta) molecules under ultraviolet light irradiation. Agostic interactions were observed in CH2ClMOH (M = Sc, Y, Nb, Ta) and CH2ClM(O)OH (M = Nb, Ta) between the chlorine atom

104 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

We gratefully acknowledge the financial support from National Natural Science Foundation of China (Grants No. 21273202 and 21473162). Y. Zhao is grateful to the Project Grants 521 Talents Cultivation of Zhejiang Sci-Tech University and China Scholarship Council (CSC) Foundation. This work is also supported by Zhejiang Provincial Top Key Academic Discipline

2 State Key Laboratory of Advanced Textiles Materials and Manufacture Technology, MOE,

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Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Molecular Spectroscopic Studies of Organic Materials**

110 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

## **Vibrational and Electronic Structure, Electron-Electron and Electron-Phonon Interactions in Organic Conductors Investigated by Optical Spectroscopy Vibrational and Electronic Structure, Electron-Electron and Electron-Phonon Interactions in Organic Conductors Investigated by Optical Spectroscopy**

## Andrzej Łapiński Andrzej Łapiński

Additional information is available at the end of the chapter

Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/63242

#### **Abstract**

The physical properties of organic conductors formed by tetrathiafulvalene (TTF) derivatives have been discussed in this chapter. The results were obtained using spectroscopic methods including infrared (IR), Raman, and UV-Vis. The experimental data were supported by theoretical DFT and TD-DFT calculations. Special attention has been paid to the description of electronic and vibrational structures, electron-electron and electron-phonon interactions and determination of transport parameters.

**Keywords:** organic conductors, electron-electron and electron-phonon interactions, vibrational end electronic structures, infrared and Raman spectroscopy, DFT calculations

## **1. Introduction**

Research on the development of organic metals and superconductors was stimulated by finding the first organic metal—charge-transfer (CT) complex composed of tetrathiafulvalene (TTF) and tetracyanoquinodimethane (TCNQ) [1–2] and by the discovery of superconductivity in CT salts of tetramethyltetraselenafulvalene (TMTSF) [3].

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

At the beginning, one of the most important targets in the field of molecular conductors was to search for high electrical conductivity systems [4]. Nowadays, the organic conductors based on the π-electron donors with various anions show a wealth of structural modifications and variety of physical properties [5–8]. They have attracted broad interest from the experimental and theoretical side because they exhibit a lot of fascinating phenomena related to the electronic states near the Fermi level and to relevant interactions. Superconductivity, metal-insulator phase transitions associated with charge-density wave (CDW) or spin-density wave (SDW) condensates and other cooperative states leading to antiferromagnetic-, charge- and dielectric order [9] are highly topical subjects in this field.

The great interest in this field has been sustained by chemists, who produced a huge number of π-electron donors for organic conductors. In many laboratories molecular conductors formed by the organic donors derived from TTF molecule are intensively studied. In designing π-donors, one can distinguish two main strategies. One has evolved mainly from: (a) the planarity for a facile formation of donor stacking, (b) the extension of π-conjugation for a decrease of on-site Coulombic repulsion involved in the formation of a dicationic species, and (c) the introduction of chalcogen atoms for an increase in dimensionality of the conduction pathway. The second approach to the donors design is totally different and it is based on the following requirements: (a) extension of the σ-bond framework which will lead to the lack of planarity, and (b) reduction of the π-electron system, which will increase the on-site Coulombic repulsion. The latter strategy was proposed by Yamada et al. [10]. They believe if donors are synthesized in accordance to these requirements, then it will be possible to produce superconductors using such donors.

In the last years, there is a great interest in the design and study of new molecular-based materials involving interplay between multiple physical properties. This kind of effects leads either to competition, coexistence or cooperation between the desired properties. A possible approach to reach this goal consists of building up hybrid solids formed by two molecular networks. Among these hybrid materials, the highly conducting CT salts formed by TTFderived donors with various inorganic acceptors with permanent magnetic moments are intensively investigated [7, 11]. A characteristic feature of these salts is a spatial segregation of the organic cations and inorganic anions into alternating layers. These materials are of special interest, because their properties are determined by presence of both the system of delocalized π-electron in the fulvalene-derived stacks or layers and by the localized d-electrons of anions. These systems may exist independently or can interact, leading to new physical properties of the conducting material. One of the most interesting phenomena is a possibility of the interaction between π-electrons within conducting layers and localized magnetic d-electrons in the counterions. Interaction between these two systems may lead to magnetically ordered conducting structures. The problem of magnetic order and electrical conductivity coexistence is highly topical [5, 8, 12, 13]. Magnetic interactions in these compounds are basically explained by the RKKY-type interaction mediated by the π-d coupling between the donor and the magnetic anions [14]. Moreover, Coulomb interactions between organic (cations) and inorganic (anions) subsystems may also lead to charge-ordering phenomena.

Coulomb interactions between electrons play an important role in organic conductors and have a considerable influence on optical, magnetic and conducting properties [15–17]. In many TTF based one- and two-dimensional organic conductors, the long-range Coulomb interactions are responsible for charge-ordering (CO) phenomena. In the field of CT salts, such behavior is of great interest among researches in many laboratories in the world [18–21]. In order to understand the nature of the charge localization Seo and Fukuyama [22] have performed theoretical calculations [23]. They have shown that a stripe-patterned charge ordering is stabilized in the insulating phase owing to intermolecular Coulomb repulsive forces. Moreover, Tajima *et al*. [24] have estimated the charge-ordering patterns in bis(ethylenedithio)tetrathiafulvalene (BEDT-TTF or ET) salts on the base of the spectral analysis and the mean-field calculations.

At the beginning, one of the most important targets in the field of molecular conductors was to search for high electrical conductivity systems [4]. Nowadays, the organic conductors based on the π-electron donors with various anions show a wealth of structural modifications and variety of physical properties [5–8]. They have attracted broad interest from the experimental and theoretical side because they exhibit a lot of fascinating phenomena related to the electronic states near the Fermi level and to relevant interactions. Superconductivity, metal-insulator phase transitions associated with charge-density wave (CDW) or spin-density wave (SDW) condensates and other cooperative states leading to antiferromagnetic-, charge- and dielectric

114 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

The great interest in this field has been sustained by chemists, who produced a huge number of π-electron donors for organic conductors. In many laboratories molecular conductors formed by the organic donors derived from TTF molecule are intensively studied. In designing π-donors, one can distinguish two main strategies. One has evolved mainly from: (a) the planarity for a facile formation of donor stacking, (b) the extension of π-conjugation for a decrease of on-site Coulombic repulsion involved in the formation of a dicationic species, and (c) the introduction of chalcogen atoms for an increase in dimensionality of the conduction pathway. The second approach to the donors design is totally different and it is based on the following requirements: (a) extension of the σ-bond framework which will lead to the lack of planarity, and (b) reduction of the π-electron system, which will increase the on-site Coulombic repulsion. The latter strategy was proposed by Yamada et al. [10]. They believe if donors are synthesized in accordance to these requirements, then it will be possible to produce super-

In the last years, there is a great interest in the design and study of new molecular-based materials involving interplay between multiple physical properties. This kind of effects leads either to competition, coexistence or cooperation between the desired properties. A possible approach to reach this goal consists of building up hybrid solids formed by two molecular networks. Among these hybrid materials, the highly conducting CT salts formed by TTFderived donors with various inorganic acceptors with permanent magnetic moments are intensively investigated [7, 11]. A characteristic feature of these salts is a spatial segregation of the organic cations and inorganic anions into alternating layers. These materials are of special interest, because their properties are determined by presence of both the system of delocalized π-electron in the fulvalene-derived stacks or layers and by the localized d-electrons of anions. These systems may exist independently or can interact, leading to new physical properties of the conducting material. One of the most interesting phenomena is a possibility of the

order [9] are highly topical subjects in this field.

conductors using such donors.

The most convenient experimental method to investigate charge distribution in conducting layers [25] and effects of electron-molecular vibration coupling [26, 27] is the vibrational spectroscopy, therefore, study of the vibrational structure in many cases is crucial to understand physical properties of organic conductors. Electron-molecular vibration (EMV) coupling constant is one of the parameters in estimating of critical temperature (*T*c) of organic superconductors, whereas the degree of ionicity, or average charge per molecule (*ρ*) is one of the fundamental parameters characterizing the physical properties of CT salts [28]. When Coulomb interaction prevails, the salts may undergo a charge-order instability. For the determination of *ρ* in TTF derivatives, the C=C stretching modes of TTF framework are mainly taken into account. It was shown that such modes are very sensitive to the ionization degree of the molecule [20, 25, 27]. Nevertheless, one should keep in mind that C=C modes can be coupled to the electronic system [29, 30] and hence their positions in infrared (IR) spectra can shift towards lower frequencies [31] due to this coupling; the frequencies of molecular modes may exhibit a non-linear dependence on *ρ* [30, 31].

The main purpose of the chapter is to present a description of physical properties of the organic conductors using experimental and theoretical methods of molecular spectroscopy. The special attention will be paid to the description of the electronic structure and determination of transport parameters. It will be shown that the most powerful method to investigate the charge ordering phenomena is the vibrational spectroscopy [32–34]. The results presented in this chapter were obtained by the spectroscopic methods including IR, Raman and UV-Vis. The experimental data were supported by theoretical DFT and TD-DFT calculations. It should be emphasized that the spectroscopic methods are very suitable tools for investigations of crystalline organic conductors because they provide a lot of information about electronic and vibrational structures, electron-electron and electron-phonon interactions [35].

## **2. Electronic structure investigated by optical spectroscopy**

The electronic transitions that appear in the spectra of organic conductors recorded in IR, Vis and UV regions fall into two classes. On the one hand, those at high frequencies generally are a result of localized excitations, which are related to intramolecular transitions in which an electron is excited to a higher level on the same molecule. For characterization of such type of excitations, the time-dependent DFT method (TD-DFT) can be applied for organic conductors [36, 37]. The quantitative understanding of such molecular electronic excited states is important in many domains, including spectroscopy, photochemistry and the design of new optical materials.

On the other hand, transitions at lower frequencies that are along the stacking directions or along to the S⋅⋅⋅S short contacts correspond to CT excitations between the molecules. The frequencies and oscillator strengths of these CT bands are clearly related to the electronic structure of these compounds, but they are a consequence of three types of interactions among the unpaired electrons occupying the highest molecular orbital (HOMO): (i) the overlap of the electronic wave functions between sites, (ii) the Coulomb repulsion of two electrons on the same or adjacent sites, and (iii) interactions of the electron with phonons. Theoretical models for the electronic structure of organic conductors have shown the importance of one or the other of these interactions, e.g. tight-binding theory [38], the Hubbard model [39] and the Peierls model [40].


**Table 1.** Electronic transitions (in cm−1) observed for selected organic conductors.

The CT bands (denoted as A and B) and intramolecular excitations for selected organic conductors are shown in **Table 1**. The band A corresponds to a charge transfer of an electron from an occupied A+ to a neutral A0 molecule (A+ +A0 →A0 +A+ ), whereas band B is associated with the CT from one A+ anion to a neighboring A+ (A+ +A+ →A0 +A2+). Within the Hubbard theory the position of A band relates to the Coulomb repulsion energy between two electrons on adjacent molecules (*V*) and hopping integrals (*t*). The position of B band depends on the value of the effective Coulomb interaction between two electrons reside on the same site. The energy of its transition is proportional to (*U*-*V*); *U* and *V* are the Hubbard parameters for onsite and nearest-neighbor Coulomb repulsion, respectively. From the center position of B band and assuming *V* to be small, we can estimate the on-site Coulomb repulsion. Hubbard has also shown that the electron distribution in the ground state can be periodic and may be considered as a generalization of the classical Wigner lattice. The arrangement of the electrons within the period can be non-uniform and then it will give rise to electric fields that can distort the ordinary lattice; distortions can manifest themselves as satellites in the X-ray diffraction pattern. For example, the ground-state configuration for ρ=1/2 may be presented by two patterns: …10101010… and …11001100… (0 indicates the neutral molecule and 1 corresponds to the monocation). Furthermore, it was also shown that the observed polarizations of optical transitions are consistent with the proposed model [39].

**2. Electronic structure investigated by optical spectroscopy**

116 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

materials.

Peierls model [40].

κ-(ET)4[Co(CN)6][N(C2H5)4]

τ-(P-*S*,*S*-DMEDT-TTF)2 (AuBr2)(AuBr2)y

from an occupied A+

with the CT from one A+

2H2O

**Compounds Charge-transfer**

**bands**

**A band B band**

β"-(ET)4NH4[Cr(C2O4)3] DMF 3400 10,200 16,300; 20,600; 30,800 [41] β"-(ET)4K[Cr(C2O4)3] DMF 3620 9900 16,000; 21,000; 30,000 [42] (ET)6(Mo8O26)(DMF)3 2500 7300 11,200; 21,900; 35,400 [43]

β-(EDT-DTDSF)4Hg3I8 2800 11,700 26,000; 32,500; 40,000 [46]

The CT bands (denoted as A and B) and intramolecular excitations for selected organic conductors are shown in **Table 1**. The band A corresponds to a charge transfer of an electron

> +A0 →A0 +A+

> > (A+ +A+ →A0

molecule (A+

anion to a neighboring A+

(DOEO)4HgBr4 TCE 3600 11,500 19,500; 21,800; 28,400; 30,600;

**Table 1.** Electronic transitions (in cm−1) observed for selected organic conductors.

to a neutral A0

The electronic transitions that appear in the spectra of organic conductors recorded in IR, Vis and UV regions fall into two classes. On the one hand, those at high frequencies generally are a result of localized excitations, which are related to intramolecular transitions in which an electron is excited to a higher level on the same molecule. For characterization of such type of excitations, the time-dependent DFT method (TD-DFT) can be applied for organic conductors [36, 37]. The quantitative understanding of such molecular electronic excited states is important in many domains, including spectroscopy, photochemistry and the design of new optical

On the other hand, transitions at lower frequencies that are along the stacking directions or along to the S⋅⋅⋅S short contacts correspond to CT excitations between the molecules. The frequencies and oscillator strengths of these CT bands are clearly related to the electronic structure of these compounds, but they are a consequence of three types of interactions among the unpaired electrons occupying the highest molecular orbital (HOMO): (i) the overlap of the electronic wave functions between sites, (ii) the Coulomb repulsion of two electrons on the same or adjacent sites, and (iii) interactions of the electron with phonons. Theoretical models for the electronic structure of organic conductors have shown the importance of one or the other of these interactions, e.g. tight-binding theory [38], the Hubbard model [39] and the

> **Intramolecular excitations**

2500, 3390 7200 10,000 [44]

1000, 5900 12,300 18,100; 22,900; 31,400; 33,500 [45]

32,000; 33,200

**References**

[37]

), whereas band B is associated

+A2+). Within the Hubbard

Considerable information about the electronic structure can also be extracted from the oscillator strength sum rule [47]. Such an approach is used very often for organic conductors [41, 42, 46, 48, 49]. The effective number of electrons (*N*eff) participating in optical transitions for energies less than ℏω is given by

$$
\left[\frac{m\_0}{m\_{\circ\circ'}}\right] N\_{\circ\circ'}\left(\alpha\right) = \frac{m\_0}{32\pi N\_\circ e^2} \left[\sigma\left(\alpha\nu\right)d\,\alpha\nu\right] \tag{1}
$$

where *m*eff is the effective mass of the carriers; *mo* means the electronic mass; *N*c is the number of molecules per unit volume and *σ* means optical conductivity.

In order to analyze the electronic dispersion for organic metals and semiconductors the leastsquares fits to the experimental data of the reflectance calculated from the Drude and Drude-Lorentz dielectric functions can be performed [41–43, 45, 46, 48, 50, 51]. The Drude model is used for describing the intraband transitions of the free charge carriers, whereas interband transitions can be investigated using the Lorentz model. Within the Drude-Lorentz model the complex dielectric constant can be written as [47]:

$$\mathcal{L}\left(\boldsymbol{\phi}\right) = \boldsymbol{\varepsilon}\_{\text{core}} - \frac{\left\|\boldsymbol{\alpha}\right\|^2}{\left\|\boldsymbol{\phi}\right\|\left(\boldsymbol{\phi} + i\boldsymbol{\Gamma}\right)} + \frac{\left\|\boldsymbol{\Omega}\_p^2}{\left\|\boldsymbol{\alpha}\right\|^2 - \left\|\boldsymbol{\alpha}\right\|^2} \tag{2}$$

where *ω*p is the plasma frequency of the free charge carries, *Γ* the relaxation constant of the free charge carries (*Γ* is related to the relaxation time of carriers *τ* by *Γ*=1/*τ*), *ε*core represents all higher frequency contributions to the dielectric function, *Ω*p, *ω*0 and *γ* are the oscillator strength, the resonance frequency and the linewidth of the Lorentz oscillators, respectively.

The polarized reflectance and optical conductivity spectra measured for ethylenedithiodithiadiselenafulvalene (EDT-DTDSF) salt: β-(EDT-DTDSF)4Hg3I8 is presented in the **Figure 1** [46]. In the bottom panel of this figure there is the inset with sum rule calculations performed for two polarizations of electrical vector. For *E*max, (*mo*/*m*eff)*N*eff increases rapidly at first and begins to level off at a value near 0.18 and then rises rapidly above 1 eV. The function rises much more slowly and smoothly for the other polarization. For this salt the effective masses of holes (*m*eff= 1.1*m*o for Emaxand*m*eff= 3.8*m*o for Emin) suggest that it belongs to quasi-twodimensional material with a closed Fermi surface [46].

**Figure 1.** Polarized reflectance (upper panel) and optical conductivity (lower panel) spectra of β-(EDT-DTDSF)4Hg3I8 at room temperature. Least-squares fits to the reflectance assuming a Drude dielectric function (upper panel, dotted line) and sum rule calculations based on the optical conductivity data (in the inset). (Reprinted with permission from Łapiński et al. [46]. Copyright© 2006, Elsevier).

The polarized reflectance and optical conductivity spectra measured for pyrazino-*S,S*dimethyl-ethylenedithio-tetrathiafulvalene (P-*S,S*-DMEDT-TTF) salt: τ-(P-S,S-DMEDT-TTF)2(AuBr2)(AuBr2)y are shown in **Figure 2** [45].

Dotted line in the upper panel of this figure was used for display Drude-Lorentz model. The electronic band centered between 5500 and 6050 cm−1 observed for this organic conductor is related to the transitions between the lower and upper Hubbard bands. Within the basic Hubbard framework, the optical conductivity spectrum at low-temperature is predicted to show: a Drude-type band centered at zero frequency due to quasi-particle transitions, a resonance at *ω*≈*U*/2 (where *U* means the on-site Coulomb repulsion) due to transitions between the Hubbard bands and quasi-particle band; and a contribution which appears at *ω*≈*U* due to transitions between lower and upper Hubbard bands [52].

Among the two-dimensional organic CT salts, the κ-phase ET salts are of particular interest, because the constituting cationic dimers are arranged in an anisotropic lattice [53–55]. To understand the electronic properties of such group of organic conductors Kino and Fukuyama [56–58] considered a triangular lattice. For κ-(ET)2X family the electronic transition observed in mid-infrared has the double nature origin. One can identify intraband transitions within the correlated manifold and interband transitions due to CT within the ET dimer. Two-dimensional metallic properties are related to the carriers which can move between the dimer "lattice sites." In the Mott-insulating state, the strong electronic repulsion limits their mobility and immobilizes them. The other types of carriers are localized on the sites of a triangular lattice. The effective on-site Coulomb interaction is related to the intradimer overlap integrals, whereas the interdimer overlap integrals define the hopping *t* between the sites.

[46]. In the bottom panel of this figure there is the inset with sum rule calculations performed for two polarizations of electrical vector. For *E*max, (*mo*/*m*eff)*N*eff increases rapidly at first and begins to level off at a value near 0.18 and then rises rapidly above 1 eV. The function rises much more slowly and smoothly for the other polarization. For this salt the effective masses of holes (*m*eff= 1.1*m*o for Emaxand*m*eff= 3.8*m*o for Emin) suggest that it belongs to quasi-two-

118 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 1.** Polarized reflectance (upper panel) and optical conductivity (lower panel) spectra of β-(EDT-DTDSF)4Hg3I8 at room temperature. Least-squares fits to the reflectance assuming a Drude dielectric function (upper panel, dotted line) and sum rule calculations based on the optical conductivity data (in the inset). (Reprinted with permission from Łapiń-

The polarized reflectance and optical conductivity spectra measured for pyrazino-*S,S*dimethyl-ethylenedithio-tetrathiafulvalene (P-*S,S*-DMEDT-TTF) salt: τ-(P-S,S-DMEDT-

Dotted line in the upper panel of this figure was used for display Drude-Lorentz model. The electronic band centered between 5500 and 6050 cm−1 observed for this organic conductor is related to the transitions between the lower and upper Hubbard bands. Within the basic Hubbard framework, the optical conductivity spectrum at low-temperature is predicted to show: a Drude-type band centered at zero frequency due to quasi-particle transitions, a resonance at *ω*≈*U*/2 (where *U* means the on-site Coulomb repulsion) due to transitions between the Hubbard bands and quasi-particle band; and a contribution which appears at *ω*≈*U* due to

Among the two-dimensional organic CT salts, the κ-phase ET salts are of particular interest, because the constituting cationic dimers are arranged in an anisotropic lattice [53–55]. To understand the electronic properties of such group of organic conductors Kino and Fukuyama [56–58] considered a triangular lattice. For κ-(ET)2X family the electronic transition observed

dimensional material with a closed Fermi surface [46].

ski et al. [46]. Copyright© 2006, Elsevier).

TTF)2(AuBr2)(AuBr2)y are shown in **Figure 2** [45].

transitions between lower and upper Hubbard bands [52].

**Figure 2.** Polarized reflectance spectra of τ-(P-S,S-DMEDT-TTF)2(AuBr2)(AuBr2)y at room temperature and 10 K (represented by solid and dashed lines, respectively). Least-squares fits to the reflectance assuming a Drude-Lorentz dielectric function (upper panel, dotted line) and the optical conductivity spectra derived from the reflectance spectra by the Kramers-Krönig transformation. (Reprinted with permission from Łapiński et al. [45]. Copyright© 2003, Elsevier).

**Figure 3** shows the electronic feature A for κ-(ET)4[Co(CN)6][N(C2H5)4] 2H2O [44] which can be explained by two contributions: CT inside the dimer "lattice sites" (from 3300 to 4700 cm−1) and interdimer CT by correlated charge carriers (from 2500 to 3000 cm−1).

Rice [59], Yartsev and coworkers [60–62] have shown that the electronic feature with a maximum at around 3500 cm−1 is related to the CT within a dimer; Ag vibrations of ET molecule can be coupled with such transition. Moreover, the electronic band at about 2700 cm−1 reveals transitions between the Hubbard bands formed by the correlated conduction electrons [15, 16, 52, 63].

The family of two-dimensional ET salts with half-filled band are especially interesting for the charge disproportionation phenomena and has been extensively investigated [64–71], with the special focus on the κ-phase salts [72–79]. However, such phenomenon in such group of salts with an effectively half-filled band was very rarely observed. It has been reported only for a few salts, such as for κ-(ET)4PtCl6 C6H5CN, the triclinic κ-(ET)4[M(CN)6][N(C2H5)4] 3H2O and the monoclinic κ-(ET)4[M(CN)6][N(C2H5)4] 2H2O (with M = CoIII, FeIII and CrIII). For κ- (ET)4[Co(CN)6][N(C2H5)4] 2H2O and κ-(ET)4[Fe(CN)6][N(C2H5)4] 2H2O salts [44] the crystallographic studies have been performed at different temperatures at about 100, 200 and 293 K [78]. At ambient temperature, both salts exhibit rather poor conductivity and large paramagnetic susceptibility, which allows us to assert that they are on the insulator side of the Mott-Hubbard criterion as in κ-(ET)2Cu2(CN)3 and κ-(ET)2Cu[N(CN)2]Cl [80, 81]. Both investigated salts undergo a charge-ordering phase transitions at TCO=150 K [78]. Above 150 K they are in the Mott insulating state with a uniform charge distribution among ET molecules (ETA +0.5ETA +0.5, ETB +0.5ETB +0.5), whereas below this temperature a charge pattern (ETA +1ETA +1, ETB 0 ETB 0 ) is observed.

**Figure 3.** Temperature dependence of the optical conductivity spectra of κ-(ET)4[Co(CN)6][N(C2H5)4] 2H2O. Dotted lines show the deconvolution of the charge-transfer band into two components. (Reprinted with permission from Łapiński et al. [44]. Copyright© 2013, American Chemical Society).

The phase transition at 150 K induces considerable modifications in electronic structures. Due to the charge ordering phase transition, some new bands related to the fully ionized and neutral ET molecules appear in the spectra. One of the most important spectral changes is appearance of the new band at about 7000 cm−1 [44] (see **Figure 3**; band B). This electronic band can be attributed to intermolecular electronic transitions between neighboring ET+ cations. The appearance of this feature is a consequence of the charge-ordering phenomenon. Below 150 K the intensity of this band increases on cooling down. For polarisation E⊥b we can also find this band above 150 K which means that even at room temperature charge density fluctuations are present and hence we can expect that the relatively short-living dimers (ETA)2 2+ exist in our system.

## **3. Vibrational structure studied by IR and Raman spectroscopy**

with an effectively half-filled band was very rarely observed. It has been reported only for a few salts, such as for κ-(ET)4PtCl6 C6H5CN, the triclinic κ-(ET)4[M(CN)6][N(C2H5)4] 3H2O and the monoclinic κ-(ET)4[M(CN)6][N(C2H5)4] 2H2O (with M = CoIII, FeIII and CrIII). For κ- (ET)4[Co(CN)6][N(C2H5)4] 2H2O and κ-(ET)4[Fe(CN)6][N(C2H5)4] 2H2O salts [44] the crystallographic studies have been performed at different temperatures at about 100, 200 and 293 K [78]. At ambient temperature, both salts exhibit rather poor conductivity and large paramagnetic susceptibility, which allows us to assert that they are on the insulator side of the Mott-Hubbard criterion as in κ-(ET)2Cu2(CN)3 and κ-(ET)2Cu[N(CN)2]Cl [80, 81]. Both investigated salts undergo a charge-ordering phase transitions at TCO=150 K [78]. Above 150 K they are in the

120 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Mott insulating state with a uniform charge distribution among ET molecules (ETA

**Figure 3.** Temperature dependence of the optical conductivity spectra of κ-(ET)4[Co(CN)6][N(C2H5)4] 2H2O. Dotted lines show the deconvolution of the charge-transfer band into two components. (Reprinted with permission from Ła-

The phase transition at 150 K induces considerable modifications in electronic structures. Due to the charge ordering phase transition, some new bands related to the fully ionized and neutral ET molecules appear in the spectra. One of the most important spectral changes is appearance of the new band at about 7000 cm−1 [44] (see **Figure 3**; band B). This electronic band can be

appearance of this feature is a consequence of the charge-ordering phenomenon. Below 150 K the intensity of this band increases on cooling down. For polarisation E⊥b we can also find this band above 150 K which means that even at room temperature charge density fluctuations

attributed to intermolecular electronic transitions between neighboring ET+

are present and hence we can expect that the relatively short-living dimers (ETA)2

piński et al. [44]. Copyright© 2013, American Chemical Society).

+0.5), whereas below this temperature a charge pattern (ETA

ETB

+0.5ETB

observed.

system.

+0.5ETA +0.5,

cations. The

2+ exist in our

+1ETA

+1, ETB 0 ETB 0 ) is The most well-known donor in organic conductors is ET molecule. In the solid state, they are never flat and their symmetry is lowered caused by the deformations of outer CH2-CH2 groups. Nevertheless, for the classification of normal modes, a planar *D*2h molecular symmetry was often taken by many authors, e.g. by Kozlov *et al*. [82, 83] and Eldridge *et al*. [84]. The equilibrium geometry of a neutral ET has a boat conformation (*C*2 symmetry). An ionized ET can be either staggered (*D*2 molecular symmetry) or eclipsed (*C*2h symmetry) [85]. Correlations between the spectral predictions based on *D*2h and on *D*2 symmetry can be easily made, the difference being associated with the lack of inversion center (Ag and Au become A, B1g and B1u become B1, B2g and B2u become B2, B3g and B3u become B3. Moreover, A and B1 modes in *D*<sup>2</sup> correlate with A in *C*2 and B2, B3 in *D*2 with B in *C*2).

For ET molecule, there are three normal modes related to C=C stretching vibrations, which exhibit the largest ionization frequency shift (120–130 cm−1) [25, 31, 54]. Assuming D2h symmetry for the free ET molecule, these modes are called ν2(Ag), ν3(Ag) and ν27(B1u) (see **Figure 4**) where the symbols in parentheses denote the symmetry species [82, 83].

**Figure 4.** Schematic views of the three C=C stretching modes in ET molecule.

They have been the first ones to be proposed for the determination of *ρ* in ET [25] and the linear dependence of ν2(Ag) and ν27(B1u) modes against charge density has been experimentally verified. The Raman-active ν2 and ν3 modes involve the central and symmetric ring C=C stretching vibrations. For the neutral ET molecule, C=C stretching vibrations are mixed almost equally in ν2 and ν3 modes, whereas for the ionized ET, they are almost separated; in the latter case the ν2 and ν3 modes are mainly assigned to ring C=C stretching and bridge C=C stretching, respectively [86, 87]. The IR-active ν27(B1u) mode is due to the anti-symmetric ring C=C stretching and is thus completely separated from the central C=C stretching.

**Figure 5** shows that for ET salts in their IR spectra a group of strong bands related to C=C bonds vibrations can be found within the spectral region from 1100 to 1400 cm−1. The ionization results in the meaningful red shift of these modes 95 and 60 cm−1 [20, 25, 88]. For organic metals, where electrical conductivity is relatively high, situation becomes a little more complicated, because instead of well defined group of vibrational features, additional broad maxima can be observed (e.g. β"-(ET)4A[M(C2O4)3] DMF where A=NH4 + , K+ and M=CrIII, FeIII [41–42], (ET)6(Mo8O26)(DMF)3 [43]). Such broad bands are a consequence of the coupling of ν2(Ag) and ν3(Ag) modes with conducting electrons, for which their proximity leads to a strong mixing.

Nevertheless, it should be emphasized that the C=C modes are often used in the study of the nature of different phase transitions. For example, for the salts κ-(ET)4[Co(CN)6] [N(C2H5)4] 2H2O and κ-(ET)4[Fe(CN)6][N(C2H5)4] 2H2O where the phase transition from the Mott insulator state to the charge-ordering state is present, the C=C modes have been discussed [44]. The considerable modifications in vibrational structure due to this phase transition at 150 K are presented in **Figure 5a**. The new bands related to the fully ionized and neutral ET molecules appear in the IR spectra. One of the most important spectral changes is appearance of new bands at 1347 cm−1 and 1289, 1297 cm−1 related to the ν3(Ag) and ν5(Ag) modes of ET+1 cation, which are activated by coupling with the CT transition observed at about 7000 cm−1 [44]. It gives an evidence of doubly charged ET2 2+ dimers. The appearance of these features is a consequence of the charge-ordering phenomenon and EMV coupling in these dimers.

**Figure 5.** Temperature dependence of the conductivity spectra of κ (ET)4[Co(CN)6][N(C2H5)4] 2H2O salt (a) and temperature variation of the ν60(B3g) (*D*2h) mode (ν10(A)for *D*2 symmetry) (frequency and intensity) (b). (Reprinted with permission from Łapiński et al. [44]. Copyright© 2013, American Chemical Society).

For the determination of *ρ* in ET salts, other vibrational modes asν29(B1) and ν44(B2) (for *D*<sup>2</sup> molecular symmetry) can also be used [89]. For example, for κ-(ET)4[M(CN)6][N(C2H5)4] 2H2O (M= CoIII and FeIII) salts [44], the ν44(B2) mode is assigned to weak bands observed in the experimental spectra at 863 cm−1 (for ET0 ), at 875 cm−1 (for ET0.5+) and at 900 cm−1 (for ET+ ) which are in good agreement with calculated by Girlando values 864, 876 and 903 cm−1 for ET0 , ET0.5+ and ET+ , respectively [89]. The 890 cm−1 mode, assigned to ν60(B3g) in the *D*2h symmetry [84] and to ν10(A) in the *D*2 symmetry [89], has attracted a special attention as a spectral feature which is so sensitive to the charge disproportion in ET salts [85]. Moreover, if we consider this mode as a totally symmetric one of a distorted, not a perfectly flat ET molecule (*D*2h symmetry) then this mode can be coupled to the electronic system [89]. This mode appears in the experimental spectra for the ET0.5+ at 878 cm−1 [90] and for ET+ at 899 cm−1 [91]. In the optical conductivity spectra of κ-(ET)4[M(CN)6][N(C2H5)4] 2H2O (M= CoIII and FeIII) salts this mode at 868 cm−1 (for ET0 ), at 883 cm−1 (for ET0.5+) and at 894 cm−1 (for ET+ ) can be observed [44]. **Figure 5b** shows the temperature dependence of the position of the ν10(A)mode.

(ET)6(Mo8O26)(DMF)3 [43]). Such broad bands are a consequence of the coupling of ν2(Ag) and ν3(Ag) modes with conducting electrons, for which their proximity leads to a strong mixing.

122 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Nevertheless, it should be emphasized that the C=C modes are often used in the study of the nature of different phase transitions. For example, for the salts κ-(ET)4[Co(CN)6] [N(C2H5)4] 2H2O and κ-(ET)4[Fe(CN)6][N(C2H5)4] 2H2O where the phase transition from the Mott insulator state to the charge-ordering state is present, the C=C modes have been discussed [44]. The considerable modifications in vibrational structure due to this phase transition at 150 K are presented in **Figure 5a**. The new bands related to the fully ionized and neutral ET molecules appear in the IR spectra. One of the most important spectral changes is appearance of new bands at 1347 cm−1 and 1289, 1297 cm−1 related to the ν3(Ag) and ν5(Ag) modes of ET+1 cation, which are activated by coupling with the CT transition observed at about 7000 cm−1 [44].

consequence of the charge-ordering phenomenon and EMV coupling in these dimers.

**Figure 5.** Temperature dependence of the conductivity spectra of κ (ET)4[Co(CN)6][N(C2H5)4] 2H2O salt (a) and temperature variation of the ν60(B3g) (*D*2h) mode (ν10(A)for *D*2 symmetry) (frequency and intensity) (b). (Reprinted with per-

For the determination of *ρ* in ET salts, other vibrational modes asν29(B1) and ν44(B2) (for *D*<sup>2</sup> molecular symmetry) can also be used [89]. For example, for κ-(ET)4[M(CN)6][N(C2H5)4] 2H2O (M= CoIII and FeIII) salts [44], the ν44(B2) mode is assigned to weak bands observed in the

and to ν10(A) in the *D*2 symmetry [89], has attracted a special attention as a spectral feature which is so sensitive to the charge disproportion in ET salts [85]. Moreover, if we consider this mode as a totally symmetric one of a distorted, not a perfectly flat ET molecule (*D*2h symmetry) then this mode can be coupled to the electronic system [89]. This mode appears in the exper-

conductivity spectra of κ-(ET)4[M(CN)6][N(C2H5)4] 2H2O (M= CoIII and FeIII) salts this mode at

, respectively [89]. The 890 cm−1 mode, assigned to ν60(B3g) in the *D*2h symmetry [84]

are in good agreement with calculated by Girlando values 864, 876 and 903 cm−1 for ET0

), at 875 cm−1 (for ET0.5+) and at 900 cm−1 (for ET+

) which

, ET0.5+

at 899 cm−1 [91]. In the optical

mission from Łapiński et al. [44]. Copyright© 2013, American Chemical Society).

imental spectra for the ET0.5+ at 878 cm−1 [90] and for ET+

experimental spectra at 863 cm−1 (for ET0

and ET+

2+ dimers. The appearance of these features is a

It gives an evidence of doubly charged ET2

**Figure 6.** Schematic atomic displacements of C=C in vibrational modes for DIETS, DIET and DIEDO molecules. Note: the position of C=C stretching modes is given for the experimental spectra of these donors. (Reprinted with permission from Łapiński et al. [36]. Copyright© 2010, Elsevier).

In the case of organic unsymmetrical donors derived from TTF molecule: e.g. pyrazino-*S,S*dimethyl-ethylenedithio-tetrathiafulvalene (P-*S,S*-DMEDT-TTF) [45],2-(4,5-ethylenedithio-1,3-dithiol-2-ylidene)-5-(1,3-dithiolan-2-ylidene)-1,3,4,6-tetrathiapentalene (EDDH-TTP) [48],2,5-bis(1,3-dithiolan-2-ylidene)-1,3,4,6-tetrathiapentalene (BDH-TTP) [48], ethylenedithio-dithiadiselenafulvalene (EDT-DTDSF) [46],diiodoethylenedithio-dithiaselenafulvalene (DIETS) [36, 50], diiodoethylenedithiotetrathiafulvalene (DIET) [50], diiodoethylene-dioxotetrathiafulvalene (DIEDO) [36, 50], (1,4-dioxane-diyl-2,3-ditio) ethylenedioxytetrathiafulvalene (DOEO) [37, 51, 92],dimethyltrimethylenetetrathiafulvalene

**Figure 7.** Simulated IR absorption spectra of EDT-DTDSF+ (a) and EDT-DTDSF0 (b). (Reprinted with permission from Łapiński et al. [46]. Copyright© 2006, Elsevier).

(DMtTTF) [93], *o* dimethyl-tetrathiafulvalene (*o*-DMTTF) [93] one can find three types of nonequivalent C=C bonds - one central bond and two ring bonds. The schematic picture of atomic displacement of carbon atoms for DIEDO, DIETS, DIET is shown in **Figure 6**. The theoretical calculations show that a strong mixing of all C=C stretching vibrations is present for all modes related to C=C stretching vibrations.

Except the modes related to the C=C stretching vibration, which show the largest lowfrequency shifts when the molecule is oxidized, other active modes also exhibit a significant shift due to the ionicity [36, 46, 51], what is schematically illustrated by dashed line for EDT-DTDSF (see **Figure 7**).

For the isolated donor molecules, the optimized geometry depends on whether we have a neutral or charged molecule. The TTF framework for neutral molecules is non-planar deforming to a boat conformation, in contrast with cations where the TTF framework is planar (see **Figure 8**) [36]. The similar situation has also been observed for the other organic donors [37, 51, 94]. In crystal structures of salts derived from TTF, where donors are not isolated molecules, the TTF framework can be flat with small deviations from planarity [95, 96]. For example, for the CT salts derived from DIET, DIEDO and DIETS and the anion [Fe(bpca)(CN)3] − the donors are almost flat [97]. In Raman spectra of these salts bands assigned to the C=C stretching vibrations are strongly shifted towards lower frequency and this effect is due to ionization [50].

**Figure 8.** Optimized geometry of the neutral DIETS, DIET, DIEDO molecules and cations. (Reprinted with permission from Łapiński et al. [36]. Copyright© 2010, Elsevier).

Infrared spectroscopy is a powerful method not only in investigating the charge disproportion phenomena but also in the study of interaction between the organic and inorganic layers in organic conductors and its impact on the physical properties. For κ-(ET)4[Co(CN)6] [N(C2H5)4] 2H2O and κ-(ET)4[Fe(CN)6][N(C2H5)4] 2H2O salts Ota and co-workers [78] showed that the strong electron–electron correlations and Coulomb interaction between ET and inorganic layers play an important role in the phase transition from the Mott insulator state to the charge-ordering state. The role of such interactions and their contributions to the phase transition has been investigated and discussed in Ref. [44]. The temperature dependence of the modes related to C≡N triple bond vibrations (~2100 cm−1) in M(CN)6 3− (M=CoIII and FeIII) anions and C-H stretching in ET molecules (~3400 cm−1) is presented in **Figure 9**. For these modes, the frequency dependences reflect the sensitivity of the CN-CH2 interaction to the 150 K phase transition. The blue shift of the CN stretching frequency with decreasing temperature proves that the interaction between the hydrogen atom and the CN group of the anions is present. Moreover, the examination of the CH2 stretching frequencies in κ-(ET)4[Co(CN)6] [N(C2H5)4] 2H2O and κ-(ET)4[Fe(CN)6][N(C2H5)4] 2H2O salts leads us to the conclusion that in the last salt the degree of donor-anion interaction is slightly smaller.

(DMtTTF) [93], *o* dimethyl-tetrathiafulvalene (*o*-DMTTF) [93] one can find three types of nonequivalent C=C bonds - one central bond and two ring bonds. The schematic picture of atomic displacement of carbon atoms for DIEDO, DIETS, DIET is shown in **Figure 6**. The theoretical calculations show that a strong mixing of all C=C stretching vibrations is present for all modes

124 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Except the modes related to the C=C stretching vibration, which show the largest lowfrequency shifts when the molecule is oxidized, other active modes also exhibit a significant shift due to the ionicity [36, 46, 51], what is schematically illustrated by dashed line for EDT-

For the isolated donor molecules, the optimized geometry depends on whether we have a neutral or charged molecule. The TTF framework for neutral molecules is non-planar deforming to a boat conformation, in contrast with cations where the TTF framework is planar (see **Figure 8**) [36]. The similar situation has also been observed for the other organic donors [37, 51, 94]. In crystal structures of salts derived from TTF, where donors are not isolated molecules, the TTF framework can be flat with small deviations from planarity [95, 96]. For example, for

are almost flat [97]. In Raman spectra of these salts bands assigned to the C=C stretching vibrations are strongly shifted towards lower frequency and this effect is due to ionization [50].

**Figure 8.** Optimized geometry of the neutral DIETS, DIET, DIEDO molecules and cations. (Reprinted with permission

Infrared spectroscopy is a powerful method not only in investigating the charge disproportion phenomena but also in the study of interaction between the organic and inorganic layers in organic conductors and its impact on the physical properties. For κ-(ET)4[Co(CN)6] [N(C2H5)4] 2H2O and κ-(ET)4[Fe(CN)6][N(C2H5)4] 2H2O salts Ota and co-workers [78] showed that the strong electron–electron correlations and Coulomb interaction between ET and inorganic layers play an important role in the phase transition from the Mott insulator state to the charge-ordering state. The role of such interactions and their contributions to the phase transition has been investigated and discussed in Ref. [44]. The temperature dependence of

anions and C-H stretching in ET molecules (~3400 cm−1) is presented in **Figure 9**. For these modes, the frequency dependences reflect the sensitivity of the CN-CH2 interaction to the 150 K phase transition. The blue shift of the CN stretching frequency with decreasing temperature proves that the interaction between the hydrogen atom and the CN group of the anions is

the modes related to C≡N triple bond vibrations (~2100 cm−1) in M(CN)6

−

3− (M=CoIII and FeIII)

the donors

the CT salts derived from DIET, DIEDO and DIETS and the anion [Fe(bpca)(CN)3]

related to C=C stretching vibrations.

from Łapiński et al. [36]. Copyright© 2010, Elsevier).

DTDSF (see **Figure 7**).

**Figure 9.** Temperature variation of the C-H (a) and C≡N (b) modes (frequency and intensity). (Reprinted with permission from Łapiński et al. [44]. Copyright© 2013, American Chemical Society).

What should be emphasized at this point is the fact that the temperature variation of bands related to C-H stretching indicate that apart from the long-range Coulomb interactions between electrons within the conducting layers, the anions have an influence on the formation of the charge-ordered state as well [44]. Laversanne and co-workers [98] showed that periodic distribution of the anions could play an important role in the physical properties of organic conductors.

They drew attention that the anion potential effects on an terminal part of the donors. The orientation of the anions along the chain influences on the charge density distribution within conducting layers and the description of the anion potential should be taken into account in calculations [98]. Moldenhower *et al*. [88] investigated the correlation between the *T*c temperature and frequencies of the CH2 stretching modes of ET radical salts with the superconducting phase transition. The position of these modes is evidently not charge dependent but it can reflect the strength of the interaction of the donor molecule with the respective anion. They showed that phases with a higher *T*c of their superconducting transition exhibit a smaller red shift of these frequencies, which is due to the hydrogen-bonding like interaction of the donor with the anion, i.e., a less attractive donor-anion interaction [88].

For (DOEO)4HgBr4 TCE salt it has been shown in [92] that the role of anion layers cannot be neglected. The temperature evolution of vibrational features reveals that only the bands related to the deformation of the outer ring of DOEO molecule (e.g. 1371, 1092 cm−1) are sensitive to the metal-insulator phase transitions (**Figure 10a**), whereas the bands related to the deformation of C-O bonds in inner part of donor molecule observed at 1000 and 902 cm−1 do not show such behavior (**Figure 10b**). The systematic analysis of vibrational and electronic structure performed for DOEO salt one can find in [37] and [51].

**Figure 10.** Temperature dependence of the wave number of the selected bands: 1371 and 1092 cm−1 (a) and 902 and 1000 cm−1 (b). Note: lines are used as a guide for the eyes. (Reprinted with permission from Łapiński et al. [92]. Copyright© 2012, Elsevier).

In the case of organic conductors formed by iodinated TTFs as DIEDO, DIET, DIETS [36], the position of modes related to C-I and C-S vibrations could be also sensitive to strong interaction between the iodo group of donor and the cyano group or halogen of acceptors [95, 97, 99, 100]. In the experimental IR spectra of these neutral donors, one can find the bands related to the simultaneous deformation of C-S and C-I bonds at 693, 817, 903 cm−1 (for DIETS), 696, 817, 917 cm−1 (for DIET) and 699, 829, 912 cm−1 (for DIEDO) [36].

The strong interaction between donors and acceptors should also have an influence on frequencies of acceptor molecules. For example, for the 2:1 salts formed by the iodine substituted donors DIEDO, DIET, DIETS with the anion [Fe(bpca)(CN)3] − (where bpca=bis(spyridylcarbonyl)amide anion) we have observed the influence of such interactions on frequencies of C≡N and C=O vibrations of acceptor molecule [50].

#### **4. Electron-phonon interaction**

Infrared spectra of organic conductors are usually dominated by strong vibrational features related to the coupling between the electrons in the highest occupied molecular orbital (HOMO) and the molecular vibrational modes of molecules [101, 102]. Because of this coupling, the vibrational modes borrow intensity from the nearby CT electronic transition and occur at frequencies lower than the corresponding Raman active modes. These strong bands are polarized perpendicularly to the molecular planes, like the CT transition.

The EMV coupling phenomenon in conducting organic salts can be analyzed in terms of various models depending on structure of the molecular stacks. Microscopic theories for regular stacks or stacks consisting of quasi-isolated dimers, trimers, tetramers or n-mers have been developed [28–30].The above mentioned models were successfully applied to IR spectra of CT salts formed by TTF and its derivatives with various acceptors [62]. More specifically, the dimer model has proven to be especially useful in determining the coupling constants for TTF-containing CT materials. For example, reliable values for the EMV constants were obtained for the salt (ET)2[Mo6O19] which contained well-isolated (ET+ )2 dimers [91].

such behavior (**Figure 10b**). The systematic analysis of vibrational and electronic structure

**Figure 10.** Temperature dependence of the wave number of the selected bands: 1371 and 1092 cm−1 (a) and 902 and 1000 cm−1 (b). Note: lines are used as a guide for the eyes. (Reprinted with permission from Łapiński et al. [92]. Copy-

In the case of organic conductors formed by iodinated TTFs as DIEDO, DIET, DIETS [36], the position of modes related to C-I and C-S vibrations could be also sensitive to strong interaction between the iodo group of donor and the cyano group or halogen of acceptors [95, 97, 99, 100]. In the experimental IR spectra of these neutral donors, one can find the bands related to the simultaneous deformation of C-S and C-I bonds at 693, 817, 903 cm−1 (for DIETS), 696, 817,

The strong interaction between donors and acceptors should also have an influence on frequencies of acceptor molecules. For example, for the 2:1 salts formed by the iodine substi-

pyridylcarbonyl)amide anion) we have observed the influence of such interactions on

Infrared spectra of organic conductors are usually dominated by strong vibrational features related to the coupling between the electrons in the highest occupied molecular orbital (HOMO) and the molecular vibrational modes of molecules [101, 102]. Because of this coupling, the vibrational modes borrow intensity from the nearby CT electronic transition and occur at frequencies lower than the corresponding Raman active modes. These strong bands

The EMV coupling phenomenon in conducting organic salts can be analyzed in terms of various models depending on structure of the molecular stacks. Microscopic theories for regular stacks or stacks consisting of quasi-isolated dimers, trimers, tetramers or n-mers have been developed [28–30].The above mentioned models were successfully applied to IR spectra

−

(where bpca=bis(s-

performed for DOEO salt one can find in [37] and [51].

126 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

917 cm−1 (for DIET) and 699, 829, 912 cm−1 (for DIEDO) [36].

tuted donors DIEDO, DIET, DIETS with the anion [Fe(bpca)(CN)3]

are polarized perpendicularly to the molecular planes, like the CT transition.

frequencies of C≡N and C=O vibrations of acceptor molecule [50].

**4. Electron-phonon interaction**

right© 2012, Elsevier).

According to symmetry considerations, only the totally symmetric vibrational modes within a specified linear approximation of non-degenerate molecular orbitals can couple with electrons [103]. For other symmetry modes, the electron–vibrational interaction is forbidden by the selection rules and is only correct if the molecules within the dimer have the same symmetry. When considering the dimer, where the molecules are asymmetric with respect to one another, if these molecules are different or inequivalent, their modes are no longer degenerate and couple both in-phase and out-of-phase. In this case, the lack of an inversion center suppresses the mutual exclusion rule leading to all of the modes for the constituent molecules within the dimer becoming both IR and Raman active. Additionally, all of their symmetric modes can then couple to the CT electron [104]. Moreover, if we consider the sufficiently fast charge transfer between the dimer molecules due to electromagnetic radiation, their nuclear configurations do not have time to change in response to the charge transfer and their molecular vibrations arise as the result of the relaxation to each molecule's respective equilibrium configuration. In this case, the symmetry type of the arising vibrational modes depends not only on the final and initial state symmetries, but also on that of the intermediate states from which the transferred charge among the neighboring molecules belongs. These facts could suggest that in some cases non-totally symmetric modes can be also coupled [105].

**Figure 11.** Experimental and calculated conductivity spectra of (DMtTTF)Br salt. Note: electric vector along the stacking axis; the logarithmic wave number scale. (Reprinted with permission from Łapiński et al. [93]. Copyright© 2014, Elsevier).

For salts formed by unsymmetrical TTF derivatives such as *o*-DMTTF, DMtTTF and DOEO in the IR spectra one observes vibrational features suggesting the EMV coupling to intramolecular vibrations of donors, especially those related to C=C stretching [106–109]. In the IR spectra of the salts (DOEO)4HgBr4 TCE [51], (DMtTTF)Br [93] and (*o* DMTTF)2[W6O19] [93] a clear evidence of the EMV coupling to C=C stretching modes have been found. The observation of vibrational bands shifted towards lower wave numbers with respect to Raman data and, moreover, with characteristic antiresonance deeps, give an evidence of their interaction with CT transition. This effect is very well visible for polarization parallel to the stacking axis; in particular there are distinct antiresonance dips at 1370 and 1379 cm−1 for (DMtTTF)Br and (*o*-DMTTF)2[W6O19], respectively [93]. Moreover, the bands at 1338 and 1345 cm−1 [93] have a characteristical asymmetric Fano-like lineshape [110]. It is observed when the electric field is polarized along the chain and the electronic absorption overlaps with the phonon frequencies; the interaction between electrons and phonons gives rise to characteristically asymmetric Fano lineshape of bands. The analysis of Fano-effect combined with Raman data can lead to quantitative predictions for the various electron phonon couplings [111].


**Table 2.** Dimer model parameters by the fit to the polarized conductivity spectrum of (DMtTTF)Br, (*o*-DMTTF)2[W6O19] and (DOEO)4HgBr4 TCE salts obtained by Kramers-Krönig transformation from the reflectance spectra.


**Table 3.** The EMV coupling constants, *g*α (meV) of the C=C stretching modes *ω* (cm−1) for several symmetrical radical cations based on TTF.

**Figure 11** shows the conductivity spectrum of (DMtTTF)Br salt obtained by Kramers-Krönig transformation from the experimental reflectance spectrum (upper panel) and conductivity spectrum calculated within the framework of the dimer model proposed by Rice et al. [103] (lower panel). **Table 2** presents the model parameters for the fit to the conductivity spectra of (DMtTTF)Br [93], (*o* DMTTF)2[W6O19] [93] and (DOEO)4HgBr4 TCE [51] salts. Comparing the relevant EMV coupling constants for unsymmetrical DMtTTF, *o*-DMTTF and DOEO donors with the corresponding ones measured for symmetrical TTF-based electron donor molecules: TTF itself [28–29], ET [91], tetramethyl-tetrathiafulvalene (TMTTF) [112], bis-fused TTF (TTP) [113] (see **Table 3**) one can see that the values of coupling constants are comparable and the most strongly coupled modes are assigned to the TTF skeleton vibrations, namely the modes related to the stretching vibrations of both central and ring C=C bonds.

It should be also emphasized that the EMV coupling plays a role in the charge-ordering instabilities, as the modulation of the frontier molecular orbitals, pushing charges back and forth, which may in turn provoke their localization on the molecular sites [89].

## **5. Conclusions**

For salts formed by unsymmetrical TTF derivatives such as *o*-DMTTF, DMtTTF and DOEO in the IR spectra one observes vibrational features suggesting the EMV coupling to intramolecular vibrations of donors, especially those related to C=C stretching [106–109]. In the IR spectra of the salts (DOEO)4HgBr4 TCE [51], (DMtTTF)Br [93] and (*o* DMTTF)2[W6O19] [93] a clear evidence of the EMV coupling to C=C stretching modes have been found. The observation of vibrational bands shifted towards lower wave numbers with respect to Raman data and, moreover, with characteristic antiresonance deeps, give an evidence of their interaction with CT transition. This effect is very well visible for polarization parallel to the stacking axis; in particular there are distinct antiresonance dips at 1370 and 1379 cm−1 for (DMtTTF)Br and (*o*-DMTTF)2[W6O19], respectively [93]. Moreover, the bands at 1338 and 1345 cm−1 [93] have a characteristical asymmetric Fano-like lineshape [110]. It is observed when the electric field is polarized along the chain and the electronic absorption overlaps with the phonon frequencies; the interaction between electrons and phonons gives rise to characteristically asymmetric Fano lineshape of bands. The analysis of Fano-effect combined with Raman data can lead to

quantitative predictions for the various electron phonon couplings [111].

128 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

*ω***<sup>α</sup>** *g***<sup>α</sup>** *λ***<sup>α</sup>** *ω***<sup>α</sup>** *g***<sup>α</sup>** *λ***<sup>α</sup>** *ω***<sup>α</sup>** *g***<sup>α</sup>** *λ***<sup>α</sup>**

Note: *ω*α and *g*α are given in cm−1.

cations based on TTF.

**(DMtTTF)Br [93] (o-DMTTF)2[W6O19] [93] (DOEO)4HgBr4 TCE [51] Assignment**

and (DOEO)4HgBr4 TCE salts obtained by Kramers-Krönig transformation from the reflectance spectra.

**TTF [28–29] ET [91] TMTTF [112] TTP [113] Assignment**

1505 *42* 1460 43 1567 32 1540 8 Ring C=C stretch

1420 133 1414 71 1418 133 1423 9 Central C=C stretch

*ω g***<sup>α</sup>** *ω g***<sup>α</sup>** *ω g***<sup>α</sup>** *ω g***<sup>α</sup>**

1587 97 0.002 1556 484 0.022 1575 183 0.040 Ring C=C stretch 1507 161 0.006 1483 645 0.042 1494 252 0.080 Ring C=C stretch 1412 597 0.095 1417 805 0.068 1460 233 0.070 Central C=C stretch

**Table 2.** Dimer model parameters by the fit to the polarized conductivity spectrum of (DMtTTF)Br, (*o*-DMTTF)2[W6O19]

**Table 3.** The EMV coupling constants, *g*α (meV) of the C=C stretching modes *ω* (cm−1) for several symmetrical radical

**Figure 11** shows the conductivity spectrum of (DMtTTF)Br salt obtained by Kramers-Krönig transformation from the experimental reflectance spectrum (upper panel) and conductivity spectrum calculated within the framework of the dimer model proposed by Rice et al. [103] (lower panel). **Table 2** presents the model parameters for the fit to the conductivity spectra of (DMtTTF)Br [93], (*o* DMTTF)2[W6O19] [93] and (DOEO)4HgBr4 TCE [51] salts. Comparing the relevant EMV coupling constants for unsymmetrical DMtTTF, *o*-DMTTF and DOEO donors

1474 54 Ring C=C stretch

In this chapter, selected problems of solid state physics of organic conductors have been discussed. The IR, Raman and UV-Vis spectroscopies were used providing the information about vibrational and electronic structures, electron-electron and electron-phonon interactions. The detailed spectral analysis led to a wider recognition and provides the necessary information about physical properties of organic conductors.

It was shown that the role of anion layers cannot be neglected. The periodic distribution of anions could play an important role in the physical properties of organic conductors. On the basis of vibration spectra it was shown that the anion potential influences on a terminal part of the molecules, which are close to anions. Apart from the long-range Coulomb interactions between electrons within layers formed by donors also the anions can have a significant influence on the formation of the charge-ordered state. Moreover, it was shown that in the case of organic unsymmetrical donors derived from TTF molecule the values of coupling constants are comparable with another symmetrical TTF derivatives and the most strongly coupled modes are assigned to the TTF skeleton vibrations, namely the modes related to the stretching vibrations of both central and ring C=C bonds. It was also shown that the special attention should be paid to the impact of the EMV coupling on the charge-ordering instabilities.

For characterization of intramolecular and intermolecular transitions the time-dependent DFT method and Drude-Lorentz models can be successfully applied. Considerable information about the electronic structure can also be extracted from the oscillator strength sum rule.

The degree of ionicity or average charge per molecule is one of the fundamental parameters characterizing the physical properties of CT salts. For the organic donors, this parameter can be studied using spectroscopic methods. It was shown that in the case of organic donors derived from TTF molecule the most convenient for this analysis are the C=C stretching modes of TTF framework which show sensitivity to the ionization degree. It was also shown that spectroscopic methods are very powerful tool in the study of the nature of different phase transitions and the interaction between the organic and inorganic layers in organic conductors and its impact on the physical properties.

## **Acknowledgements**

Author is indebted to his co-workers Barszcz B., Graja A., Ostrowski A.,Olejniczak I., Połomska M., Świetlik R., Waplak S. at Institute of Molecular Physics PAS for their contribution to this work and to Baumer V., Faulques E.,Fourmigué M., Gąsecka A., Golhen S., Golub M., Imakubo T., Jankowski D.,Kotov A.I.,Kravczenko A., Lyubovskaya R.N., Mousdis G.A., Ouahab L.,Papavassiliou G.C.,Prokhorova T.G., Reinheimer E.W.,Setifi F., Starodub V.A., Yamada J., Zhilyaeva E.I. for a fruitful collaboration.

## **Author details**

Andrzej Łapiński

Address all correspondence to: lapinski@ifmpan.poznan.pl

Institute of Molecular Physics, Polish Academy of Sciences, Poznan, Poland

## **References**


[8] Enoki T, Miyazaki A. Magnetic TTF-based charge-transfer complexes. Chem. Rev. 2004;104:5449–5477. DOI: http://dx.doi.org/10.1021/cr0306438

**Acknowledgements**

**Author details**

Andrzej Łapiński

**References**

Zhilyaeva E.I. for a fruitful collaboration.

Address all correspondence to: lapinski@ifmpan.poznan.pl

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130 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Author is indebted to his co-workers Barszcz B., Graja A., Ostrowski A.,Olejniczak I., Połomska M., Świetlik R., Waplak S. at Institute of Molecular Physics PAS for their contribution to this work and to Baumer V., Faulques E.,Fourmigué M., Gąsecka A., Golhen S., Golub M., Imakubo T., Jankowski D.,Kotov A.I.,Kravczenko A., Lyubovskaya R.N., Mousdis G.A., Ouahab L.,Papavassiliou G.C.,Prokhorova T.G., Reinheimer E.W.,Setifi F., Starodub V.A., Yamada J.,

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Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

### **Infrared and Raman Spectroscopic Characterization of Porphyrin and its Derivatives Infrared and Raman Spectroscopic Characterization of Porphyrin and its Derivatives**

Metin Aydin and Daniel L. Akins Metin Aydin and Daniel L. Akins

Additional information is available at the end of the chapter Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/64582

#### **Abstract**

140 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Density functional theory (DFT) was employed to investigate protonation, deuteration, and substitution effects on the vibrational spectra of porphyrin molecules. The results of the calculations were compared with experimental data. The calculations show that *meso*‐substitutions produced a substantial shift in frequencies when the *meso*‐carbons within the parent porphine are involved in the vibrational motion of molecules, while protonation of the N atoms leads to a significant blue shift when the H atoms covalent bonded to the N atoms that are substantially involved in the vibrational motion. Deuteration of N atoms at the porphyrin core is found to result not only in a red shift in the frequencies of the corresponding peaks below 1600 cm‐1, but also to generate new Raman bands of frequencies in the range of 2565–2595 cm‐1, resulting from N‐D bond stretching. Also, the deuteration of O atoms within the sulfonato groups (‐SO3 ‐ ) results in a new peak at near 2642 cm‐1 due to O‐D bond stretching. Calculated IR spectra of the compounds studied here showed similar differences. Finally, we discuss solvent effects on the IR spectrum of TSPP.

**Keywords:** porphyrins, protonation, Raman, IR, DFT calculation

## **1. Introduction**

Molecular vibrations may be induced through two well‐known optical excitation processes. One is the absorption of photons and the other is the inelastic scattering of photons. Excitation of molecular vibration by absorption of photons is achieved by irradiation of a species using radiation containing photons of a frequency equivalent to the frequency difference Δ*ν* between the initial (i) and the final (f) vibrational states of the species; i.e., Δ*ν* = *ν*f − *ν*<sup>i</sup> . Unlike IR spectroscopy, the scattering mechanism for exciting molecular vibrations generally exploits monochromatic radiation. In this latter case, a number of incident photons is scattered

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

inelastically such that the frequency of the scattered photons (*ν*S) differs from that of the incident photons (*ν*0). And with conversation of the energy, this energy difference is the energy change associated with a transition from the initial (i) vibrational state to the final (f) vibra‐ tional state of the scattering species; i.e., *ν*0 − *ν*S = *ν*f − *ν*<sup>i</sup> . Inelastic scattering of the photons was first discovered by the Indian scientist C. V. Raman in 1928 and is referred to as the Raman effect.

In this chapter, we discuss IR and Raman spectra of protonated, deuterated, and *meso*‐ substituted parent porphyrin using density functional theory (DFT) to calculate the IR and Raman spectra, and, where possible, make comparison to experimental spectra. We also discuss spectra of aggregates involving several of the porphyrin species, using vibrational band assignments to ascertain which motions of the vibrating molecule couple more effec‐ tively, with excitonic motion, and as a result, we derive molecular alignment information from the enhancement that certain vibronic bands in the Raman spectrum experience for the various porphyrins.

#### **2. Overview of Raman spectroscopy**

In this section, we focus on Raman scattering. It is convenient to define the Raman scattering cross‐section for the n → m vibrational transition as σn m, and to relate it to the scattering intensity as follows:

$$\mathbf{l\_{n \to m}} = \sigma\_{\mathbf{n \to m}} \mathbf{l\_0} \tag{1}$$

In this equation, <sup>0</sup> is the intensity of the incident radiation and <sup>n</sup> <sup>m</sup> the intensity of the light scattered by molecules integrated over all scattering angles and polarization directions for randomly oriented molecules. The Raman cross‐section is associated with the Raman polar‐ izability by utilizing the fact that the intensity for electric dipole radiation scales as the fourth power of the frequency:

$$\sigma\_{\mathbf{n}\rightarrow\mathbf{m}} \propto (\mathbf{v}\_{\mathbf{0}} \mp \mathbf{v}\_{\mathbf{k}})^{4} \sum\_{\rho,\sigma} \left| \mathbf{a}\_{\rho\sigma} \right|^{2} \tag{2}$$

In this equation, the indices and σ indicate the molecule‐fixed directional coordinates. Moreover, for this equation, the scattering tensor can be formulated in terms of Kramers ‐Heisenberg‐Dirac dispersion theory, as indicated in Eq. (3) below [1]:

$$\mathbf{I}\left[\mathbf{a}\_{\rho\sigma}\right]\_{\mathrm{nm}} = \frac{1}{\mathrm{h}}\Sigma\_{\mathrm{S},\mathrm{r}}\left\{\frac{(\mathrm{nG}[\mathsf{M}\_{\rho}]\mathrm{Sr})(\mathrm{rS}|\mathsf{M}\_{\sigma}|\mathsf{G}\mathrm{m})}{\mathrm{v}\_{\mathrm{Sr}} - \mathrm{v}\_{\mathrm{k}} - \mathrm{v}\_{\mathrm{0}} + \mathrm{l}\Gamma\_{\mathrm{S}}} + \frac{(\mathrm{rS}|\mathsf{M}\_{\sigma}|\mathsf{G}\mathrm{m})\mathrm{(nG}|\mathsf{M}\_{\rho}|\mathrm{Sr})}{\mathrm{v}\_{\mathrm{Sr}} - \mathrm{v}\_{\mathrm{k}} + \mathrm{v}\_{\mathrm{0}} + \mathrm{l}\Gamma\_{\mathrm{S}}}\right\}}\right),\tag{3}$$

where M*ρ* and M*σ* represent the electronic transition dipole moment in a molecule‐fixed coordinate system (Albrecht [2] and Warshel and Dauber [3]). The symbols *ν*0 and *ν*k represent the frequencies of the excitation radiation and the normal mode Qk, respectively, S and r represent the respective electronic and vibrational states of the molecule, and Γ*s* is a damping constant, which is associated with the lifetime of the vibroelectronic state Sr. The sum in Eq. (3) indicates that for the Raman transition of all vibronic states must be used, which indicates that the scattering tensor, and thus, the Raman intensity, is controlled by the transition probabilities involving all vibronic states, even though the initial and final states refer to the vibrational ground and excited states of the electronic ground state. Thus, the sum of integrals in Eq. (3) describes the transitions: When the excitation frequency *ν*0 is in resonance or preresonance with the frequency of an electronic transition, the scattering is referred to as resonance Raman (RR) scattering. In this case, Eq. (3) may be simplified to:

inelastically such that the frequency of the scattered photons (*ν*S) differs from that of the incident photons (*ν*0). And with conversation of the energy, this energy difference is the energy change associated with a transition from the initial (i) vibrational state to the final (f) vibra‐

142 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

first discovered by the Indian scientist C. V. Raman in 1928 and is referred to as the Raman

In this chapter, we discuss IR and Raman spectra of protonated, deuterated, and *meso*‐ substituted parent porphyrin using density functional theory (DFT) to calculate the IR and Raman spectra, and, where possible, make comparison to experimental spectra. We also discuss spectra of aggregates involving several of the porphyrin species, using vibrational band assignments to ascertain which motions of the vibrating molecule couple more effec‐ tively, with excitonic motion, and as a result, we derive molecular alignment information from the enhancement that certain vibronic bands in the Raman spectrum experience for the various

In this section, we focus on Raman scattering. It is convenient to define the Raman scattering cross‐section for the n → m vibrational transition as σn <sup>m</sup>, and to relate it to the scattering

scattered by molecules integrated over all scattering angles and polarization directions for randomly oriented molecules. The Raman cross‐section is associated with the Raman polar‐ izability by utilizing the fact that the intensity for electric dipole radiation scales as the fourth

In this equation, the indices and σ indicate the molecule‐fixed directional coordinates. Moreover, for this equation, the scattering tensor can be formulated in terms of Kramers

where M*ρ* and M*σ* represent the electronic transition dipole moment in a molecule‐fixed coordinate system (Albrecht [2] and Warshel and Dauber [3]). The symbols *ν*0 and *ν*k represent the frequencies of the excitation radiation and the normal mode Qk, respectively, S and r

<sup>0</sup> is the intensity of the incident radiation and

‐Heisenberg‐Dirac dispersion theory, as indicated in Eq. (3) below [1]:

. Inelastic scattering of the photons was

(1)

(2)

(3)

<sup>n</sup> <sup>m</sup> the intensity of the light

tional state of the scattering species; i.e., *ν*0 − *ν*S = *ν*f − *ν*<sup>i</sup>

**2. Overview of Raman spectroscopy**

effect.

porphyrins.

intensity as follows:

In this equation,

power of the frequency:

$$\left[\mathbf{[}\mathbf{c}\_{\rho\sigma}\right]\_{\rm nm} \cong \frac{1}{\mathbf{h}} \Sigma\_{\rm S,r} \left\{ \frac{\langle \mathbf{n} \mathbf{G} | \mathbf{M}\_{\rho} | \mathbf{S} \mathbf{r} \rangle \langle \mathbf{r} \mathbf{S} | \mathbf{M}\_{\sigma} | \mathbf{G} \mathbf{m} \rangle}{\mathbf{v}\_{\rm Sr} - \mathbf{v}\_{\rm k} - \mathbf{v}\_{\rm 0} + \mathrm{i}\Gamma\_{\rm S}} \right\},\tag{4}$$

where the summation is now restricted to the vibrational states r of the resonantly excited electronic state (Albrecht [2]; Warshel and Dauber [3]). The wave functions of the integrals in Eq. (4) depend on the electronic and nuclear coordinates and may be separated by taking into account the Born‐Oppenheimer approximation:

$$
\langle \mathbf{n} \mathbf{G} | \mathbf{M}\_{\rho} | \mathbf{S} \mathbf{r} \rangle = \langle \mathbf{G} | \mathbf{M}\_{\rho} | \mathbf{S} \rangle \langle \mathbf{n} | \mathbf{r} \rangle = \mathbf{M}\_{\text{GS},\rho} \langle \mathbf{n} | \mathbf{r} \rangle \tag{5}
$$

Here, the integral represents the Franck‐Condon factor, which is the integral over the product of two vibrational wave functions. With this approximation, Eq. (4) becomes:

$$\left[\mathbf{c}\_{\rho\sigma}\right]\_{\mathbf{n}\mathbf{m}} \cong \frac{1}{\mathbf{h}} \sum\_{\mathbf{r}} \left\{ \frac{\mathbf{M}\_{\text{GS},\rho} \mathbf{M}\_{\text{GS},\sigma}(\mathbf{n}|\mathbf{r}) \langle \mathbf{r}|\mathbf{m}\rangle}{\mathbf{v}\_{\text{Sr}} - \mathbf{v}\_{\text{K}} - \mathbf{v}\_{\text{0}} + \mathbf{i}\Gamma\_{\text{S}}} \right\},\tag{6}$$

where MGS,*ρ* is the electronic transition‐dipole moment associated with the electronic transition from the ground state G to the electronically excited state S. Thus, MGS,*ρ* can be expanded in a Taylor series with respect to the normal coordinates Qk:

$$\mathbf{M}\_{\rm GS,\rho}(\mathbf{Q}\_{\mathbf{k}}) = \mathbf{M}\_{\rm GS,\rho}(\mathbf{Q}\_{\mathbf{k}}^{0}) + \boldsymbol{\Sigma}\_{\rm k} \mathbf{Q}\_{\rm k} \left(\frac{\partial \mathbf{M}\_{\rm GS,\rho}}{\partial \mathbf{Q}\_{\rm k}}\right)\_{\mathbf{0}} + \cdots \tag{7}$$

And, within the harmonic approximation, we neglect higher order terms and combine Eqs. (6) and (7) to obtain the scattering tensor as the sum of two terms, the so‐called Albrecht A and B terms:

$$\left[\mathbf{a}\_{\rho\sigma}\right]\_{\text{nm}} \cong \mathbf{A}\_{\rho\sigma} + \mathbf{B}\_{\rho\sigma} + \dots \tag{8}$$

$$\mathbf{A}\_{\mathbf{p}\sigma} \cong \frac{1}{\mathbf{h}} \sum\_{\mathbf{r}} \left\{ \frac{\mathbb{M}\_{\text{GS},\rho}^{0} \mathbb{M}\_{\text{GS},\sigma}^{0} \langle \mathbf{n} | \mathbf{r} \rangle \langle \mathbf{r} | \mathbf{m} \rangle}{\mathbb{v}\_{\text{Sr}} - \mathbb{v}\_{\text{K}} - \mathbb{v}\_{\text{0}} + \mathrm{i}\Gamma\_{\text{S}}} \right\} \tag{9}$$

$$\mathbf{B}\_{\mathsf{p}\sigma} \cong \frac{1}{\mathbf{h}} \boldsymbol{\Sigma}\_{\mathsf{r}} \left\{ \frac{\mathbf{M}\_{\mathrm{GS},\sigma}^{0} \left( \frac{\partial \mathbf{M}\_{\mathrm{GS},\mathbf{0}}}{\partial \mathbf{Q}\_{\mathrm{k}}} \right)\_{0} \langle \mathbf{n} | \mathbf{Q}\_{\mathrm{k}} | \mathbf{r} \rangle \langle \mathbf{r} | \mathbf{m} \rangle}{\mathbf{v}\_{\mathrm{S}\mathbf{r}} - \mathbf{v}\_{\mathrm{k}} - \mathbf{v}\_{0} + \mathrm{i}\Gamma\_{\mathrm{S}}} + \frac{\mathbf{M}\_{\mathrm{GS},\mathbf{0}}^{0} \left( \frac{\partial \mathbf{M}\_{\mathrm{GS},\sigma}}{\partial \mathbf{Q}\_{\mathrm{k}}} \right)\_{0} \langle \mathbf{r} | \mathbf{Q}\_{\mathrm{k}} | \mathbf{m} \rangle \langle \mathbf{n} | \mathbf{r} \rangle}{\mathbf{v}\_{\mathrm{S}\mathbf{r}} - \mathbf{v}\_{\mathrm{k}} - \mathbf{v}\_{0} + \mathrm{i}\Gamma\_{\mathrm{S}}} \right\} \tag{10}$$

In the above equations, MGS, <sup>0</sup> and MGS,σ 0 are the components of transition dipole moment of the vertical electronic transition G → S.

The A and B terms represent different scattering mechanisms, but the dominators are mini‐ mized in both terms when the frequency of the excitation *v*0 is in preresonance or resonance with the frequency of an electronic transition. In such a case, both the A and the B terms are enhanced, leading to amplified scattering of radiation.

It is to be noted that if the resonant electronic transition exhibits a large oscillator strength, i.e., a large transition dipole moment 0 , then the A term may be increased substantially more than the B term, and therefore become the more important scattering term. In this case, the enhancement of a normal mode depends on the products of Franck‐Condon factors, i.e., the term . It is to be noted that whether or not a normal mode is resonance enhanced via the Franck‐Condon mechanism depends on the geometry of the resonant excited state.

The intensity of a vibrational band attributable to a normal mode Q of frequency *v***Q** can be estimated in the double harmonic approximation. For the nonresonant situation (for a normal mode **QK** of frequency *v***Qk** and excitation frequency *v*0), the Raman intensity **IQk** can be computed according to the following equations [1, 4]:

$$\mathbf{I}\_{\mathbf{Q}\_{\mathbf{k}}} = \frac{\mathbf{f} \left(\mathbf{v}\_{0} - \mathbf{v}\_{\mathbf{Q}}\right)^{\*}}{\mathbf{v}\_{\mathbf{Q}\_{\mathbf{k}}} \left[\mathbf{1} - \exp\left(\frac{\mathbf{h} \mathbf{v}\_{\mathbf{Q}}}{\mathbf{k} \mathbf{T}}\right)\right]} \mathbf{S}\_{\mathbf{Q}\_{\mathbf{k}}} \tag{11}$$

$$\mathbf{S}\_{\mathbf{Q}\_{\mathbf{k}}} \cong \left\{ \mathbf{4} \, \mathbf{5} \left( \frac{\partial \alpha}{\partial \mathbf{Q}\_{\mathbf{k}}} \right)^{2} + \mathbf{7} \left( \frac{\partial \mathbf{y}}{\partial \mathbf{Q}\_{\mathbf{k}}} \right)^{2} \right\} \tag{12}$$

$$\left(\frac{\partial \mathbf{a}}{\partial \mathbf{Q}\_{\mathbf{k}}}\right)^{2} = \left(\frac{1}{3}\right) \left\{ \left(\frac{\partial \mathbf{a}\_{\mathbf{X}}}{\partial \mathbf{Q}\_{\mathbf{k}}}\right) + \left(\frac{\partial \mathbf{a}\_{\mathbf{Y}}}{\partial \mathbf{Q}\_{\mathbf{k}}}\right) + \left(\frac{\partial \mathbf{a}\_{\mathbf{Z}}}{\partial \mathbf{Q}\_{\mathbf{k}}}\right) \right\}^{2} \tag{13}$$

$$\left(\frac{\partial \mathbf{y}}{\partial \mathbf{Q}\_{\mathbf{k}}}\right)^{2} = \left(\frac{1}{2}\right) \left\{ \left[ \left(\frac{\partial \mathbf{a}\_{\mathbf{X}}}{\partial \mathbf{Q}\_{\mathbf{k}}}\right) - \left(\frac{\partial \mathbf{a}\_{\mathbf{Y}}}{\partial \mathbf{Q}\_{\mathbf{k}}}\right) \right]^{2} + \left[ \left(\frac{\partial \mathbf{a}\_{\mathbf{Y}}}{\partial \mathbf{Q}\_{\mathbf{k}}}\right) - \left(\frac{\partial \mathbf{a}\_{\mathbf{Z}}}{\partial \mathbf{Q}\_{\mathbf{k}}}\right) \right]^{2} + \left[ \left(\frac{\partial \mathbf{a}\_{\mathbf{Z}}}{\partial \mathbf{Q}\_{\mathbf{k}}}\right) - \left(\frac{\partial \mathbf{a}\_{\mathbf{X}}}{\partial \mathbf{Q}\_{\mathbf{k}}}\right) \right]^{2} \right\}\tag{14}$$

In the above equations, is the Raman activity for a normal mode , ∂ ∂ and ∂ ∂ are, respectively, the derivatives of the polarizability tensor and the corresponding anisotropy with respect to the normal mode Q, and f is a physical constant that includes the intensity of the incident radiation. We have calculated Raman intensities of the Raman active modes using Eq. (11), which is implemented in Gauss Sum software [5]. The software provides (the

Raman activity, Eq. 12) and the frequency *v***Qk** from the output files of the quantum chemical calculation program (specifically, Gaussian 09).

We explore in this chapter the effect of protonation, deuteration, and *meso*‐substitutions on the vibronic spectra of porphyrin and some of its derivatives. Specific molecules considered are the following: parent porphyrin (FBP), diprotonated FBP (H4FBP), deuterated H4FBP (D4FBP); *meso*‐tetraphenylporphyrin (TPP), diprotonated TPP (H4TPP or dicationic TPP) deuterated H4TPP (D4TPP); *meso*‐tetrakis (*p*‐sulfonatophenyl) porphyrin (TSPP), diprotonated TSPP (H4TSPP or dianionic TSPP), deuterated H4TSPP (D4TSPP), dicationic TSPP (H8TSPP), as well as deuterated H8TSPP (D8TSPP). We also deal with how molecular aggregation of some of the aforementioned species affects Raman spectra. Density functional theory has been employed to calculate the vibronic structural properties for both IR and Raman spectra.

(10)

(11)

(12)

(13)

(14)

∂ are,

(the

∂ and ∂

0 are the components of transition dipole moment of

0 , then the A term may be increased substantially more

In the above equations, MGS,

the vertical electronic transition G → S.

a large transition dipole moment

In the above equations,

calculation program (specifically, Gaussian 09).

<sup>0</sup> and MGS,σ

144 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

enhanced, leading to amplified scattering of radiation.

computed according to the following equations [1, 4]:

The A and B terms represent different scattering mechanisms, but the dominators are mini‐ mized in both terms when the frequency of the excitation *v*0 is in preresonance or resonance with the frequency of an electronic transition. In such a case, both the A and the B terms are

It is to be noted that if the resonant electronic transition exhibits a large oscillator strength, i.e.,

than the B term, and therefore become the more important scattering term. In this case, the enhancement of a normal mode depends on the products of Franck‐Condon factors, i.e., the term . It is to be noted that whether or not a normal mode is resonance enhanced via the Franck‐Condon mechanism depends on the geometry of the resonant excited state.

The intensity of a vibrational band attributable to a normal mode Q of frequency *v***Q** can be estimated in the double harmonic approximation. For the nonresonant situation (for a normal mode **QK** of frequency *v***Qk** and excitation frequency *v*0), the Raman intensity **IQk** can be

is the Raman activity for a normal mode , ∂

respectively, the derivatives of the polarizability tensor and the corresponding anisotropy with respect to the normal mode Q, and f is a physical constant that includes the intensity of the incident radiation. We have calculated Raman intensities of the Raman active modes using

Raman activity, Eq. 12) and the frequency *v***Qk** from the output files of the quantum chemical

Eq. (11), which is implemented in Gauss Sum software [5]. The software provides

Our motivation for focusing on the porphyrin monomers and aggregates is that porphyrin monomers and their aggregates play fundamental roles in natural systems and increasingly in artificial photonic devices. As regards aggregates, the primary mechanism through which molecular aggregate structures are formed in both natural and artificial systems is self‐ assembly through intrinsic intermolecular interactions, without the formation of covalent linkages. Self‐assembled molecular aggregates often assume a structure that can be classified as being of J‐ or H‐type, defined by the relative orientations of induced transition dipoles of the constituent molecules, either "head‐to‐tail" or "head‐to‐head," respectively [6]. Structural pictures such as those provided by J‐ and H‐aggregates have provided a framework for theoretical analysis of structure and dynamics of aggregated systems.

Moreover, aggregated porphyrin species are model composite structures for gaining insight into the roles that optically induced transient structural changes and photon dynamics play in photosynthesis [7, 8]. And through the study of spectral properties and photodynamic behaviors of aggregated porphyrin structures, an important outcome sought is the translation of the electron transfer specificities and speeds often found for biological reactions to the realm of molecular photonic devices (i.e., biomimetics) or photonic materials; indeed, enormous interest in the applications area has been evidenced [9, 10]. Thus, experimental and quantum chemical calculations of structures and optical dynamics of porphyrin monomers and aggre‐ gates have both scientific and technological importance.

We deduce that the observed Raman bands of the TPP, TSPP, H4TSPP, and aggregated H4TSPP may most properly be characterized by the vibrations of the pyrrole and pyrroline rings, the sulfonatophenyl groups, and their combinations rather than as vibrations of isolated chemical bonds.

As regards IR spectra, we have found that calculated IR spectra of H4TSPP can be assigned by comparison with the calculated IR spectra of other porphyrin derivatives and the experimen‐ tally measured IR spectra that are obtained from the literature. We further point out that the experimental and theoretical data used in this chapter are taken from prior experimental measurements performed in our laboratories [11–13].

The Raman and IR spectra of porphyrin derivatives in water, used as solvent in the calculations, were calculated at the B3LYP/6‐311G (d, p) level of density functional theory.

## **3. The Raman spectra of porphyrin and derivatives**

**Figure 1** provides the measured Raman spectra of the TPP (**Figure 1B**) and H4TSPP (**Figure 1G**) from our previous works [11–13]. Many Raman bands with strong and medium intensity, as well as numerous weak bands are found throughout the spectrum. The Raman spectrum of the H4TSPP when compared to that of the TPP are quite similar, however, the positions of several bands are substantially shifted in frequency. As examples, in the observed Raman spectrum of the TPP, the strongest band at 1564 cm‐1 and the bands at 334, 1234, 1327, 1438, 1577, and 1595 cm‐1 (with relatively weak intensity) are respectively red shifted to 1537 cm‐1 (the most intense peak), 312, 1229, 1339, 1427, 1562, and 1494 cm‐1 in the H4TSPP spectrum. Also, the bands at 201, 334, 962, and 1002 cm‐1 are respectively blue shifted to 236, 314, 983, and 1014 cm‐1 in the H4TSPP spectrum. Additionally, the bands at 1476 and 701 cm‐1 in the H4TSPP spectrum are considerably enhanced compared to their corresponding ones in the TPP.

**Figure 1.** The predicted Raman spectra of porphyrin derivatives: (**A**) free‐base porphyrin (FBP) and deuterated FBP (D2FBP); (B) the experimentally measured Raman spectrum of the TPP; (**C**) *meso*‐tetraphenylporphyrin (TPP) and (D2TPP); (**D**) anionic *meso*‐tetrakis(*p*‐sulfonatophenyl)porphyrin (TSPP) and deuterated TSPP (D2TSPP); (**E**) diprotonat‐ ed FBP (H4FBP) and deuterated H4FBP (D4FBP); (**F**) diprotonated‐TPP (H4TPP) and deuterated H4TPP (D4TPP); (**H**) di‐ protonated TSPP (H4TSPP) and deuterated‐H4TSPP (D4TSPP); and (**I**) dicationic TSPP (H8TSPP) and deuterated H8TSPP (D8TSPP). The plotted spectra in the gray color belong to the deuterated molecules. The calculations were car‐ ried out in water at B3LYP/6‐311G(d, p) level of DFT, and the line arrows show the frequency shift in the deuterated molecule [11].

Also, calculated Raman spectra of the FBP/D2FBP, H4FBP/D4FBP, TPP/D2TPP, H4TPP/D4TPP, TSPP/D2TSPP, H4TSPP/D4TSPP, and H8TSPP/D8TSPP in water used as a solvent are given in **Figure 1**, with the observed Raman spectra of the TPP and H4TSPP for comparison. (It is important to note that the D8TSPP symbolize the dicationic TSPP where four of eight deuterium atoms (D) covalently bounded to the nitrogen atoms at the core and the other four covalent bonded to one of three oxygen atoms within each of four *meso*‐sulfonatophenyl substituted groups.)


**3. The Raman spectra of porphyrin and derivatives**

146 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

ones in the TPP.

molecule [11].

groups.)

**Figure 1** provides the measured Raman spectra of the TPP (**Figure 1B**) and H4TSPP (**Figure 1G**) from our previous works [11–13]. Many Raman bands with strong and medium intensity, as well as numerous weak bands are found throughout the spectrum. The Raman spectrum of the H4TSPP when compared to that of the TPP are quite similar, however, the positions of several bands are substantially shifted in frequency. As examples, in the observed Raman spectrum of the TPP, the strongest band at 1564 cm‐1 and the bands at 334, 1234, 1327, 1438, 1577, and 1595 cm‐1 (with relatively weak intensity) are respectively red shifted to 1537 cm‐1 (the most intense peak), 312, 1229, 1339, 1427, 1562, and 1494 cm‐1 in the H4TSPP spectrum. Also, the bands at 201, 334, 962, and 1002 cm‐1 are respectively blue shifted to 236, 314, 983, and 1014 cm‐1 in the H4TSPP spectrum. Additionally, the bands at 1476 and 701 cm‐1 in the H4TSPP spectrum are considerably enhanced compared to their corresponding

**Figure 1.** The predicted Raman spectra of porphyrin derivatives: (**A**) free‐base porphyrin (FBP) and deuterated FBP (D2FBP); (B) the experimentally measured Raman spectrum of the TPP; (**C**) *meso*‐tetraphenylporphyrin (TPP) and (D2TPP); (**D**) anionic *meso*‐tetrakis(*p*‐sulfonatophenyl)porphyrin (TSPP) and deuterated TSPP (D2TSPP); (**E**) diprotonat‐ ed FBP (H4FBP) and deuterated H4FBP (D4FBP); (**F**) diprotonated‐TPP (H4TPP) and deuterated H4TPP (D4TPP); (**H**) di‐ protonated TSPP (H4TSPP) and deuterated‐H4TSPP (D4TSPP); and (**I**) dicationic TSPP (H8TSPP) and deuterated H8TSPP (D8TSPP). The plotted spectra in the gray color belong to the deuterated molecules. The calculations were car‐ ried out in water at B3LYP/6‐311G(d, p) level of DFT, and the line arrows show the frequency shift in the deuterated

Also, calculated Raman spectra of the FBP/D2FBP, H4FBP/D4FBP, TPP/D2TPP, H4TPP/D4TPP, TSPP/D2TSPP, H4TSPP/D4TSPP, and H8TSPP/D8TSPP in water used as a solvent are given in **Figure 1**, with the observed Raman spectra of the TPP and H4TSPP for comparison. (It is important to note that the D8TSPP symbolize the dicationic TSPP where four of eight deuterium atoms (D) covalently bounded to the nitrogen atoms at the core and the other four covalent bonded to one of three oxygen atoms within each of four *meso*‐sulfonatophenyl substituted


**Table 1.** Predicted and measured Raman active modes of frequencies (in cm‐1) of the HTSPP (C42v) with the TPP (C2v) and TSPP (C2v).


**Table 2.** The predicted Raman active bands of frequencies (for the protonated and deuterated porphyrin derivatives) exhibited significant frequency shift in the range of 1040–950 cm−1.

**Figure 2.** Calculated molecular motions for some vibrational bands of the H4TSPP, from reference [11].

**TPP** **Sym ∆νsc. S I R R**

A1 815 <1 <1 A1 768 <1 <1 A1 727 <1 <1

A1 584 <1 2 A1 531 0. 3

A2 468 <1 1

A2 322 <1 17

A1 252 <1 28 respectively [11–13].

**Table 1.** Predicted and measured Raman active modes of frequencies (in cm‐1) of the H

4

TSPP (C

2v) with the TPP (C2v) and TSPP (C2v).

A1 257 <1 18 A1 252 <1 12

A1 589 <1 1 A1 596 <1 3 580 10 A1 574 0. 1 A1 566 0. 1 548 5

A1 510 0. 2 494 3 w(NH)

A1 814 <1 <1 A1 820 <1 1 821 5

**TSPP**

**Δνexp IR/exp Sym ∆νsc. S**

  **I R**

**R**

 **Sym ∆ν**

**sc. S I R**

 **∆ν R**

**exp IR/exp**

Expansion of the pyrrole/pyrroline groups along N(H)…N(H) direction due to ν(Cα‐Cβ), leading to

Expansion of the pyrrole/pyrroline groups along N(H)…N(H) direction in the same phase like macro‐

cycle getting square shape or similar to breathing of the macrocycle

Out of plane wagging of the H on the phenyl rings, w(CH)

Bending deformation inside entire molecule.

w(CH on the macrocycle and phenyl rings)

Out of plane bending deformation of whole molecule including w(CH/NH)

ν(S‐O) and expansion of the phenyl rings along S…Cm direction including w(CH/NH)

148 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Out of plane twisting of the macrocycle

w(NH and CH on the macrocycle and phenyl rings) and wagging of the macrocycle.

Wagging of entire molecule

In‐plane wagging of macrocycle and translational motion of phenyl rings.

Out of plane bending of the phenyl rings.

Breathing macrocycle and translational motion of phenyl rings in opposite phase.

Breathing of whole molecule.

Out of plane wagging of macrocycle.

Out of plane wagging of macrocycle.

The calculations were obtained in water used as solvent at B3LYP/6‐311G(d,p) level. Where ∆νsc symbolizes the scaled vibrational frequencies, ∆νsc. = 0.96 (∆νcalc) + 40, and

SR and IR represents, respectively, the predicted Raman scattering activity and intensity; and ∆νexp and IR/exp symbolize the measured Raman frequency and Intensity,

Out of plane wagging of phenyl rings and relatively weak out of plane wagging macrocycle.

363 7

macrocycle getting rectangular shape instead of square shape.

**H TSPP 4**

**Assignments**

The assignment of the observed vibrational bands in the Raman spectra of the TPP and H4TSPP were made based on the density functional prediction at the B3LYP/6‐311G (d, p) level and on the atomic displacements visualized by using the GaussView program. The calculated vibrational frequencies coincided with those observed in their Raman spectra. We used the calculated frequencies and, to some degree, the predicted intensity distribution to attribute observed vibrational frequencies and intensities to specific intramolecular motions of the H4TSPP and TPP. These latter assessments were facilitated by analysis of the calculated nuclear displacements, combined with animation of their vibrations, to identify specific motions as the dominant movements within the molecule. This is not a truly rigorous approach but should provide adequate insight. The assignments of the vibrational mode are provided in **Tables 1** and **3**, whereas **Figure 2** presents the nuclear displacement for several selected vibrational modes.



**TPP**  **Sym ∆νsc.**

**a ∆νsc.**

**b IIR ∆νexp**

**∆νexp**

**Sym ∆νsc.**

**a IIR Sym ∆νsc.**

**a IIR ∆νexp**

**Sym ∆νsc.**

**a IIR**

**[16]** 

In‐plane rotational motion of the pyrroline rings, including relatively weak out‐of‐plane twist‐

ing deformation of the phenyl rings, but no contributions come from the pyrroline rings

Rocking of phenyl rings (*ρ*(phenyl) and wagging of macrocycle w(macrocycle).

Out‐of‐plane bending of phenyl groups only.

Twisting of phenyl τ(phenyl) and w(macrocycle)

**[15]** 

**[16]** 

 A1 484 8

 A1 487 4 w(NH only)

 B1 567 10 Out of plane twisting of the molecule and θ(O‐S‐O)/w(CH and NH)

150 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Due to bending deformation of the SO

−

In plane bending deformation of phenyl rings, including w(NH and C

deformation of the macrocycle.

w(CH on phenyl) and relatively weak out of plane deformation of the phenyl rings.

w(CH on phenyl) and out of plane deformation of the phenyl rings and macrocycle.

Primarily due to ν(S‐C)/θ(phenyl) and relatively weak w(CH an NH) and out of plane bending

(or twisting) deformation of macrocycle,

β

H only) and out of plane

3 groups like closing and opening umbrella shape.

A1 510 8 B1 559 10

B1 757

 A1 753 19

Primarily due to w(C

cycle, relatively weak out of plane deformation of the phenyl.

H an NH) and out of plane bending (or twisting) deformation of

weak out of plane deformation of the phenyl.

β macrocycle, relatively

w(CH in phenyl and macrocycle) and out of plane bending (or twisting) deformation of phenyl

rings the macrocycle.

w(C

Hs an NH) and out of plane bending (or twisting) deformation of

β macro‐

**TSPP** 

 **H TSPP 4**

**H TSPP** 

**8**

**Assignments** 


**Table 3.** Assigned IR features of the *meso*‐substituted porphyrin derivatives: TPP (C2v point group), TSPP (C2v), H TSPP (C 42v), and H TSPP (C 82v).

Our assignments may be summarized as follows:


**TPP**  **Sym ∆νsc.**

1564

1597

Where ∆νsc represents the scaled vibrational frequencies ((a) ∆νsc = 0.96(∆νcalc) +40 as used for the Raman spectra for all compounds studied here) and IIR symbolizes the

predicted IR intensity. In the assignments, the symbols ν, θ, *ρ*, and w represent the bonding stretching, bending deformation, rocking, and wagging, respectively. It is

worthy to note that two different scaling factor used for the TPP: (a) ∆νsc = 0.96(∆νcalc) + 40 and (b) ∆νsc = 0.976(∆νcalc). The latter one, (b), gives best fitting to measured IR

spectrum (from ref. [15, 16]) of the TPP only; not for others. However, the scaling factor of ∆νsc = 0.96(∆νcalc) +40 gives the best fitting to measured IR spectrum of H

(from ref. [16]). The results of calculations were obtained in water used as solvent at the B3LYP/6‐311G (d,p) level of the theory.

**Table 3.** Assigned IR features of the *meso*‐substituted porphyrin derivatives: TPP (C2v point group), TSPP (C2v), H

4

TSPP (C

2v), and H

TSPP (C

2v).

8

 TSPP 4

B2 1604 1

**a ∆νsc.**

**b IIR ∆νexp**

**∆νexp**

**Sym ∆νsc.**

**a IIR Sym ∆νsc.**

**a IIR ∆νexp**

**Sym ∆νsc.**

**a IIR**

**[16]** 

 B1 1241 7

 B1 1301 2

νa(C‐N‐C)/*ρ*(NH and C

ν(Cβ‐Cα)/θ(C‐N‐C)/*ρ*(C

β

H and NH). νa(Cβ‐Cβ‐Cα)/ θ(Cα‐N‐Cα)/νa(Cϕ‐Cm‐Cα)/θ(Cϕ‐Cm‐Cα)/*ρ*(CH).

νa(C‐N‐C)/*ρ*(C

H and NH). ν(Cβ‐Cα)/ν(Cα‐Cm) which also leading to νa(Cβ‐Cα‐Cm), including *ρ*(C

*ρ*(CH on phenyl), including relatively weak νs(C‐C‐Cϕ)

N(Cβ‐Cβ)/ν(Cα‐Cm) that leading to θ(C‐N‐C)

ν(Cα‐Cm)/ν(Cβ‐Cβ')/νa(Cα‐NH‐Cβ), including *ρ*(CH) on the macrocycle only.

152 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

νa(C‐C‐C) within phenyl rings and *ρ*(H on phenyl)

ν(C‐C)/*ρ*(CH) within phenyl rings, including θ(C‐C‐C in phenyl).

 H). β

β

 H) β

**[15]** 

**[16]** 

**TSPP** 

**H TSPP 4**

**H TSPP** 

**8**

**Assignments**  tions from *ν*s(C‐N(H)‐C), *ρ*(CH) and a comparatively weak ν(Cβ‐Cβ). This vibrational mode is attributed to the measured Raman bands at 1229 cm‐1 in H4TSPP spectrum and 1234 cm‐1 in the TPP. However, in calculated spectra of the unsubstituted free‐base porphyrin (FBP and H4FBP), this peak is respectively red shifted to 1194 and 1217 cm‐1, owing to the rocking of the H atom (covalent bounded to *meso*‐carbon atom (Cm)), *ρ*(CmH), including vibrational bond stretching within the macrocycle (see **Figure 2**). There is a question here we need to answer that while the peak (at 1238 cm‐1) is not significantly shifted in the predicted Raman spectra of the diprotonated and/or *meso*‐substituted porphyrin mole‐ cules, relative to each other, but it is substantially shifted in the FBP and H4FBP spectra.

This may be explained by the electrostatic repulsive interactions or steric effect between the H atoms covalent bonded to the Cm and Cβ atoms in the FBP and H4FBP structures. The effect decreases with increasing in the distance between the H atoms on the Cβ and Cm atoms because of the out‐of‐plane distortion from planarity in the H4FBP molecule (diprotonated porphyrin). In the case of *meso*‐phenyl or meso‐sulfonatophenyl substituted porphyrin molecules, the steric effect between the H atoms on the Cβ and Cp (in the *meso*‐phenyl substituent) give rise to the rotation of these *meso*‐substituted groups about Cm‐Cϕ bond, in their ground state structure, up to the tilt angle of about 71° and 48° for their unprotonated and protonated structures, respectively. Due to reduced electrostatic repulsion or steric effect by the Cm‐Cϕ bond rotation, the calculations do not reveal a substantial frequency shift in this peak position (∼1238 cm‐1) in the *meso*‐substituted porphyrin molecules.

(5) In region of 1050–950 cm‐1, there are two Raman peaks that are affected by diprotonated and deuterated parent porphyrin molecule. For instance, the observed two peaks at 1002 and 962 cm‐1 in the TPP spectrum (exc. at 488 nm) are respectively blue shifted to 1016 and 1002 cm‐1 in the H4TSPP (exc. at 514 nm). Calculation indicates that the peaks at 1020 and 983 cm‐1 in the TPP spectrum occurs at 1020 and 986 cm‐1 in the TSPP. These same bands are blue shifted to 1036 and 1005 cm‐1 in the calculated spectrum of the protonated‐TSPP (H4TSPP). Our results clearly show that these shifts in the observed peak positions are due to protona‐ tion of the porphyrin core that leads to saddle‐type distortions of the porphyrin core (i.e., leads to an increase in the degree of freedom of the rocking of the N‐H bonds as a consequence of the reduced repulsive interaction or steric effect between these hydrogen atoms). Moreover, GaussView visualization software shows that the peak at 1036 cm‐1 (in H4TSPP) is caused by expansion of the pyrrole groups along N(H)…N(H) direction, but in opposite phase (**Figure 2**), as a consequence of ν(Cα‐Cβ), which causes the macrocycle to assume a rectangular shape rather than square shape. The band at 1005 cm‐1 (H4TSPP) is caused by expansion of the pyrroles along N(H)…N(H) direction likewise macrocycle breathing (or breathing of pyrroles in the same phase) as assigned by Rich and McHale [14].

(6) Another two fundamental Raman bands in the range of low frequency are found at 248 and 338 cm‐1 in the H4TSPP spectrum, and at 235 and 365 cm‐1 in the TPP are respectively attributed to out‐of‐plane twisting of the macrocycle and breathing of whole molecule, which are in agreement with their experimental values of 242 and 338 cm‐1 for the H4TSPP; 235 and 334 cm‐1 for the TPP. These blue and red shifted bands in the measured and predicted Raman spectrum of the H4TSPP (dianionic or diprotonated‐TSPP) result from the protonation of the nitrogen atoms at the core, not owing to the *meso*‐sulfonato substituted groups. Additional assignments are provided in **Table 1**.

## **3.1. Isotope effect on the Raman spectrum**

tions from *ν*s(C‐N(H)‐C), *ρ*(CH) and a comparatively weak ν(Cβ‐Cβ). This vibrational mode is attributed to the measured Raman bands at 1229 cm‐1 in H4TSPP spectrum and 1234 cm‐1 in the TPP. However, in calculated spectra of the unsubstituted free‐base porphyrin (FBP and H4FBP), this peak is respectively red shifted to 1194 and 1217 cm‐1, owing to the rocking of the H atom (covalent bounded to *meso*‐carbon atom (Cm)), *ρ*(CmH), including vibrational bond stretching within the macrocycle (see **Figure 2**). There is a question here we need to answer that while the peak (at 1238 cm‐1) is not significantly shifted in the predicted Raman spectra of the diprotonated and/or *meso*‐substituted porphyrin mole‐ cules, relative to each other, but it is substantially shifted in the FBP and H4FBP spectra.

154 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

This may be explained by the electrostatic repulsive interactions or steric effect between the H atoms covalent bonded to the Cm and Cβ atoms in the FBP and H4FBP structures. The effect decreases with increasing in the distance between the H atoms on the Cβ and Cm atoms because of the out‐of‐plane distortion from planarity in the H4FBP molecule (diprotonated porphyrin). In the case of *meso*‐phenyl or meso‐sulfonatophenyl substituted porphyrin molecules, the steric effect between the H atoms on the Cβ and Cp (in the *meso*‐phenyl substituent) give rise to the rotation of these *meso*‐substituted groups about Cm‐Cϕ bond, in their ground state structure, up to the tilt angle of about 71° and 48° for their unprotonated and protonated structures, respectively. Due to reduced electrostatic repulsion or steric effect by the Cm‐Cϕ bond rotation, the calculations do not reveal a substantial frequency shift in this peak position (∼1238 cm‐1)

(5) In region of 1050–950 cm‐1, there are two Raman peaks that are affected by diprotonated and deuterated parent porphyrin molecule. For instance, the observed two peaks at 1002 and 962 cm‐1 in the TPP spectrum (exc. at 488 nm) are respectively blue shifted to 1016 and 1002 cm‐1 in the H4TSPP (exc. at 514 nm). Calculation indicates that the peaks at 1020 and 983 cm‐1 in the TPP spectrum occurs at 1020 and 986 cm‐1 in the TSPP. These same bands are blue shifted to 1036 and 1005 cm‐1 in the calculated spectrum of the protonated‐TSPP (H4TSPP). Our results clearly show that these shifts in the observed peak positions are due to protona‐ tion of the porphyrin core that leads to saddle‐type distortions of the porphyrin core (i.e., leads to an increase in the degree of freedom of the rocking of the N‐H bonds as a consequence of the reduced repulsive interaction or steric effect between these hydrogen atoms). Moreover, GaussView visualization software shows that the peak at 1036 cm‐1 (in H4TSPP) is caused by expansion of the pyrrole groups along N(H)…N(H) direction, but in opposite phase (**Figure 2**), as a consequence of ν(Cα‐Cβ), which causes the macrocycle to assume a rectangular shape rather than square shape. The band at 1005 cm‐1 (H4TSPP) is caused by expansion of the pyrroles along N(H)…N(H) direction likewise macrocycle breathing (or breathing of

(6) Another two fundamental Raman bands in the range of low frequency are found at 248 and 338 cm‐1 in the H4TSPP spectrum, and at 235 and 365 cm‐1 in the TPP are respectively attributed to out‐of‐plane twisting of the macrocycle and breathing of whole molecule, which are in agreement with their experimental values of 242 and 338 cm‐1 for the H4TSPP; 235 and 334 cm‐1 for the TPP. These blue and red shifted bands in the measured and predicted Raman spectrum of the H4TSPP (dianionic or diprotonated‐TSPP) result from the protonation of the

in the *meso*‐substituted porphyrin molecules.

pyrroles in the same phase) as assigned by Rich and McHale [14].

The polarized resonance Raman scattering (RRS) spectra, exc. at 488 nm, of the aggregated H4TSPP (diprotonated TSPP) and deuterated TSPP (D2TSPP) by Rich and McHale [14] displayed a frequency shifts in the positions of some of the well‐known Raman peaks, in addition to changes in the relative intensities of the Raman bands upon deuteration. The authors have reported that the observed Raman bands at 983 and 1013 cm‐1 in the aggregated H4TSPP (or diprotonated‐TSPP) spectrum are respectively shifted to 957 and 1004 cm‐1 in the aggregated D4TSPP spectrum. Additionally, they suggested that these two modes are pyrrole breathing modes and thus these red shifts may be attributed to the substitution of deuterium ions with the labile protons in the porphyrin core [14].

By comparing the spectral positions of these two peaks in the calculated Raman spectra of diprotonated and deuterated porphyrin core with their corresponding nonprotonated ones (see **Table 2**), we see that while the protonated and *meso*‐substituted parent porphyrin cause a blue shift in frequency of the two Raman peaks, the deuteration causes a red shift. For example, in the calculated spectrum of the TSPP, while these bands at 1020 and 985 cm‐1 are blue shifted respectively to 1036 and 1005 cm‐1 in the H4TSPP (diprotonated TSPP), they are red shifted to 1012 and 977 cm‐1 in the D2TSPP (deuterated TSPP) spectrum, respectively. When all four nitrogen atoms at the porphyrin core are deuterated, these Raman bands are shifted from 1036 and 1005 cm‐1 (in the H4TSPP) to 1026 and 983 cm‐1 in the D4TSPP (deuterated H4TSPP), respectively.

For the other moderately intense Raman peaks in the predicted spectrum, the shift in their spectral positions, due to the deuterated nitrogen atoms at the core, is not more than 5 cm‐1, which is in agreement with the experimental observation [14]. However, there are several weaker bands in the calculated spectra that displayed a significant shift in frequency (**Figure 1**). The other *meso*‐substituted and free‐base porphyrin derivatives displayed analogous results, which are in agreement with the experimental findings as argued above. Moreover, the results of calculations suggest that the *meso*‐substituted groups do not significantly alter the spectral position of these two Raman bands.

Consequently, the blue shift of the two Raman bands associated with diprotonated nitrogen atoms at the core is not unexpected when considering the steric effect (or electrostatic repulsive effect) between the hydrogen atoms bounded to nitrogen atoms at the core. This effect may be reduced by departing from the planarity of the porphyrin core (or macrocycle) as argued earlier. The red shift also is to be expected because of the isotopic effect since the vibrational frequency is inversely related to the square root of atomic mass that contributes to the vibrational mode. The deuterated nitrogen atoms at the core and one of three oxygen atoms in each of four sulfonato groups (‐SO3D) revealed new Raman peaks in the 2630–2720 cm‐1 region, which could be an experimental evidence for the presence of the deuterated TSPP (D4TSPP) or deuterated H4TSPP (D8TSPP) in samples.

## **4. IR spectra of porphyrin and derivatives**

We also calculated (at the same level of the DFT) the IR spectra of FBP, TPP, TSPP, H4FBP, H4TPP, H4TSPP, and H8TSPP, as well as their deuterated structures (D2FBP, D2TPP, D2TSPP, D4FBP, D4TPP, D4TSPP, and D8TSPP). It is worthy to note that the D8 represent that the four of eight deuterium atoms covalent bounded to nitrogen at the core and another four bounded to four sulfonato groups (‐SO3D). Calculated spectra exhibit dispersed about the full spectral range many IR features with medium and relatively weak intense, in addition to intense IR bands (see **Figure 3**). The results of the calculations together with their animated motions indicate that the predicted IR vibrational modes are predominantly linked with: (1) symmetric and asymmetric skeletal deformations of the macrocycle and phenyl rings; (2) wagging and rocking of the hydrogen atoms bonded to carbon and nitrogen atoms, CH and NH; and (3) out‐of‐plane distortion of the phenyl rings and the parent porphyrin or macrocycle. The selected IR bands in the calculated spectra of these compounds studied here are assigned using GaussView animation software. The assigned IR features are given in **Table 3**.

To test the reliability of the calculated IR spectra of the molecules investigated, we compared the IR bands in the calculated spectra of TPP and H4TSPP (diprotonated TSPP) with experi‐ mentally measured IR spectra of TPP [15] and H4TSPP [16]; as seen in **Table 3**, the spectra correlate quite well. This analysis indicates that the calculated IR spectra of these compounds (FBP/H4FBP, TPP/H4TPP, and TSPP/H8TSPP) are reasonable. We assigned the predicted IR features for the H4TSPP in connection with the predicted IR spectra of the FBP/H4FBP, TPP/

**Figure 3.** The predicted IR spectra of parent porphyrin and its derivatives: (**A**) free‐base porphyrin (FBP) and deuterat‐ ed FBP (D2FBP); (**B**) *meso*‐tetraphenylporphyrin (TPP) and (D2TPP); (**C**) anionic *meso*‐tetrakis(*p*‐sulfonatophenyl)por‐ phyrin (TSPP) and deuterated TSPP (D2TSPP), and (**D**) diprotonated FBP (H4FBP) and deuterated H4FBP (D4FBP); (**E**) diprotonated TPP (H4TPP) and deuterated H4TPP (D4TPP); (**F**) diprotonated TSPP (H4TSPP) and deuterated H4TSPP (D4TSPP); and (**G**) dicationic TSPP (H8TSPP) and deuterated H8TSPP (D8TSPP). It should be noted that the plotted IR spectra (grey in color) corresponds to that for their deuterated structures. The calculations were carried out in water used as solvent at the B3LYP/6‐311G(d, p) level of the theory.

H4TPP, and TSPP/H4TSPP/H8TSPP (in water used as solvent) by taking into account their vibrational motions. Our key conclusions concerning the calculated IR spectra are as following:

**4. IR spectra of porphyrin and derivatives**

156 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

We also calculated (at the same level of the DFT) the IR spectra of FBP, TPP, TSPP, H4FBP, H4TPP, H4TSPP, and H8TSPP, as well as their deuterated structures (D2FBP, D2TPP, D2TSPP, D4FBP, D4TPP, D4TSPP, and D8TSPP). It is worthy to note that the D8 represent that the four of eight deuterium atoms covalent bounded to nitrogen at the core and another four bounded to four sulfonato groups (‐SO3D). Calculated spectra exhibit dispersed about the full spectral range many IR features with medium and relatively weak intense, in addition to intense IR bands (see **Figure 3**). The results of the calculations together with their animated motions indicate that the predicted IR vibrational modes are predominantly linked with: (1) symmetric and asymmetric skeletal deformations of the macrocycle and phenyl rings; (2) wagging and rocking of the hydrogen atoms bonded to carbon and nitrogen atoms, CH and NH; and (3) out‐of‐plane distortion of the phenyl rings and the parent porphyrin or macrocycle. The selected IR bands in the calculated spectra of these compounds studied here are assigned using

To test the reliability of the calculated IR spectra of the molecules investigated, we compared the IR bands in the calculated spectra of TPP and H4TSPP (diprotonated TSPP) with experi‐ mentally measured IR spectra of TPP [15] and H4TSPP [16]; as seen in **Table 3**, the spectra correlate quite well. This analysis indicates that the calculated IR spectra of these compounds (FBP/H4FBP, TPP/H4TPP, and TSPP/H8TSPP) are reasonable. We assigned the predicted IR features for the H4TSPP in connection with the predicted IR spectra of the FBP/H4FBP, TPP/

**Figure 3.** The predicted IR spectra of parent porphyrin and its derivatives: (**A**) free‐base porphyrin (FBP) and deuterat‐ ed FBP (D2FBP); (**B**) *meso*‐tetraphenylporphyrin (TPP) and (D2TPP); (**C**) anionic *meso*‐tetrakis(*p*‐sulfonatophenyl)por‐ phyrin (TSPP) and deuterated TSPP (D2TSPP), and (**D**) diprotonated FBP (H4FBP) and deuterated H4FBP (D4FBP); (**E**) diprotonated TPP (H4TPP) and deuterated H4TPP (D4TPP); (**F**) diprotonated TSPP (H4TSPP) and deuterated H4TSPP (D4TSPP); and (**G**) dicationic TSPP (H8TSPP) and deuterated H8TSPP (D8TSPP). It should be noted that the plotted IR spectra (grey in color) corresponds to that for their deuterated structures. The calculations were carried out in water

used as solvent at the B3LYP/6‐311G(d, p) level of the theory.

GaussView animation software. The assigned IR features are given in **Table 3**.


#### **4.1. Isotopic (or deuteration) effect on the IR spectrum**

Calculated IR spectra of the molecules clearly indicate that deuterated porphyrin exhibits relatively intense IR peaks in the range of 2565–2600 cm‐1. Such bands are associated with N‐ D bond stretching. And bands around 2640 cm‐1 are attributable to O‐D bond stretching. The largest frequency shifts are calculated for bands at 540 and 490 cm‐1 (H4TSPP, where all N atoms at porphyrin core are protonated) that are shifted to 396 and 366 cm‐1 in the D4HTSPP (deu‐ terated‐H4TSPP); in the low‐frequency region (below 700 cm‐1) bands are attributable to wagging of the N‐D bond, w(ND).

In the region of high or mid frequency, where deuterium atom is included in vibrational mode frequency, a red shift in frequency by up to 10 cm‐1 is shown in the D2TSPP. Deuteration also has an influence on the intensity of the IR bands; see **Figure 3**. Shift in the region of high frequency of D2FBP, D4FBP, and D4TPP spectra are more significant than those in the spectra of the D2TSPP and D4TSPP. These results imply that above the low‐frequency region, the frequency shifts as a result of the deuteration decrease with increasing size of the substituent group.

## **5. Solvent effect on the IR spectrum**

We investigated the solvent effect on the IR spectrum of the H4TSPP by using toluene, dimethyl sulfoxide (DMSO) and water as a solvent. Calculations indicate that below 1100 cm‐1 there is no significant frequency, shift in peak positions H4TSPP, but above 1100 cm‐1 shifts do occur. Specifically, the IR peak centered at around 1200 cm‐1 is shifted to 1188 cm‐1 (toluene), 1166 cm‐1 (DMSO), and 1160 cm‐1 (water). Also, the IR peaks centered about 1453 and 1477 cm‐1 in the gas phase spectrum are shifted to 1468 and 1490 cm‐1 (toluene), 1480 and 1497 cm‐1 (DMSO), and 1481 and 1499 cm‐1 (water), respectively. This observation suggests that the IR features, especially in high energy region, of the parent porphyrin and its derivatives, at least for H4TSPP, are responsive to its surroundings.

## **6. Resonance Raman spectra of aggregated diprotonated‐TSPP**

In the section, we will discuss the results vibroelectronic properties of the aggregated‐H4TSPP (known as acidic‐, dianionic‐, or diprotonated‐TSPP). Several structural and spectroscopic studies have shown that TSPP aggregates in acidic aqueous solution. **Figure 4** shows the absorption spectra of free‐base TSPP (pH = 12), H4TSPP (pH = 4.5), and aggregated H4TSPP (pH = 1.6), with concentration of 5 × 10‐5 M in aqueous solution.

While the spectrum of the TSPP [17] exhibited a Soret band at 410 nm and several weak Q bands in the region of 500–640 nm, the monomeric H4TSPP spectrum exhibited the Soret band at 432 nm, and Q‐bands at 594 and 642 nm. **Figure 4** shows the Soret band of the H4TSPP is split into H‐ and J‐band components in the H4TSPP aggregate as a sharp and intense absorption

**4.1. Isotopic (or deuteration) effect on the IR spectrum**

158 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

wagging of the N‐D bond, w(ND).

**5. Solvent effect on the IR spectrum**

H4TSPP, are responsive to its surroundings.

group.

Calculated IR spectra of the molecules clearly indicate that deuterated porphyrin exhibits relatively intense IR peaks in the range of 2565–2600 cm‐1. Such bands are associated with N‐ D bond stretching. And bands around 2640 cm‐1 are attributable to O‐D bond stretching. The largest frequency shifts are calculated for bands at 540 and 490 cm‐1 (H4TSPP, where all N atoms at porphyrin core are protonated) that are shifted to 396 and 366 cm‐1 in the D4HTSPP (deu‐ terated‐H4TSPP); in the low‐frequency region (below 700 cm‐1) bands are attributable to

In the region of high or mid frequency, where deuterium atom is included in vibrational mode frequency, a red shift in frequency by up to 10 cm‐1 is shown in the D2TSPP. Deuteration also has an influence on the intensity of the IR bands; see **Figure 3**. Shift in the region of high frequency of D2FBP, D4FBP, and D4TPP spectra are more significant than those in the spectra of the D2TSPP and D4TSPP. These results imply that above the low‐frequency region, the frequency shifts as a result of the deuteration decrease with increasing size of the substituent

We investigated the solvent effect on the IR spectrum of the H4TSPP by using toluene, dimethyl sulfoxide (DMSO) and water as a solvent. Calculations indicate that below 1100 cm‐1 there is no significant frequency, shift in peak positions H4TSPP, but above 1100 cm‐1 shifts do occur. Specifically, the IR peak centered at around 1200 cm‐1 is shifted to 1188 cm‐1 (toluene), 1166 cm‐1 (DMSO), and 1160 cm‐1 (water). Also, the IR peaks centered about 1453 and 1477 cm‐1 in the gas phase spectrum are shifted to 1468 and 1490 cm‐1 (toluene), 1480 and 1497 cm‐1 (DMSO), and 1481 and 1499 cm‐1 (water), respectively. This observation suggests that the IR features, especially in high energy region, of the parent porphyrin and its derivatives, at least for

In the section, we will discuss the results vibroelectronic properties of the aggregated‐H4TSPP (known as acidic‐, dianionic‐, or diprotonated‐TSPP). Several structural and spectroscopic studies have shown that TSPP aggregates in acidic aqueous solution. **Figure 4** shows the absorption spectra of free‐base TSPP (pH = 12), H4TSPP (pH = 4.5), and aggregated H4TSPP

While the spectrum of the TSPP [17] exhibited a Soret band at 410 nm and several weak Q bands in the region of 500–640 nm, the monomeric H4TSPP spectrum exhibited the Soret band at 432 nm, and Q‐bands at 594 and 642 nm. **Figure 4** shows the Soret band of the H4TSPP is split into H‐ and J‐band components in the H4TSPP aggregate as a sharp and intense absorption

**6. Resonance Raman spectra of aggregated diprotonated‐TSPP**

(pH = 1.6), with concentration of 5 × 10‐5 M in aqueous solution.

**Figure 4.** UV‐vis spectra of the free‐base TSPP (the maximum of the absorption band at 410 nm), monomeric H4TSPP (the maximum at 432 nm) and aggregated H4TSPP (the maximum at 489 nm) [20]. The concentration of compounds in each case is 5 × 10‐5 M in the aqueous solution. The pH = 12 for the free‐base TSPP; pH = 4.5 for the monomeric H4TSPP; pH = 1.6 for the aggregated H4TSPP, and [KCl] = 0.1 M. Spectra above ca. 500 nm have been offset by +0.2 absorbance units and amplified by the indicated factor to aid presentation. The structure on the band at around 500 nm for the free‐base TSPP is an artifact attributable to the absorption spectrometer.

band at 489 nm (J‐aggregate) and a broad and weak absorption band at 422 nm (H‐aggregate) are formed. The Q‐bands at 594 and 642 nm (in the monomeric H4TSPP) is also shifted to ca. 670 and 706 nm in the aggregated H4TSPP spectrum, respectively. The UV‐vis spectra results suggest that aggregation evolves through the formation of diprotonated TSPP (H4TSPP), and only occurs at a pH below 5. These observations have also reported by other researchers [18, 19].

**Figure 5** presents the Raman spectra of free‐base (TSPP), monomeric dianion (H4TSPP) and aggregated H4TSPP resonantly excited at their respective Soret‐band absorption wavelengths (**Figure 4**). Analysis of the resonance Raman (RR) spectra of the H4TSPP and aggregated H4TSPP reveal the presence of bands that do not accommodate bands of the free‐base por‐ phyrin. However, an in‐depth examination indicates that subtle differences bands of the aggregate and the dianionic monomer are correlated. The most important correlation in spectra is found in the low‐frequency region, where two bands of dianionic TSPP monomer at 233 and 310 cm‐1 correlate with two dramatically enhanced aggregate bands at 241 and 317 cm‐1, in addition to two weak satellite bands at 205 and 362 cm‐1.

Moreover, DFT calculations (at B3LYP/6‐311G(d, p) level) show that while the band at 317 cm‐1 is due to breathing of the whole molecule, the enhanced band at 241 cm‐1 results from the out‐of‐plane wagging of the macrocycle. Hence, computationally these two Raman bands of porphyrins originate from out‐of‐plane modes—in conjunction with bending of the Cm‐ph

**Figure 5.** Resonance Raman spectrum (RRS) of the TSPP [20]: (A) free‐base TSPP, exc. at = 416 nm; (B) diprotonated TSPP (H4TSPP), exc. at 432 nm; (C) aggregated H4TSPP, exc. at 488 nm. Where the solutions used here were the same as used for the measured absorption spectra in **Figure 4**.

bond (ph representing phenyl) and deformation of the core of the porphinato macrocycle caused by pyrrole ring tilt and swivel [20–22]. Moreover, in the case of lanthanide sandwich dimer porphyrins, low‐frequency Raman bands have been hypothesized to reflex the degree of intramolecular *π‐π* interaction and to be connected with the intradimer vibration that modulates the separation between the two porphyrin moieties, or owing to symmetrical linear combinations of out‐of‐plane distortions of the neighboring porphinato macrocycles [23].

Given the enhancement of scattering associated with bands having motions that can strongly couple with excitonic motion, which helps define the aggregate's structure, we report in **Table 1** assignments made through such a scheme and by comparison to the literature. It is to be noted that a theoretical construct known as "aggregation‐enhanced Raman scattering (AERS)," has been advanced by one of us (DLA) to explain which bands would experience significant enhancement upon aggregation of the scattering species. And, indeed, the two bands discussed above that show enormous enhancement upon aggregation of H4TSPP have motions that couple to exciton movement through the aggregate and would be expected to experience significantly enhanced Raman intensities [12].

## **Acknowledgements**

We would like to thank Ömer Andaç (Chemistry Department of Ondokuz Mayıs University) for kindly providing computing facilities and software expertise. We also thank staff at TUBITAK ULAKBIM, the high performance and Grid Computing Center (TR‐Grid e‐Infra‐ structure), for performing the calculations reported herein. Also, we would like to thank the U.S. National Science Foundation (NSF) for support of research efforts under grant No. HRD‐ 08‐33180.

## **Author details**

Metin Aydin1\* and Daniel L. Akins2

\*Address all correspondence to: aydn123@netscape.net

1 Department of Chemistry, Faculty of Art and Sciences, Ondokuz Mayıs University, Samsun, Turkey

2 Department of Chemistry and Biochemistry, Center for Analysis of Structures and Interfa‐ ces (CASI), The City College of the City University of New York, New York, USA

## **References**

bond (ph representing phenyl) and deformation of the core of the porphinato macrocycle caused by pyrrole ring tilt and swivel [20–22]. Moreover, in the case of lanthanide sandwich dimer porphyrins, low‐frequency Raman bands have been hypothesized to reflex the degree of intramolecular *π‐π* interaction and to be connected with the intradimer vibration that modulates the separation between the two porphyrin moieties, or owing to symmetrical linear combinations of out‐of‐plane distortions of the neighboring porphinato macrocycles [23].

**Figure 5.** Resonance Raman spectrum (RRS) of the TSPP [20]: (A) free‐base TSPP, exc. at = 416 nm; (B) diprotonated TSPP (H4TSPP), exc. at 432 nm; (C) aggregated H4TSPP, exc. at 488 nm. Where the solutions used here were the same as

160 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Given the enhancement of scattering associated with bands having motions that can strongly couple with excitonic motion, which helps define the aggregate's structure, we report in **Table 1** assignments made through such a scheme and by comparison to the literature. It is to be noted that a theoretical construct known as "aggregation‐enhanced Raman scattering (AERS)," has been advanced by one of us (DLA) to explain which bands would experience significant enhancement upon aggregation of the scattering species. And, indeed, the two bands discussed above that show enormous enhancement upon aggregation of H4TSPP have motions that couple to exciton movement through the aggregate and would be expected to experience

We would like to thank Ömer Andaç (Chemistry Department of Ondokuz Mayıs University) for kindly providing computing facilities and software expertise. We also thank staff at TUBITAK ULAKBIM, the high performance and Grid Computing Center (TR‐Grid e‐Infra‐

significantly enhanced Raman intensities [12].

used for the measured absorption spectra in **Figure 4**.

**Acknowledgements**


## **Novel Pressure-Induced Molecular Transformations Probed by** *In Situ* **Vibrational Spectroscopy Novel Pressure-Induced Molecular Transformations Probed by** *In Situ* **Vibrational Spectroscopy**

Yang Song Yang Song

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[18] Pasternack, R. F.; Huber, P. R.; Boyd, Engasser, P.; Francesconi, G.; Gibbs, L.; Fasella, E.; Venturo, P.; Cerio, G.; Hinds, L. deC. On the aggregation of meso‐substituted water‐

[19] Ohno, O.; Kaizu, Y.; Kobayashi, H. *J*‐aggregate formation of a water‐soluble porphyrin

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[23] Donohoe, R. J.; Duchowski, J. K.; Bocian, D. F. Hole delocalization in oxidized ceri‐ um(IV) porphyrin sandwich complexes, J. Am. Chem. Soc. 1988, 110, 6119.

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162 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Additional information is available at the end of the chapter Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/64617

#### **Abstract**

Pressure-induced structural change in molecular systems has demonstrated strong promises to access previously unexplored, novel structures and new properties in molecular materials with practical applications. The *in situ* structural characterization is of fundamental importance to understand the exotic structures and the possible transformation mechanisms. Among all the spectroscopic probes, vibrational spectroscopy that include Raman and Fourier-transform infrared (FTIR) spectroscopy and microscopy allow for highly efficient, sensitive and qualitative characterization of pressure-induced new structures and transformation processes *in situ*. Supported by state-of-the-art, highly customized spectroscopic systems in-house and at synchrotron facilities, molecular structures and materials properties can be probed in a broad pressure-temperature range with very high spectral and spatial resolutions. Complementary to each other, Raman and IR spectroscopy provide valuable information in molecular structures, nature of bonding, lattice dynamics as well as intermolecular interactions. In this chapter, a comprehensive and critical review of examples of pressure-induced molecular transformations in a wide variety of molecules and materials probed by vibrational spectroscopy is provided. The purpose of this chapter is to give readers the most recent advances in high-pressure chemistry and materials research by demonstrating the power of vibrational spectroscopy as a highly effective *in situ* structural characterization tool.

**Keywords:** high pressure, diamond anvil cells, Raman spectroscopy, FTIR spectroscopy, conformation, hydrogen bonding, phase transitions, guest-host interactions

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

## **1. Introduction**

As one of three principal thermodynamic variables, pressure (P) plays an important role to alter the interatomic distances and thus the nature of intermolecular interactions, chemical bonding, molecular configurations, crystal structures and stability of materials. Extreme pressure can even induce transformations involving the strongest chemical interactions that exceed 10 eV (965 kJ mol−1) such that chemical bonds and even the well-known properties of atoms and molecules can be completely changed. As a result, investigation of pressure-induced structural transformations and formation of novel functional materials has become a vibrant frontier in chemistry and materials science [1]. On one hand, major advances in high-pressure techniques such as diamond anvil cell have allowed the study of molecules and materials in an unprecedented pressure-temperature (P-T) range. On the other hand, the compatible micro-spectroscopic probes have made possible the characterization of structures and transformational processes *in situ* with great spectral and spatial resolution. The recent advances in high-pressure science and technology and their applications in materials research have been provided in several excellent review articles [2–8].

Among all the available *in situ* structural characterization probes for materials under extreme conditions, in particular, vibrational spectroscopy that include Raman and Infrared (IR) spectroscopy has demonstrated strong sensitivity and accuracy as well as efficiency in monitoring the pressure-induced transformations. Raman and IR spectroscopy, complementary to each other, provide valuable information on molecular structures, nature of bonding, lattice dynamics as well as intermolecular interactions. In this chapter, a comprehensive and critical review of examples of pressure-induced molecular transformations in a wide variety of molecules and materials probed by vibrational spectroscopy is given. The examples include (1) conformational change; (2) pressure-mediated hydrogen bonding; (3) phase and structural transitions; (4) pressure-induced chemical reactions; and (5) porous materials and guest-host interactions. Through these examples, the readers are provided the most recent advances in high-pressure chemistry and materials research by demonstrating the power of vibrational spectroscopy as an effective tool for structural characterizations for materials under extreme conditions.

## **2. Experimental methods**

## **2.1. The diamond anvil cell**

The recent advances in high-pressure technology have enabled the generation of extreme conditions in a broad P-T range with great controllability and accuracy. In particular, diamond anvil cell (DAC) is a fundamental apparatus to achieve static high pressures. Diamonds are known as the hardest material in nature and thus suitable as anvils to generate very high pressure. Moreover, diamonds are transparent to a wide spectral range of electromagnetic radiation from far-IR to hard X-ray. As a result, various analytical probes, including optical spectroscopy, synchrotron and neutron sources, have enabled structural characterization of material under extreme P-T conditions with unprecedented spatial, temporal and spectral resolutions.

**Figure 1.** Schematic diagram of a diamond anvil cell.

**1. Introduction**

excellent review articles [2–8].

**2. Experimental methods**

**2.1. The diamond anvil cell**

conditions.

As one of three principal thermodynamic variables, pressure (P) plays an important role to alter the interatomic distances and thus the nature of intermolecular interactions, chemical bonding, molecular configurations, crystal structures and stability of materials. Extreme pressure can even induce transformations involving the strongest chemical interactions that exceed 10 eV (965 kJ mol−1) such that chemical bonds and even the well-known properties of atoms and molecules can be completely changed. As a result, investigation of pressure-induced structural transformations and formation of novel functional materials has become a vibrant frontier in chemistry and materials science [1]. On one hand, major advances in high-pressure techniques such as diamond anvil cell have allowed the study of molecules and materials in an unprecedented pressure-temperature (P-T) range. On the other hand, the compatible micro-spectroscopic probes have made possible the characterization of structures and transformational processes *in situ* with great spectral and spatial resolution. The recent advances in high-pressure science and technology and their applications in materials research have been provided in several

164 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Among all the available *in situ* structural characterization probes for materials under extreme conditions, in particular, vibrational spectroscopy that include Raman and Infrared (IR) spectroscopy has demonstrated strong sensitivity and accuracy as well as efficiency in monitoring the pressure-induced transformations. Raman and IR spectroscopy, complementary to each other, provide valuable information on molecular structures, nature of bonding, lattice dynamics as well as intermolecular interactions. In this chapter, a comprehensive and critical review of examples of pressure-induced molecular transformations in a wide variety of molecules and materials probed by vibrational spectroscopy is given. The examples include (1) conformational change; (2) pressure-mediated hydrogen bonding; (3) phase and structural transitions; (4) pressure-induced chemical reactions; and (5) porous materials and guest-host interactions. Through these examples, the readers are provided the most recent advances in high-pressure chemistry and materials research by demonstrating the power of vibrational spectroscopy as an effective tool for structural characterizations for materials under extreme

The recent advances in high-pressure technology have enabled the generation of extreme conditions in a broad P-T range with great controllability and accuracy. In particular, diamond anvil cell (DAC) is a fundamental apparatus to achieve static high pressures. Diamonds are known as the hardest material in nature and thus suitable as anvils to generate very high pressure. Moreover, diamonds are transparent to a wide spectral range of electromagnetic radiation from far-IR to hard X-ray. As a result, various analytical probes, including optical spectroscopy, synchrotron and neutron sources, have enabled structural characterization of **Figure 1** shows a typical DAC apparatus where two brilliant cut diamonds are used as anvils to exert static pressure up to several million atmospheres (or several hundred GPa) with only moderate force. A metal gasket with a hole drilled at the center serves as the sample chamber. Most of the time the sample to be studied is loaded together with pressure-transmitting medium (PTM) to enhance the hydrostaticity, and a ruby chip which is used for pressure calibration. The extreme pressures can be accurately determined by monitoring ruby fluorescence lines using the following relationship [9]:

$$P = \frac{1904}{B} \left[ \left( 1 + \frac{\Delta \mathcal{L}}{694.24} \right)^{B} - 1 \right] \tag{1}$$

where *P* is the pressure in GPa, Δ*λ* is the ruby R1 line shift in nm, and parameter *B* is 7.665 for quasi-hydrostatic conditions and is 5 for non-hydrostatic conditions. The ruby fluorescence can be conveniently collected using a Raman system such as described below.

To conduct vibrational spectroscopy on materials loaded in DAC effectively, optical transparency is a prime factor in selecting diamond anvils. Two types of diamonds (i.e., type I and type II) are typically used for different spectroscopic probes. Both types have the intense first-order Raman line at 1332 cm−1 (*F*2g mode of the diamond). The difference between the two types is in the infrared absorption spectrum. Type I anvils (with more nitrogen impurities) have two strong IR absorption regions around 2000 and 1000–1350 cm−1, respectively. In contrast, type II anvils (nitrogen free) have a relatively clean IR window bellow 2000 cm−1 allowing effective IR absorption measurements on samples. Therefore, the low-fluorescent type I diamonds are only suitable for Raman spectroscopy, while the type II diamonds are mainly used in IR spectroscopy.

## **2.2. Raman spectroscopy**

Raman spectroscopy is a vibrational spectroscopy based on the inelastic scattering of visible photons (typically from a laser source) by materials, a process with a much smaller crosssection than other spectroscopic processes (e.g., absorption, fluorescence, etc.). Although many commercial Raman microscopy systems are available, they generally have a rigid design that does not allow *in situ* measurements with different DAC configurations. Therefore, a state-ofthe-art customized Raman system was constructed to allow the DAC-based measurements in a broad P-T range with multiple excitation laser sources that cover the spectral range from near UV to near IR, such as 488–514 nm lines from an Innova Ar+ laser (Coherent Inc.), 532 and 782 mn lines from diode-pumped solid-state lasers, as well as 700–1100 nm lines from a Ti: sapphire laser (Spectral Physics) [10]. Using a 20× Mitutoyo objective, the laser can be focused to less than 5 μm on the sample. The combination of a 15× eyepiece and a digital camera allows precise alignment of the focused laser beam on the sample. With backscattering geometry, the Raman signal is collected by the same objective lens. The elastic Rayleigh scattering is removed by either a pair of notch filters or an edge filter that enabled a spectral range above 100 cm−1 to be measured before the total scattered photons are focused on the entrance slit of a spectrometer. The scattered light is then dispersed using an imaging spectrograph (SpectroPro-2500i, Acton Research Corporation) that houses a 0.5 m focal distance monochromator equipped with multiple gratings, such as a 1800 lines/mm grating, allowing a spectral resolution of ±0.1 cm−1 to be achieved. The Raman signal was recorded using an ultrasensitive back-illuminated, liquid nitrogen cooled, charge-coupled device (CCD) detector from Acton. The Raman system is first calibrated by using a neon lamp giving an uncertainty of ±1 cm−1 before each experiment.

#### **2.3. FTIR spectroscopy**

Complementary to Raman spectroscopy, IR absorption spectroscopy provides sensitive and fingerprints information on materials loaded in DAC, especially those with high fluorescence that prohibits effective Raman measurements. The IR measurements for the examples demonstrated in this chapter were mostly carried out using a customized IR micro-spectroscopy system constructed in-house [11]. Specifically, a commercial FTIR spectrometer (model Vertex 80v from Bruker Optics Inc.) containing a Globar IR source constitutes the major component of the micro-IR system. The spectrometer is operated under a vacuum of <5 mbar to efficiently remove the absorption by H2O and CO2. The IR beam is collimated with varying diameters achieved by using apertures from 0.25 to 8 mm, and then is directed into a relay box through a KBr window. Using the combination of iris optics and 15× reflective objective lens (numerical aperture of 0.4), the IR beam is then focused onto the sample in the DAC. Using an XYZ precision stage with the aid of an optical microscope equipped with a 20× eyepiece from Edmond Optics and an objective lens of variable magnifications, the sample loaded in DAC can be easily aligned to allow the maximum transmission of the IR beam. Using a series of iris apertures, the size of the IR beam was set to be identical to the entire sample size (e.g., ~200 μm). Another identical reflective objective as the condenser is used to collect the transmitted IR beam, which is subsequently directed to a midband mercury cadmium telluride (MCT) detector. A ZnSe window equipped on the midband MCT detector allows efficient measurements in the spectral range of 600–12,000 cm−1. The combination of 512 scans and a resolution setting of 4 cm−1 is typically used for each spectrum measurement that gives an excellent signalto-noise ratio. The absorption of diamond anvils loaded with KBr but without any sample is used as the reference spectrum, which is divided as background from each sample spectrum to obtain the absorbance.

## **2.4. Synchrotron-based FTIR spectroscopy**

Raman line at 1332 cm−1 (*F*2g mode of the diamond). The difference between the two types is in the infrared absorption spectrum. Type I anvils (with more nitrogen impurities) have two strong IR absorption regions around 2000 and 1000–1350 cm−1, respectively. In contrast, type II anvils (nitrogen free) have a relatively clean IR window bellow 2000 cm−1 allowing effective IR absorption measurements on samples. Therefore, the low-fluorescent type I diamonds are only suitable for Raman spectroscopy, while the type II diamonds are mainly used in IR

166 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Raman spectroscopy is a vibrational spectroscopy based on the inelastic scattering of visible photons (typically from a laser source) by materials, a process with a much smaller crosssection than other spectroscopic processes (e.g., absorption, fluorescence, etc.). Although many commercial Raman microscopy systems are available, they generally have a rigid design that does not allow *in situ* measurements with different DAC configurations. Therefore, a state-ofthe-art customized Raman system was constructed to allow the DAC-based measurements in a broad P-T range with multiple excitation laser sources that cover the spectral range from near

mn lines from diode-pumped solid-state lasers, as well as 700–1100 nm lines from a Ti: sapphire laser (Spectral Physics) [10]. Using a 20× Mitutoyo objective, the laser can be focused to less than 5 μm on the sample. The combination of a 15× eyepiece and a digital camera allows precise alignment of the focused laser beam on the sample. With backscattering geometry, the Raman signal is collected by the same objective lens. The elastic Rayleigh scattering is removed by either a pair of notch filters or an edge filter that enabled a spectral range above 100 cm−1 to be measured before the total scattered photons are focused on the entrance slit of a spectrometer. The scattered light is then dispersed using an imaging spectrograph (SpectroPro-2500i, Acton Research Corporation) that houses a 0.5 m focal distance monochromator equipped with multiple gratings, such as a 1800 lines/mm grating, allowing a spectral resolution of ±0.1 cm−1 to be achieved. The Raman signal was recorded using an ultrasensitive back-illuminated, liquid nitrogen cooled, charge-coupled device (CCD) detector from Acton. The Raman system is first calibrated by using a neon lamp giving an uncertainty of ±1 cm−1 before each experiment.

Complementary to Raman spectroscopy, IR absorption spectroscopy provides sensitive and fingerprints information on materials loaded in DAC, especially those with high fluorescence that prohibits effective Raman measurements. The IR measurements for the examples demonstrated in this chapter were mostly carried out using a customized IR micro-spectroscopy system constructed in-house [11]. Specifically, a commercial FTIR spectrometer (model Vertex 80v from Bruker Optics Inc.) containing a Globar IR source constitutes the major component of the micro-IR system. The spectrometer is operated under a vacuum of <5 mbar to efficiently remove the absorption by H2O and CO2. The IR beam is collimated with varying diameters achieved by using apertures from 0.25 to 8 mm, and then is directed into a relay box through a KBr window. Using the combination of iris optics and 15× reflective objective lens (numerical

laser (Coherent Inc.), 532 and 782

UV to near IR, such as 488–514 nm lines from an Innova Ar+

spectroscopy.

**2.2. Raman spectroscopy**

**2.3. FTIR spectroscopy**

Synchrotron light is a source of electromagnetic radiation produced by a storage ring housing traveling electrons with a near speed of light. Although synchrotron source provides enormous advantages typically in the X-ray region, the infrared synchrotron light has unique applications for DAC-based measurements due to the very intense, very broad and highly focused IR source that allows very high spatial resolution and far-IR measurements. Some examples in this chapter are based on the experiments performed at the U2A beamline at the National Synchrotron Light Source (NSLS) of Brookhaven National Laboratory (BNL). Briefly, the IR beam from the synchrotron storage ring is first extracted through a wedged diamond window from a source with a 40 × 40 mrad solid angle. Then it is collimated to a 1.5″ diameter beam and directed into a vacuum FTIR spectrometer (Bruker IFS 66V) equipped with three independent microscope systems. The spectrometer is equipped with a number of combinations of IR beam splitters and detectors (e.g., silicon bolometer and MCT). For mid-IR measurements, a Bruker IR microscope is used to focus the IR beam onto the sample. The absorption spectrum is collected in transmission mode by the MCT detector in the spectral range of 600–4000 cm−1. The far-IR spectra are collected using a customized IR microscope allowing very high collection efficiency and recorded by the bolometer in the spectral region of 100 to 600 cm−1. A resolution of 4 cm−1 was used in all IR measurements. For all measurements, mid-IR spectra were collected through a 30 × 30 μm2 aperture, whereas the effective IR transmission area covered the entire sample (i.e., a circle of about 90 μm in diameter) for the far-IR measurements. The data acquisition, processing and analysis are similar to those obtained using the in-house mid-IR spectroscopy system.

## **3. Pressure-induced conformational change**

Pressure-mediated conformational equilibrium is of particular interests because the reactivity of many organic reagents, product yields, and even reaction pathways are strongly correlated with molecular conformations. Here, two simple halogen substituted alkane molecules, that is, 1,2-dichloroethane (DCE) [12] and chlorocyclohexane (CCH) [13], were investigated under high pressures for conformational and structural changes using *in situ* Raman spectroscopy.

#### **3.1. 1,2-Dichloroethane**

As a model molecule, DCE has two representative conformations, that is, *gauche* and *trans* depending on the relative orientations of the halogens attached to the two carbons, making it an interesting candidate for conformational studies under high pressures. At pressures below 0.6 GPa, fluid DCE exhibits two conformations, that is, *gauche* and *trans* in equilibrium. Upon compression, the equilibrium appears to shift toward *gauche* conformation (**Figure 2**). Upon further compression, DCE was found to transform to a solid phase with exclusive *trans* conformation. In fluid phase, all the characteristic Raman shifts remain constant whereas in the solid phase they move to higher frequencies with increasing pressure. At about 4–5 GPa, DCE transforms into a crystalline phase from a possible disordered phase as indicated by the appearance of several new lattice modes and bandwidth narrowing. Dramatic changes in Raman spectra of DCE were observed when compressed to ~8–9 GPa. For instance, the C─C─Cl bending mode at 325 cm−1 splits, the inactive internal mode at 684 cm−1 becomes observable, and new lattice modes appear. All these observations suggest another pressure-induced phase transformation. Significant changes in pressure dependence of representative Raman modes at the distinctive pressures further confirm the transition and allow the identification of phase boundaries. Although with a likely lower symmetry, the new phase remains crystalline. The transformations are found reversible in the entire pressure region upon decompression. Quantitative analysis on Raman intensities associated with each conformer even allows the determination of the transformation volume of 0.58 ± 0.10 cm3 /mol (**Figure 3**).

**Figure 2.** Representative Raman spectra of DCE on compression in the pressure region of (a) 0–5.0 GPa and (b) 5.7–29.2 GPa and the spectral region of 120–1300 cm−1 and 2900–3100 cm−1. The assignments of Raman active mode are labeled below for *gauche* (a) and *trans* (b) conformations. Reproduced with permission from reference [12].

**Figure 3.** Representative Raman spectra of DCE in the magnified spectral region of 600–800 cm−1 for fluid phase. The inset is the plot of logarithm of relative intensities of the first two peaks over the third peak as a function of pressure. Reproduced with permission from reference [12].

#### **3.2. Chlorocyclohexane**

with molecular conformations. Here, two simple halogen substituted alkane molecules, that is, 1,2-dichloroethane (DCE) [12] and chlorocyclohexane (CCH) [13], were investigated under high pressures for conformational and structural changes using *in situ* Raman spectroscopy.

168 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

As a model molecule, DCE has two representative conformations, that is, *gauche* and *trans* depending on the relative orientations of the halogens attached to the two carbons, making it an interesting candidate for conformational studies under high pressures. At pressures below 0.6 GPa, fluid DCE exhibits two conformations, that is, *gauche* and *trans* in equilibrium. Upon compression, the equilibrium appears to shift toward *gauche* conformation (**Figure 2**). Upon further compression, DCE was found to transform to a solid phase with exclusive *trans* conformation. In fluid phase, all the characteristic Raman shifts remain constant whereas in the solid phase they move to higher frequencies with increasing pressure. At about 4–5 GPa, DCE transforms into a crystalline phase from a possible disordered phase as indicated by the appearance of several new lattice modes and bandwidth narrowing. Dramatic changes in Raman spectra of DCE were observed when compressed to ~8–9 GPa. For instance, the C─C─Cl bending mode at 325 cm−1 splits, the inactive internal mode at 684 cm−1 becomes observable, and new lattice modes appear. All these observations suggest another pressure-induced phase transformation. Significant changes in pressure dependence of representative Raman modes at the distinctive pressures further confirm the transition and allow the identification of phase boundaries. Although with a likely lower symmetry, the new phase remains crystalline. The transformations are found reversible in the entire pressure region upon decompression. Quantitative analysis on Raman intensities associated with each conformer even allows the

**Figure 2.** Representative Raman spectra of DCE on compression in the pressure region of (a) 0–5.0 GPa and (b) 5.7–29.2 GPa and the spectral region of 120–1300 cm−1 and 2900–3100 cm−1. The assignments of Raman active mode are labeled

below for *gauche* (a) and *trans* (b) conformations. Reproduced with permission from reference [12].

/mol (**Figure 3**).

determination of the transformation volume of 0.58 ± 0.10 cm3

**3.1. 1,2-Dichloroethane**

*In situ* Raman measurements on CCH at room temperature and high pressures up to 20 GPa also show interesting pressure-dependent conformational changes [13]. Below 0.7 GPa, CCH exists as a fluid phase with a mixture of axial and equatorial conformations in equilibrium, which is shifted to axial upon compression (**Figure 4a**). The shift was attributed to the smaller volume of axial conformer with a volume difference of −2.2 cm3 mol−1 relative to equatorial conformation, which is consistent with previous studies. When compressed to 2.4 GPa, the depletion of C─H stretching mode at high frequency as well as the splittings of the ν22 mode suggest a phase transition (**Figure 4b**). The splittings are further enhanced at 4.8 GPa together with the observation of a new lattice mode, suggesting another phase transition. Upon careful comparison, these high-pressure phases are likely different from the low-temperature phases observed previously. Significant broadening of Raman profiles was observed above 9.5 GPa, indicating that CCH is undergoing gradual disordering at high pressures (**Figure 4b**). Upon releasing of pressure, CCH is fully recoverable indicating that the six-member ring can sustain high pressures up to 20 GPa. The observation of two new modes upon decompression, however, suggests that phase transformation of CCH is partially irreversible above 2.5 GPa. The phase produced by decompression exhibits a contribution from axial conformation of CCH. These pressure-induced hysteresis and partial irreversibility can be attributed to the plastic nature of the CCH crystals.

**Figure 4.** (a) Raman spectra of CCH collected at ambient pressure (top) in comparison with that collected upon slight compression (i.e., at 0.03 GPa, bottom). CCH exists as a mixture of axial and equatorial conformer with the latter dominant at condition and thus the assignment labeled above each Raman modes refers to equatorial conformation for the top spectrum. Axial and equatorial conformers share majority of common Raman modes and thus only those exclusively associated with axial conformer are labeled in the bottom spectrum. (b) Selective Raman spectra of CCH on compression in the pressure region 0–14 GPa in the spectral range of 120–1300 cm−1 and 2800–3200 cm−1. Reproduced with permission from reference [13].

## **4. Pressure-mediated hydrogen bonding**

Hydrogen bonding plays an important role in stabilizing a wide range of molecular structures and influences the chemical and physical properties of molecular systems. Typically, the characterizations of hydrogen bonding are inferred from crystal structures or by theoretical modeling. Here two examples are shown to demonstrate that vibrational spectroscopy on materials loaded in DAC can reveal interesting pressure-mediated hydrogen bonding interactions.

#### **4.1. Ethylene glycol**

Ethylene glycol (EG) serves as a prototype for understanding hydroxyl group interactions in biological compounds such as sugars and polysaccharides. Using *in situ* high-pressure Raman and infrared absorption spectroscopy, the structural and conformational transformations of EG were found to be substantially influenced by hydrogen bonding interactions under pressure up to 10 GPa [14]. The high-pressure behavior of Raman modes suggests that EG exists as a liquid with a mixture of *trans* and *gauche* conformations up to 3.1 GPa. In the pressure range 4–7 GPa, the solid phase has a varied proportion of *trans* and *gauche* conformations. At pressures above 7 GPa, the EG structure is stabilized to *gauche* conformation and remains stable up to 10 GPa. The increase in the intensity and the large pressure induced red shift of the infrared active OH mode *ν***ε** suggest that intra-molecular hydrogen bond is formed and strengthened during the stabilization of *gauche* conformation (**Figure 5**). The observed pressure induced changes were found to be completely reversible on decompression to ambient conditions.

**Figure 5.** Infrared absorption spectra of ethylene glycol at different pressures under compression in the spectral region of 2500–4000 cm−1 (a) and variation of OH stretching infrared active modes of ethylene glycol with pressure (b). Reproduced with permission from reference [14].

### **4.2. Bis(1H-tetrazol-5-yl)amine monohydrate**

**Figure 4.** (a) Raman spectra of CCH collected at ambient pressure (top) in comparison with that collected upon slight compression (i.e., at 0.03 GPa, bottom). CCH exists as a mixture of axial and equatorial conformer with the latter dominant at condition and thus the assignment labeled above each Raman modes refers to equatorial conformation for the top spectrum. Axial and equatorial conformers share majority of common Raman modes and thus only those exclusively associated with axial conformer are labeled in the bottom spectrum. (b) Selective Raman spectra of CCH on compression in the pressure region 0–14 GPa in the spectral range of 120–1300 cm−1 and 2800–3200 cm−1. Reproduced with

170 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Hydrogen bonding plays an important role in stabilizing a wide range of molecular structures and influences the chemical and physical properties of molecular systems. Typically, the characterizations of hydrogen bonding are inferred from crystal structures or by theoretical modeling. Here two examples are shown to demonstrate that vibrational spectroscopy on materials loaded in DAC can reveal interesting pressure-mediated hydrogen bonding

Ethylene glycol (EG) serves as a prototype for understanding hydroxyl group interactions in biological compounds such as sugars and polysaccharides. Using *in situ* high-pressure Raman and infrared absorption spectroscopy, the structural and conformational transformations of EG were found to be substantially influenced by hydrogen bonding interactions under pressure up to 10 GPa [14]. The high-pressure behavior of Raman modes suggests that EG exists as a liquid with a mixture of *trans* and *gauche* conformations up to 3.1 GPa. In the pressure range 4–7 GPa, the solid phase has a varied proportion of *trans* and *gauche* conformations. At pressures above 7 GPa, the EG structure is stabilized to *gauche* conformation and remains stable up to 10 GPa. The increase in the intensity and the large pressure induced red shift of the infrared active OH mode *ν***ε** suggest that intra-molecular hydrogen bond is formed and

permission from reference [13].

interactions.

**4.1. Ethylene glycol**

**4. Pressure-mediated hydrogen bonding**

Bis(1H-tetrazol-5-yl)amine (BTA) with two tetrazole rings linked by one nitrogen atom that contains 82.5 wt% nitrogen has been considered a promising high energy density material. Moreover, examining the possibility of converting this high nitrogen content precursor to other polymorphs with higher energy density using high pressure is of great interest. *In situ* highpressure study of BTA H2O was carried out up to 25 GPa at room temperature using Raman and IR spectroscopy, X-ray diffraction as well as *ab initio* simulations [15]. Upon compression, both the Raman and IR vibrational bands were found to undergo continuous and gradual broadening without significant change of the profile, indicating pressure-induced structural disordering rather than phase transition. X-ray diffraction patterns confirmed the pressure effect on the structural evolutions of BTA H2O. Interestingly, in contrast to all other Raman and IR modes of BTA H2O which exhibit blue shifts, the N-H stretching mode shows a prominent red shift upon compression to ~8 GPa, strongly suggesting pressure enhanced hydrogen bonding between BTA and H2O (**Figure 6**). The analysis of X-ray diffraction patterns of BTA H2O indicates that the unit cell parameters undergo anisotropic compression rate. The pressure dependence of the unit cell parameters and volumes coincides with the behavior of the hydrogen bonding enhancement (**Figure 7**). Aided with first-principles simulations, these pressure-mediated structural modifications consistently suggest that hydrogen bonding played an important role in the compression behavior and structural stability of BTA H2O under high pressures (**Figure 8**).

**Figure 6.** Pressure dependence of IR modes of BTA H2O on compression. Reproduced with permission from reference [15].

**Figure 7.** Normalized unit cell volume versus pressure (black squares) for BTA H2O on compression and fitted equation of state (red curve) using second-order Birch-Murnaghan equation. The inset shows normalized monoclinic unit cell parameters for *a, b* and *c* of BTA H2O on compression. The vertical dashed line denotes the pressure at which the monotonic contraction of *a* and *c* axes changed. Reproduced with permission from reference [15].

Novel Pressure-Induced Molecular Transformations Probed by *In Situ* Vibrational Spectroscopy http://dx.doi.org/10.5772/64617 173

**Figure 8.** Proton hopping and molecular interactions of BTA H2O system based on first-principles simulations.

## **5. Structural and phase transitions**

#### **5.1. Boron nitride nanotubes**

**Figure 6.** Pressure dependence of IR modes of BTA H2O on compression. Reproduced with permission from reference

172 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 7.** Normalized unit cell volume versus pressure (black squares) for BTA H2O on compression and fitted equation of state (red curve) using second-order Birch-Murnaghan equation. The inset shows normalized monoclinic unit cell parameters for *a, b* and *c* of BTA H2O on compression. The vertical dashed line denotes the pressure at which the

monotonic contraction of *a* and *c* axes changed. Reproduced with permission from reference [15].

[15].

Compared to carbon nanotube, boron nitride nanotube (BNNT) has structure-independent wide band gap, enhanced thermal stability, high resistance to oxidation at high temperatures, high thermal conductivity and remarkable yield strength, making it a promising advanced material for a wide range of applications. Multiwalled boron nitride nanotubes (BNNTs) were compressed at room temperature in diamond anvil cells up to 35 GPa followed by decompression and characterized by *in situ* FTIR absorption spectroscopy [11]. Pressure-induced transformations from a hexagonal to a more closely packed wurtzite structure were observed at 11 GPa, which is similar to that reported for bulk BN (**Figure 9**). However, BNNTs exhibit quantitative differences compared to bulk h-BN in terms of transformation completeness and reversibility (**Figure 10**). These findings provide strong evidence that significantly different yield of sp3 bonding formation originated from different morphologies of the starting BN materials (**Figure 11**). The unique transformation mechanism for BNNTs provides new useful information for developing BNNTs as potential advanced materials with more desirable properties than carbon nanotubes.

**Figure 9.** Infrared spectra of BNNTs at selected pressures upon compression (red lines) and decompression (blue lines) in the spectra region of 600–1900 cm−1. The solid and dashed arrows indicate the compression and decompression sequence. The inset shows spectra from another run at a highest pressure of 34.6 GPa on compression (red line) and complete pressure release (blue line). Reproduced with permission from reference [11].

**Figure 10.** Pressure dependence of representative IR modes of BNNTs (open symbols) and in comparison with those for bulk h-BN (solid symbols) on compression. The squares and circles are the respective A2u and E1u modes of h-BN structure, while other symbols represent IR modes for w-BN structure. The dashed line at around 11 GPa denotes the transition onset for both BNNTs and bulk h-BN. The vertical bars for A2u mode represent the full width at half maximum for BNNTs. The inset shows the ratio of the IR band intensity of the mode at 1125 cm−1 for w-BN over the E1u mode for h-BN observed in BNNTs labeled as Iw/Ih. The solid lines are for eye guidance showing three distinctive conversion regions. Reproduced with permission from reference [11].

Novel Pressure-Induced Molecular Transformations Probed by *In Situ* Vibrational Spectroscopy http://dx.doi.org/10.5772/64617 175

**Figure 11.** Crystal structures and bonding patterns of (a) h-BN and (b) w-BN with the transformation conditions for BNNTs and bulk h-BN denoted. The red and blue balls represent boron and nitrogen, respectively. The dashed arrow for BNNT indicates incomplete irreversible transformation, while the solid arrows with different length for bulk h-BN indicate partial reversibility. Reproduced with permission from reference [11].

#### **5.2. Aromatic compounds**

**Figure 9.** Infrared spectra of BNNTs at selected pressures upon compression (red lines) and decompression (blue lines) in the spectra region of 600–1900 cm−1. The solid and dashed arrows indicate the compression and decompression sequence. The inset shows spectra from another run at a highest pressure of 34.6 GPa on compression (red line) and com-

**Figure 10.** Pressure dependence of representative IR modes of BNNTs (open symbols) and in comparison with those for bulk h-BN (solid symbols) on compression. The squares and circles are the respective A2u and E1u modes of h-BN structure, while other symbols represent IR modes for w-BN structure. The dashed line at around 11 GPa denotes the transition onset for both BNNTs and bulk h-BN. The vertical bars for A2u mode represent the full width at half maximum for BNNTs. The inset shows the ratio of the IR band intensity of the mode at 1125 cm−1 for w-BN over the E1u mode for h-BN observed in BNNTs labeled as Iw/Ih. The solid lines are for eye guidance showing three distinctive con-

plete pressure release (blue line). Reproduced with permission from reference [11].

174 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

version regions. Reproduced with permission from reference [11].

Aromatic compounds have been investigated under non-ambient conditions over the past few decades due to their great importance in both fundamental and applied science. In particular, they have been widely studied in chemical synthesis under elevated temperatures and pressures as the precursors of technological materials, such as amorphous solids and conjugated polymers [16]. For instance, using *in situ* Raman spectroscopy and infrared absorption spectroscopy, structural transitions of pyridine have been investigated as a function of pressure up to 26 GPa [17]. By monitoring the band profiles in both Raman and IR spectra and especially the Raman shifts in the lattice region, a liquid-to-solid transition at 1 GPa followed by solidto-solid transitions at 2, 8, 11 and 16 GPa were observed upon compression (**Figure 12**). All these transitions were reversible upon decompression from 22 GPa. When compressed beyond 22 GPa, a further chemical transformation was observed which is evidenced by the substantial and irreversible changes of the Raman and infrared spectra. This transformation could be attributed to the destruction of the ring structure. The high-pressure behavior of pyridine was also compared to that of benzene. The similar transition sequence with well-aligned transition pressures indicates that aromatic compounds with isoelectronic structures may have similar structural stabilities and thus transition behaviors under high pressure.

**Figure 12.** Selected Raman spectra of pyridine on compression in the spectral region of 60–500 cm−1 (a), 400–1160 cm−1 (b) and 1100–3300 cm−1 (c). Reproduced with permission from reference [17].

#### **5.3. Metal and chemical hydrides**

High-pressure investigations of potential hydrogen storage materials, especially hydrogenrich metal and chemical hydrides have received increasing attentions [8]. Not only has pressure demonstrated great promises for producing new structures and materials but also many known hydrogen-rich materials have exhibited new transformations as well as totally different thermodynamic and kinetic behaviors under higher pressures than under ambient conditions. Hydrides in a wide range of different categories, such as calcium borohydride, sodium amide and ammonia borane, have been extensively investigated under high pressures by vibrational spectroscopy, X-ray diffraction and theoretical calculations [18–21]. Here ammonia borane (NH3BH3) is chosen as an example to demonstrate that vibrational spectroscopy can be an effective tool to elucidate novel high-pressure structures [18, 21].

Using *in situ* Raman and synchrotron IR spectroscopy, the pressure behavior of ammonia borane complex as a promising hydrogen storage material was investigated up to 14 GPa [18]. In the low-pressure region (<2 GPa), the complex was found to undergo a structural transformation to, an ordered, possibly orthorhombic structure from originally a disordered tetragonal phase. With increasing pressure, the Raman and IR spectra suggest several solid-to-solid transformations at about 2.4, 5.5, 8.5 and 10.4 GPa, as evidenced by the distinctive profiles and the pressure dependences of characteristic modes (**Figure 13**). Upon decompression, these pressure-induced transformations are found completely reversible with intact chemical structure of the NH3BH3 complex, but possible modifications to the crystal structures. Analysis of combined Raman and IR measurements, especially the lattice features (**Figure 13a**), suggests that NH3BH3 structures below 5.5 GPa resemble a low-pressure orthorhombic structure, while in the higher pressure regions, NH3BH3 complexes may undergo transformations to disordered or amorphous structures.

**Figure 13.** Pressure dependences of Raman shift of NH3BH3 on compression for (a) the lattice modes; (b) the 11B-N/10B-N stretch (ν5/ν5′) modes; and (c) the NBH rock (ν12a, ν12b, ν11a, ν11b and ν11c) modes. The solid lines crossing the solid symbols are based on linear fit. The vertical dashed lines indicate the proposed phase boundaries. Reproduced with permission from reference [18].

Novel Pressure-Induced Molecular Transformations Probed by *In Situ* Vibrational Spectroscopy http://dx.doi.org/10.5772/64617 177

**5.3. Metal and chemical hydrides**

dered or amorphous structures.

permission from reference [18].

High-pressure investigations of potential hydrogen storage materials, especially hydrogenrich metal and chemical hydrides have received increasing attentions [8]. Not only has pressure demonstrated great promises for producing new structures and materials but also many known hydrogen-rich materials have exhibited new transformations as well as totally different thermodynamic and kinetic behaviors under higher pressures than under ambient conditions. Hydrides in a wide range of different categories, such as calcium borohydride, sodium amide and ammonia borane, have been extensively investigated under high pressures by vibrational spectroscopy, X-ray diffraction and theoretical calculations [18–21]. Here ammonia borane (NH3BH3) is chosen as an example to demonstrate that vibrational spectroscopy can be an

Using *in situ* Raman and synchrotron IR spectroscopy, the pressure behavior of ammonia borane complex as a promising hydrogen storage material was investigated up to 14 GPa [18]. In the low-pressure region (<2 GPa), the complex was found to undergo a structural transformation to, an ordered, possibly orthorhombic structure from originally a disordered tetragonal phase. With increasing pressure, the Raman and IR spectra suggest several solid-to-solid transformations at about 2.4, 5.5, 8.5 and 10.4 GPa, as evidenced by the distinctive profiles and the pressure dependences of characteristic modes (**Figure 13**). Upon decompression, these pressure-induced transformations are found completely reversible with intact chemical structure of the NH3BH3 complex, but possible modifications to the crystal structures. Analysis of combined Raman and IR measurements, especially the lattice features (**Figure 13a**), suggests that NH3BH3 structures below 5.5 GPa resemble a low-pressure orthorhombic structure, while in the higher pressure regions, NH3BH3 complexes may undergo transformations to disor-

**Figure 13.** Pressure dependences of Raman shift of NH3BH3 on compression for (a) the lattice modes; (b) the 11B-N/10B-N stretch (ν5/ν5′) modes; and (c) the NBH rock (ν12a, ν12b, ν11a, ν11b and ν11c) modes. The solid lines crossing the solid symbols are based on linear fit. The vertical dashed lines indicate the proposed phase boundaries. Reproduced with

effective tool to elucidate novel high-pressure structures [18, 21].

176 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 14.** Selected Raman spectra of NH3BH3 collected on compression up to 15.92 GPa at 180 K in the region of 50– 300 cm−1 (a), 1000–1300 cm−1 (b), and 3100–3400 cm−1 (c). The assignments are labeled for selected Raman mode at selected pressures. Reproduced with permission from reference [21].

**Figure 15.** Schematic P-T phase diagram of NH3BH3 in the pressure region of 0–15 GPa (in log2 scale) and temperature region of 80–350 K. Solid symbols are experimental data from this study, with squares for *I4mm* phase, circles for *Pmn*21 phase and diamonds for *Cmc*21 phase. The open squares are adopted from reference [22]. The solid lines denote the rough boundaries among the three known phases. The *P*1 phase labeled is considered tentative. Reproduced with permission from reference [21].

Subsequently, ammonia borane was investigated at simultaneous high pressures (up to 15 GPa) and low temperatures (down to 80 K) by *in situ* Raman spectroscopy [21]. Upon cooling to 220 K from room temperature at ambient pressure, ammonia borane transforms from *I*4*mm* to *Pmn*21. Upon isothermal compression to 15 GPa at 180 K, another three pressure-induced structural transformations were observed. These transitions can be evidenced by the change in the Raman profile as well as the pressure dependence of the major Raman modes (**Figure 14**). Upon decompression and warming-up, these P-T-induced transformations are found completely reversible. With the aid of factor group analysis, the phases above 1.5 GPa were found consistent with the crystal structure with space group *Cmc*21, and that the transitions at 5 and 8 GPa are second order in nature, which can be interpreted as enhanced inter-molecular interactions within the same or possibly a slightly modified crystal lattice. Further compression above 15 GPa leads to the gradual transformation to an amorphous phase. When combined with previously reported high-pressure and room-temperature data, our Raman measurements from multiple runs covering various P-T paths allowed the significant update of the P-T phase diagram of ammonia borane in the pressure range of 0–15 GPa and the temperature range of 80–350 K (**Figure 15**).

## **6. Pressure-induced chemical reactions**

#### **6.1. Acrylic acid**

Pressure-induced polymerization is a chemical process pertaining to green chemistry as the reactions can be carried out in the absence of any solvent or catalyst, which implies a lesser environmental impact. Poly(acrylic acid) is a well-known polymer with a wide variety of industrial applications such as being super absorbent materials, biocompatible polymers, polyelectrolytes and nanopolymers in molecular devices. Therefore, it is very significant in the polymer industry to explore pressure-induced polymerization from this monomer, as the polymer product with improved properties distinct from that obtained using conventional synthetic methods might be obtained. The first pressure-induced structural and polymeric transformations of acrylic acid were studied by *in situ* Raman spectroscopy [23]. Upon compression to 0.3 GPa, a liquid-to-solid transformation was observed, followed by a solid-tosolid transition at ~2.7 GPa. The two new high-pressure crystalline phases are labeled as phase I and II, respectively (**Figure 16a**). Phase I had a possibly similar structure that resembles lowtemperature phase reported previously. Phase II can be interpreted as a denser phase with strong intermolecular interactions leading to polymerization or oligomerization ultimately. When compressed to above 8 GPa, acrylic acid transforms into a disordered polymeric phase (**Figure 16b**). Upon decompression to ambient pressure, the retrieved polymeric phase exhibits a significant amount of acrylic acid monomers or oligomers. Comparative Raman measurements on standard commercial poly(acrylic acid) (**Figure 17**) allowed the understanding of possible structures of the polymeric phase of acrylic acid produced in this study. Overall, our analysis suggests that hydrogen bonding played a significant role in the pressure-induced polymerization/oligomerization process.

Novel Pressure-Induced Molecular Transformations Probed by *In Situ* Vibrational Spectroscopy http://dx.doi.org/10.5772/64617 179

**Figure 16.** Raman spectra of acrylic acid at selected pressures upon compression in the pressure region of 0.3–4.5 GPa (a) and 3.3–10 GPa (b) in the spectral region of 100–1300 cm−1. Reproduced with permission from reference [23].

**Figure 17.** Raman spectrum of poly(acrylic acid) purchased from Aldrich with an average molecular weight of 1800 g/mol (a) and 450,000 g/mol (b) in comparison with that of recovered acrylic acid by decompression from 10 GPa (c) and that of acrylic acid at 10 GPa (d). Reproduced with permission from reference [23].

#### **6.2. Ethylene glycol**

Subsequently, ammonia borane was investigated at simultaneous high pressures (up to 15 GPa) and low temperatures (down to 80 K) by *in situ* Raman spectroscopy [21]. Upon cooling to 220 K from room temperature at ambient pressure, ammonia borane transforms from *I*4*mm* to *Pmn*21. Upon isothermal compression to 15 GPa at 180 K, another three pressure-induced structural transformations were observed. These transitions can be evidenced by the change in the Raman profile as well as the pressure dependence of the major Raman modes (**Figure 14**). Upon decompression and warming-up, these P-T-induced transformations are found completely reversible. With the aid of factor group analysis, the phases above 1.5 GPa were found consistent with the crystal structure with space group *Cmc*21, and that the transitions at 5 and 8 GPa are second order in nature, which can be interpreted as enhanced inter-molecular interactions within the same or possibly a slightly modified crystal lattice. Further compression above 15 GPa leads to the gradual transformation to an amorphous phase. When combined with previously reported high-pressure and room-temperature data, our Raman measurements from multiple runs covering various P-T paths allowed the significant update of the P-T phase diagram of ammonia borane in the pressure range of 0–15 GPa and the temperature

178 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Pressure-induced polymerization is a chemical process pertaining to green chemistry as the reactions can be carried out in the absence of any solvent or catalyst, which implies a lesser environmental impact. Poly(acrylic acid) is a well-known polymer with a wide variety of industrial applications such as being super absorbent materials, biocompatible polymers, polyelectrolytes and nanopolymers in molecular devices. Therefore, it is very significant in the polymer industry to explore pressure-induced polymerization from this monomer, as the polymer product with improved properties distinct from that obtained using conventional synthetic methods might be obtained. The first pressure-induced structural and polymeric transformations of acrylic acid were studied by *in situ* Raman spectroscopy [23]. Upon compression to 0.3 GPa, a liquid-to-solid transformation was observed, followed by a solid-tosolid transition at ~2.7 GPa. The two new high-pressure crystalline phases are labeled as phase I and II, respectively (**Figure 16a**). Phase I had a possibly similar structure that resembles lowtemperature phase reported previously. Phase II can be interpreted as a denser phase with strong intermolecular interactions leading to polymerization or oligomerization ultimately. When compressed to above 8 GPa, acrylic acid transforms into a disordered polymeric phase (**Figure 16b**). Upon decompression to ambient pressure, the retrieved polymeric phase exhibits a significant amount of acrylic acid monomers or oligomers. Comparative Raman measurements on standard commercial poly(acrylic acid) (**Figure 17**) allowed the understanding of possible structures of the polymeric phase of acrylic acid produced in this study. Overall, our analysis suggests that hydrogen bonding played a significant role in the pressure-induced

range of 80–350 K (**Figure 15**).

**6.1. Acrylic acid**

**6. Pressure-induced chemical reactions**

polymerization/oligomerization process.

Using combined high-pressure and photon excitations especially in the UV range has demonstrated strong potential to produce new molecular materials in a highly efficient way. Using multi-line UV radiation at ~350 nm, the photon-induced reactivity of liquid ethylene glycol (EG) at room temperature was investigated by FTIR spectroscopy [24]. Upon UV irradiation, IR spectra of EG show two sets of distinctive profiles after specific reaction time, indicating multiple photon-induced chemical reactions, which can be designated as primary and secondary processes (**Figure 18**). Careful spectral analysis allows the identification of primary reaction products that include glycolaldehyde, acetaldehyde and methanol. Further photoreactions of these primary products led to the formation of the secondary products, which were identified as methane, formaldehyde, methoxymethanol, methylformate and carbon dioxide. Based on these reaction products, possible reaction mechanisms and production pathways were proposed. We also found that the initial loading pressure of EG plays an important role in influencing the reaction kinetics as well as in controlling the accessibilities for some reaction channels such as for CH4 (**Figure 19a**). Quantitative analysis of the antisymmetric stretching mode of CO2 formed at different loading pressures suggests the formation of CO2 clathrate hydrates well as CO2 clusters. The stabilities as well as relative abundance of these CO2 species are found to be dependent on both pressure and radiation time (**Figure 19b**). These observations revealed interesting pressure-induced CO2 sequestration behaviors as a result of photochemical reactions of ethylene glycol.

**Figure 18.** Selected FTIR spectra of EG with an initial loading pressure of 0.1 GPa upon UV irradiation (with *λ* of ~350 nm and power of ~700 mW) collected at different radiation time. The most characteristic new IR bands emerged at 13.5 h and observed at 22.5 h indicating sequential photochemical reactions are labeled. The spectral region in 3000–3500 cm−1 before 13.5 h is truncated due to the saturated IR absorption intensity. Reproduced with permission from reference [24].

Novel Pressure-Induced Molecular Transformations Probed by *In Situ* Vibrational Spectroscopy http://dx.doi.org/10.5772/64617 181

**Figure 19.** Relative photochemical reaction yields of CH4 (a) and CO2 (b) derived by integrating the intensity of the respective characteristic IR modes (*ν*4 of CH4 and *ν*3 of CO2) as a function of radiation time for EG samples with an initial loading pressure of 0.1, 0.5, 1.0 and 2.0 GPa. The pressures labeled for each sample indicate the final system pressure. Reproduced with permission from reference [24].

#### **7. Porous materials and guest-host interactions**

#### **7.1. ZIF-8**

IR spectra of EG show two sets of distinctive profiles after specific reaction time, indicating multiple photon-induced chemical reactions, which can be designated as primary and secondary processes (**Figure 18**). Careful spectral analysis allows the identification of primary reaction products that include glycolaldehyde, acetaldehyde and methanol. Further photoreactions of these primary products led to the formation of the secondary products, which were identified as methane, formaldehyde, methoxymethanol, methylformate and carbon dioxide. Based on these reaction products, possible reaction mechanisms and production pathways were proposed. We also found that the initial loading pressure of EG plays an important role in influencing the reaction kinetics as well as in controlling the accessibilities for some reaction channels such as for CH4 (**Figure 19a**). Quantitative analysis of the antisymmetric stretching mode of CO2 formed at different loading pressures suggests the formation of CO2 clathrate hydrates well as CO2 clusters. The stabilities as well as relative abundance of these CO2 species are found to be dependent on both pressure and radiation time (**Figure 19b**). These observations revealed interesting pressure-induced CO2 sequestration behaviors as a result of

180 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 18.** Selected FTIR spectra of EG with an initial loading pressure of 0.1 GPa upon UV irradiation (with *λ* of ~350 nm and power of ~700 mW) collected at different radiation time. The most characteristic new IR bands emerged at 13.5 h and observed at 22.5 h indicating sequential photochemical reactions are labeled. The spectral region in 3000–3500 cm−1 before 13.5 h is truncated due to the saturated IR absorption intensity. Reproduced with permission from refer-

photochemical reactions of ethylene glycol.

ence [24].

ZIF-8 is a representative member of the zeolitic imidazolate framework (ZIF) family, an emerging class of porous materials with promising applications in gas storage and catalysis, etc. As a result, substantial interest has been focused on the investigation of its structure and properties under different conditions. Pressure tuning has proven an important and effective means to modify the structures and thus the associated properties of porous materials. Therefore, ZIF-8 was investigated under high pressures up to ~39 GPa using *in situ* IR spectroscopy [25]. Upon compression to 1.6 GPa followed by decompression, the structural modifications on ZIF-8 framework appear reversible (**Figure 20a**). However, further compression to higher pressures led to irreversible structural transitions to an amorphous phase characterized by the very broad IR profiles (**Figure 20b**). Nevertheless, the chemical structure of the framework was found to sustain extreme compression without permanent breaking down. Overall, the high-pressure behavior and especially the surprising chemical stability probed by *in situ* IR spectroscopy demonstrate strong promises storage applications of ZIF-8 under extreme conditions.

In a subsequent study, ZIF-8 framework was investigated when loaded with CO2 in a diamond anvil cell at high pressures of 0.8 GPa, far beyond the conventional gas adsorption pressure also using *in situ* FTIR spectroscopy [26]. Upon loading, CO2 molecules in two types of environment (i.e., outside as bulk medium and inside the framework) can be unambiguously differentiated by monitoring the combination IR bands of CO2 (**Figure 21**). Furthermore, pressure was found to play a regulating role in the migration of CO2 molecules with respect to the framework even at room temperature. The strong interactions between CO2 and framework are evident from the IR features of the framework (e.g., C═C stretching region), providing valuable information about the possible interaction site. As guest molecules, CO2 in turn can substantially enhance the structural stability of the ZIF-8 framework as compared to the empty framework (**Figure 22**). The enhanced CO2 storage capacity of ZIF-8 at high pressure provides new insight into the gas capture and storage applications of ZIFs.

**Figure 20.** Selected IR spectra of ZIF-8 on compression to a highest pressure of 1.60 GPa and as recovered (a), and to another highest pressure of 39.15 GPa and as recovered (b). Reproduced with permission from reference [25].

**Figure 21.** (a) The comparison of IR spectrum of pure CO2 (top), ZIF-8 loaded with CO2 (middle) and that of pure ZIF-8 (bottom) at similar pressures. The inset shows the spectral region for the combination modes of CO2 loaded with ZIF-8 loaded (top) and pure CO2 (bottom). (b) Photograph of ZIF-8 loaded with CO2 obtained under an optical microscope. The arrows denote the positions of the C═C stretching mode of the imidazole ring. Reproduced with permission from reference [26].

**Figure 22.** Far-IR spectra of empty ZIF-8 framework upon compression to 2.61 GPa and decompression to ambient pressure. These far-IR spectra suggest that pressure can significantly modify the crystal structures of empty ZIF-8 framework irreversibly. Reproduced with permission from reference [26].

#### **7.2. MIL-68**

to the framework even at room temperature. The strong interactions between CO2 and framework are evident from the IR features of the framework (e.g., C═C stretching region), providing valuable information about the possible interaction site. As guest molecules, CO2 in turn can substantially enhance the structural stability of the ZIF-8 framework as compared to the empty framework (**Figure 22**). The enhanced CO2 storage capacity of ZIF-8 at high pressure

**Figure 20.** Selected IR spectra of ZIF-8 on compression to a highest pressure of 1.60 GPa and as recovered (a), and to another highest pressure of 39.15 GPa and as recovered (b). Reproduced with permission from reference [25].

**Figure 21.** (a) The comparison of IR spectrum of pure CO2 (top), ZIF-8 loaded with CO2 (middle) and that of pure ZIF-8 (bottom) at similar pressures. The inset shows the spectral region for the combination modes of CO2 loaded with ZIF-8 loaded (top) and pure CO2 (bottom). (b) Photograph of ZIF-8 loaded with CO2 obtained under an optical microscope. The arrows denote the positions of the C═C stretching mode of the imidazole ring. Reproduced with permission from

reference [26].

provides new insight into the gas capture and storage applications of ZIFs.

182 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

As a promising candidate for the application of gas storage and separation, metal-organic framework (MOF) MIL-68 has unique structural topology that contains two types of channels with distinct pore sizes. Using *in situ* IR spectroscopy, the behavior of as-made and activated MIL-68 (In) and their structural reversibilities were investigated under high pressures [27]. Overall, the structures of both frameworks were found highly stable upon compression to 9 GPa. However, some modifications on the local structure especially the bridging O─H units, which are very sensitive to compression, can be clearly identified. The structural modifications are found to be completely reversible upon decompression for asmade MIL-68 (In) but irreversible for the activated framework. The different reversibility of framework is most likely associated with the solvent DMF molecules contained in the framework channels. Furthermore, the stability of the activated framework was investigated using PTM to achieve hydrostatic compression. The pressure-induced inclusion of PTM makes the framework more resilient to compression (18 GPa). As a result, structural modifications of the framework with PTM are completely reversible upon decompression (**Figure 23a**). Moreover, the performance of MIL-68 (In) for CO2 adsorption under high pressure was investigated. Our results show that at relative low pressures such as below 0.35 GPa, the hexagonal pores are readily accessible for CO2, while the triangular pores become accessible for CO2 at higher pressures such as above 1.5 GPa (**Figure 23b**). Such pressure-regulated CO2 occupation in different channels of the MIL-68 framework is completely reversible between compression and decompression (**Figure 23c**). The unique adsorption behavior of CO2 in the MIL-68 is strongly correlated with the OH units contributing as the primary binding sites through hydrogen bonding with CO2. Molecular dynamics simulations further support our analysis (**Figure 24**). The high framework stability and enhanced CO2 adsorption of MIL-68 (In) under high pressure make it a promising candidate for greenhouse gas storage.

**Figure 23.** (a) IR spectra of activated MIL-68 (In) with PTM upon compression. (b) IR spectra of activated MIL-68 (In) and MIL-68 (In) loaded with CO2 at around 0.4 GPa in the frequency region of 600–3800 cm−1. (c) IR spectra of MIL-68 (In) loaded with CO2 upon compression. Reproduced with permission from reference [27].

**Figure 24.** Simulated contour plots of the CO2 probability density distributions along the hexagonal and triangular channels of MIL-68 (In) framework at (a) 1 bar, (b) 1000 bar or 0.1 GPa and (c) 105 bar (or 10 GPa). Reproduced with permission from reference [27].

## **8. Summary and future perspectives**

pressure was investigated. Our results show that at relative low pressures such as below 0.35 GPa, the hexagonal pores are readily accessible for CO2, while the triangular pores become accessible for CO2 at higher pressures such as above 1.5 GPa (**Figure 23b**). Such pressure-regulated CO2 occupation in different channels of the MIL-68 framework is completely reversible between compression and decompression (**Figure 23c**). The unique adsorption behavior of CO2 in the MIL-68 is strongly correlated with the OH units contributing as the primary binding sites through hydrogen bonding with CO2. Molecular dynamics simulations further support our analysis (**Figure 24**). The high framework stability and enhanced CO2 adsorption of MIL-68 (In) under high pressure make it a promising

184 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 23.** (a) IR spectra of activated MIL-68 (In) with PTM upon compression. (b) IR spectra of activated MIL-68 (In) and MIL-68 (In) loaded with CO2 at around 0.4 GPa in the frequency region of 600–3800 cm−1. (c) IR spectra of MIL-68

**Figure 24.** Simulated contour plots of the CO2 probability density distributions along the hexagonal and triangular

bar (or 10 GPa). Reproduced with

(In) loaded with CO2 upon compression. Reproduced with permission from reference [27].

channels of MIL-68 (In) framework at (a) 1 bar, (b) 1000 bar or 0.1 GPa and (c) 105

permission from reference [27].

candidate for greenhouse gas storage.

In summary, this chapter demonstrated the application of *in situ* vibrational spectroscopy including Raman and FTIR spectroscopy in the elucidation of molecular structures and transformation mechanism for a wide variety of materials rendered under high-pressure conditions. Specifically, conformational changes, pressure-mediated hydrogen bonding interactions, molecular and crystal structural transitions, polymerizations and photon-assisted chemical reactions, as well as guest-host interactions of respective selected systems can be efficiently and accurately probed and characterized using *in situ* high-pressure Raman spectroscopy, FTIR spectroscopy or combination of both. These spectroscopic data provided enormously valuable information for us to understand the pressure-induced phenomena at microscopic level in-depth. Thus, vibrational micro-spectroscopy can be considered a routine but indispensable technique in any high-pressure materials research laboratories.

In addition to extreme pressure, extreme temperatures such as several Kelvin and several hundred degrees Celsius, and especially their combinations pose experimental challenges yet offer new and unexplored P-T domains for novel structures and properties of materials to be discovered. *In situ* vibrational micro-spectroscopy is expected to play an important role in structural characterization under these tough conditions. Although extremely convenient, one should realize that vibrational spectroscopy itself alone is seldom successful in solving totally unknown structures. Therefore, to realize the full potential of vibrational spectroscopy on materials under extreme conditions, other experimental techniques such as X-ray diffraction, synchrotron probes as well as theoretical modeling are essential to obtain the full structural information of novel materials.

## **Acknowledgements**

This work was supported by a Discovery Grant, a Research Tools and Instruments Grant from the Natural Science and Engineering Research Council of Canada, a Leaders Opportunity Fund from the Canadian Foundation for Innovation, an Early Researcher Award from the Ontario Ministry of Research and Innovation, a Petro-Canada Young Innovator Award and by Defense Research and Development Canada under contract No. W7702-135601. The synchrotron IR measurements presented were performed at U2A beamline of National Synchrotron Light Source of US Brookhaven National Laboratory.

## **Author details**

Yang Song

Address all correspondence to: yang.song@uwo.ca

Department of Chemistry, University of Western Ontario, London, Ontario, Canada

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Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

## **Conformational Analysis of Molecules: Combined Vibrational Spectroscopy and Density Functional Theory Study Conformational Analysis of Molecules: Combined Vibrational Spectroscopy and Density Functional Theory Study**

Partha P. Kundu and Chandrabhas Narayana Partha P. Kundu and Chandrabhas Narayana

Additional information is available at the end of the chapter Additional information is available at the end of the chapter

http://dx.doi.org/ 10.5772/64452

#### **Abstract**

188 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Vibrational spectroscopy can be broadly classified into Raman and infrared (IR). These two techniques are complementary to each other as the mechanisms behind these are different. Vibrational spectroscopy provides detail information about the structure of molecules. The advantage of this technique over X‐ray diffraction is that it can be used to probe molecules in solid, liquid or gas phase. This is especially helpful for studying biomolecules as those molecules can be probed in their physiological environment. Over the last few decades, quantum mechanical calculation has become important tool to assign bands from vibrational spectra. Combination of these two techniques has been used widely in the field of chemistry and biochemistry. In this chapter, we review some of the works that combine both of these techniques. A brief theoretical background is given for understanding the principle of these two techniques.

**Keywords:** Raman, infrared (IR), density functional theory (DFT), conformation

## **1. Introduction**

Spectroscopy is a subject that is related to the interaction of electromagnetic radiation with the atoms or molecules. It provides rich information about the structures, physical and chemical properties of the materials. Energy of a stationary molecule can be written as a sum of three parts: electronic, vibrational and rotational. In vibrational spectroscopy, the vibra‐ tional levels of a molecule are probed. Vibrational spectroscopy can be broadly classified into two: infrared (IR) and Raman. Even though both techniques probe the vibrational energy

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

levels, physical processes leading to these spectra are different. Thus, these two techniques offer different information about the molecule and regarded as complementary to each other. To get the structural information from a vibrational spectrum, the first task is to assign the bands. Band assignments can be performed by comparing the modes of similar molecule already existing in literature. However, vibrational frequencies are sensitive to the small difference in the structure and also to the environment. Moreover, it is difficult to assign the large number of closely spaced bands arising from even a medium size molecule. Hence, for reliable assignments of these bands, it is essential to calculate the normal modes theoretically and compare those with the experimental spectra. Over the last few decades, calculation of molecular spectra using quantum mechanics has become a common practice. There are many quantum mechanical‐based methods for calculation, of which density functional theory (DFT) is most popular as its computational cost is less without compromising significantly with the accuracy.

Here, we will introduce the basic theory behind these vibrational techniques. Also, the principle of DFT will be discussed in brief. We will provide references so that the interested readers can gain insights about these topics.

## **2. Theoretical background**

#### **2.1. Raman scattering**

When a molecule is irradiated with a monochromatic light of wave number 0, a small fraction of the incident light will be scattered. In the scattered radiation, major portion of the light will have the same wave number as the incident light; however, a tiny fraction of light will have the wave number ′ = 0 ± . The first kind of scattering is called Rayleigh scattering while the latter is called Raman scattering. Classically, the phenomenon of Raman scattering can be explained in the following paragraphs.

When a molecule is in an oscillating electric field () with angular frequency , an induced dipole will be created, Which in the linear approximation can be written (in complex notation) as,

$$
\underline{\mathbf{p}}(\boldsymbol{\alpha}\_{L}) = \boldsymbol{\hat{\alpha}}\_{L}(\boldsymbol{\alpha}\_{L}) \, \underline{\mathbf{E}}(\boldsymbol{\alpha}\_{L}) \tag{1}
$$

where is the *polarizability tensor* and . Here, it is to be mentioned that as the molecule vibrates, the polarizability tensor gets modulated. Polarizability thus not only depends on frequency but also on the atomic positions. To describe the vibrational pattern, *normal coordinates* () are introduced. For a specific normal mode *k* (*k* = 1, 2, …, 3*N*‐6, where *N* is the total number of atoms in the molecule), all the atoms in the molecule will oscillate with the same frequency . If the polarizability tensor is expanded in Taylor series around the equilibrium position, it can be shown [1] that the induced dipole (real) can be expressed as

$$\mathbf{p}(t) = \mathbf{p}\_{\perp}(t) + \mathbf{p}\_{\circ}(t) + \mathbf{p}\_{\circ}(t),\tag{2}$$

where

levels, physical processes leading to these spectra are different. Thus, these two techniques offer different information about the molecule and regarded as complementary to each other. To get the structural information from a vibrational spectrum, the first task is to assign the bands. Band assignments can be performed by comparing the modes of similar molecule already existing in literature. However, vibrational frequencies are sensitive to the small difference in the structure and also to the environment. Moreover, it is difficult to assign the large number of closely spaced bands arising from even a medium size molecule. Hence, for reliable assignments of these bands, it is essential to calculate the normal modes theoretically and compare those with the experimental spectra. Over the last few decades, calculation of molecular spectra using quantum mechanics has become a common practice. There are many quantum mechanical‐based methods for calculation, of which density functional theory (DFT) is most popular as its computational cost is less without compromising significantly with the

190 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Here, we will introduce the basic theory behind these vibrational techniques. Also, the principle of DFT will be discussed in brief. We will provide references so that the interested

When a molecule is irradiated with a monochromatic light of wave number 0, a small fraction of the incident light will be scattered. In the scattered radiation, major portion of the light will have the same wave number as the incident light; however, a tiny fraction of light will have the wave number ′ = 0 ± . The first kind of scattering is called Rayleigh scattering while the latter is called Raman scattering. Classically, the phenomenon of Raman scattering can be

When a molecule is in an oscillating electric field () with angular frequency , an induced dipole will be created, Which in the linear approximation can be written (in complex notation)

where is the *polarizability tensor* and . Here, it is to be mentioned that as the molecule vibrates, the polarizability tensor gets modulated. Polarizability thus not only depends on frequency but also on the atomic positions. To describe the vibrational pattern, *normal coordinates* () are introduced. For a specific normal mode *k* (*k* = 1, 2, …, 3*N*‐6, where *N* is the total number of atoms in the molecule), all the atoms in the molecule will oscillate with

^ (1)

accuracy.

as,

readers can gain insights about these topics.

**2. Theoretical background**

explained in the following paragraphs.

**2.1. Raman scattering**

$$\mathbf{p}\_{\perp}(t) = \text{Re}[\hat{\alpha}\_{\perp}(\alpha\_{\perp}, 0)\underline{\mathbf{E}}(\alpha\_{\perp})\mathbf{e}^{-\alpha\_{\perp}t}] \tag{3}$$

is the oscillating dipole with frequency representing Rayleigh scattering,

$$\mathbf{p}\_s(t) = \frac{\underline{Q}\_\*^{\circ}}{2} \text{Re}[\hat{R}\_\*(a\boldsymbol{\nu}\_\iota)\underline{\mathbf{E}}(a\boldsymbol{\nu}\_\iota)\mathbf{e}^{-i(a\_\iota - a\_\iota) \times \iota \boldsymbol{\nu}}] \tag{4}$$

is oscillating with a frequency = − and produce Stokes Raman scattering,

$$\boldsymbol{\mathfrak{p}}\_{\boldsymbol{\omega}^{\boldsymbol{\phi}}}(t) = \frac{\underline{\mathbf{Q}}\_{\boldsymbol{\cdot}}^{\boldsymbol{0}}}{2} \text{Re}[\hat{\boldsymbol{R}}\_{\boldsymbol{s}}(\boldsymbol{\alpha}\_{\boldsymbol{\cdot}}) \underline{\mathbf{E}}(\boldsymbol{\alpha}\_{\boldsymbol{\cdot}}) \mathbf{e}^{-i(\boldsymbol{\alpha}\_{\boldsymbol{\cdot}} + \boldsymbol{\alpha}\_{\boldsymbol{\cdot}}) \boldsymbol{s} - \boldsymbol{\omega}}] \tag{5}$$

represents oscillating dipole with frequency = + and gives rise to anti‐Stokes Raman scattering. Here, () is called Raman tensor, 0 is the amplitude of oscillation of mode *k* and is an arbitrary phase.

Although classical approach could successfully explained the change in the frequency observed in the scattered radiation, it failed to account for the difference in the intensity observed in Stokes and anti‐Stokes Raman. Also, it could not give reasons for the *resonant Raman scattering* phenomenon. Thus, quantum mechanics is required to understand the Raman scattering. According to the quantum picture, when a molecule makes a transition from one state to another with different discrete energies, radiation is absorbed or emitted. To describe the scattering process, it is necessary to treat both the molecule and radiation quantum mechanically. Such a rigorous treatment can be avoided by considering *semi‐classical* approach, where the molecule is considered to be a quantum mechanical system, whereas the incident light can be considered as a perturbation to the energy level of the molecule. In this treatment,

scattering is viewed as transition probabilities between initial state of the molecule to the final state in the presence of perturbing incident light. It can be shown that for such a transition, a Raman polatizability component is given by [1, 2],

$$\alpha\_{\boldsymbol{\omega}} = \frac{1}{h} \sum\_{\boldsymbol{\cdot}, \boldsymbol{\cdot}, \boldsymbol{\cdot}} \left\{ \frac{\left\{ f \left| \boldsymbol{p}\_{\boldsymbol{\cdot}} \right| \boldsymbol{r} \right\} \left\{ r \left| \boldsymbol{p}\_{\boldsymbol{\cdot}} \right| \boldsymbol{i} \right\}}{\left\{ \boldsymbol{\alpha}\_{\boldsymbol{\cdot}} - \boldsymbol{\alpha}\_{\boldsymbol{\cdot}} - \boldsymbol{\alpha}\_{\boldsymbol{\cdot}} - \boldsymbol{\epsilon} \Gamma\_{\boldsymbol{\cdot}} \right\}} + \frac{\left\{ f \left| \boldsymbol{p}\_{\boldsymbol{\cdot}} \right| \boldsymbol{r} \right\} \left\{ r \left| \boldsymbol{p}\_{\boldsymbol{\cdot}} \right| \boldsymbol{i} \right\}}{\left\{ \boldsymbol{\alpha}\_{\boldsymbol{\cdot}} - \boldsymbol{\alpha}\_{\boldsymbol{\cdot}} + \boldsymbol{\alpha}\_{\boldsymbol{\cdot}} + \boldsymbol{\epsilon} \Gamma\_{\boldsymbol{\cdot}} \right\}} \right\} \tag{6}$$

where the sum is over all possible states of the molecule (except for the initial and final states), and called quantum dipole moment operators, ℏ( − ) is the energy difference between state and , and is inversely proportional to the lifetime of the state . As it can be seen from the expression, polarizability depends on the excitation frequency . Thus by choosing close to the frequency corresponding to the transition between two states, transition polarizability can be enormously increased, which is essentially the resonance Raman scattering. Quantum mechanics also successfully explained the difference observed in the intensity of Stokes and anti‐Stokes Raman.

Let us now consider the vibrational motion of a molecule consisting of *N* atoms. Since the motion of the electrons moves much faster than the nucleus, we can consider the motion of the nucleus separately. It can be shown [1] that potential energy of the nucleus can be approxi‐ mately expressed by,

$$\begin{aligned} V'' &= \frac{1}{2} \sum\_{i,j=1}^{3N} f\_{i,j} q\_i q\_j \\ f\_{i,j} &= \left( \frac{\partial^2 V''}{\partial q\_i \partial q\_j} \right)\_{q\_i, q\_j=0} \end{aligned} \tag{7}$$

where *qi* s are called *reduced mass coordinates*. The scalar terms , are called *force constants* represented as a real symmetric matrix called Hessian matrix . The dynamics of a molecule can be written as [1],

$$
\stackrel{\triangle}{F} \mathcal{A} = \stackrel{\triangle}{\alpha^2} \mathcal{A} \tag{8}
$$

where . For a particular mode, these quantities completely describe the dynam‐ ics of the system. These 3*N* normal modes form a complete system, any arbitrary pattern of the motion of the atoms can be expressed as a combination of these modes. In a molecule, there are 3*N*‐6 (3*N*‐5, for linear molecule) eigenvectors correspond to the *normal vibrational modes*. The atomic displacement can also be described by set of coordinates , called *normal coordi‐ nates*, defined as = . . For a single vibrational mode *k*, a single scalar can describe the atomic displacements.

#### **2.2. Infrared (IR) spectroscopy**

Like Raman spectroscopy, IR spectroscopy also involves the interaction of electromagnetic radiation with the molecule, but the nature of interaction is different. Here, the transition from a state *n* to *m* takes place as a result of absorption of photon. The process is mediated through the electric dipole moment operator , given by,

$$
\bigwedge\_{a} = \sum\_{a} e\_{a}.q\_{a} \tag{9}
$$

where is the effective charge on the atom and is the distance from the centre of gravity. It can be shown [3] that the transition probability is given by,

$$\left[\bigwedge\limits\_{q}\right] = \sum\_{k=1}^{3N-6} \hat{\boldsymbol{\mu}}\_{q}^{k} \left\langle \boldsymbol{\nu}\_{\boldsymbol{m}}^{\*} \left| \boldsymbol{Q}\_{k} \right| \boldsymbol{\nu}\_{\boldsymbol{n}} \right\rangle \tag{10}$$

where

,

¹

*kl*

a

the intensity of Stokes and anti‐Stokes Raman.

states), and

mately expressed by,

can be written as [1],

atomic displacements.

where *qi*

between state and , and

1 *kl lk*

*hii*

called quantum dipole moment operators, ℏ( −

www

= +

192 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

*r if riL r r f L r f p r rpi f p r rp i*

 ww


where the sum is over all possible states of the molecule (except for the initial and final

can be seen from the expression, polarizability depends on the excitation frequency . Thus by choosing close to the frequency corresponding to the transition between two states, transition polarizability can be enormously increased, which is essentially the resonance Raman scattering. Quantum mechanics also successfully explained the difference observed in

Let us now consider the vibrational motion of a molecule consisting of *N* atoms. Since the motion of the electrons moves much faster than the nucleus, we can consider the motion of the nucleus separately. It can be shown [1] that potential energy of the nucleus can be approxi‐

3

*V f qq*

å

*i j*

=

æ ö ¶ <sup>=</sup> ç ÷ ç ÷ ¶ ¶ è ø

1 2

*<sup>V</sup> <sup>f</sup>*

*<sup>N</sup> <sup>n</sup>*

=

,

*i j*

, , 1 2

*n*

*q q*

*i j q q*

represented as a real symmetric matrix called Hessian matrix . The dynamics of a molecule

where . For a particular mode, these quantities completely describe the dynam‐ ics of the system. These 3*N* normal modes form a complete system, any arbitrary pattern of the motion of the atoms can be expressed as a combination of these modes. In a molecule, there are 3*N*‐6 (3*N*‐5, for linear molecule) eigenvectors correspond to the *normal vibrational modes*. The atomic displacement can also be described by set of coordinates , called *normal coordi‐ nates*, defined as = . . For a single vibrational mode *k*, a single scalar can describe the

*ij i j*

, 0

=

s are called *reduced mass coordinates*. The scalar terms , are called *force constants*

^ (8)

*i j*

 w

î þ <sup>å</sup> (6)

is inversely proportional to the lifetime of the state . As it

) is the energy difference

(7)

$$
\hat{\boldsymbol{\mu}}\_{q}^{k} = \left(\frac{\partial \boldsymbol{\mu}\_{k}}{\partial \boldsymbol{Q}\_{k}}\right)\_{0} \tag{11}
$$

A particular mode *k* is IR active if both and \* are non‐zero.

#### **2.3. Density functional theory**

Over the past few decades, *density functional theory* has gain its popularity as computational tool in quantum chemistry because of its computational cost comparable to that of Hartree‐ Fock (HF) theory [4], yet accuracy similar to the computationally demanding post‐Hartree‐ Fock methods. Earlier attempts were made to express energy in terms of electron density alone [5–7]. The most successful attempt, suggested by Kohn and Sham [8], was to divide the kinetic energy into two parts. The major contribution is analogous to the HF kinetic energy, which can be calculated precisely, with a small contribution due to correlation. The main idea of Kohn‐ Sham theory is to calculate the kinetic energy by assuming a non‐interacting system. The missing kinetic energy term, existing in real system, is absorbed in a term called *exchange‐ correlation.* According to the Kohn‐Sham approach, the DFT energy can be written as

$$E\_{\rm DFT}[\rho] = T\_{\rm s}[\rho] + E\_{\rm w}[\rho] + J[\rho] + E\_{\rm w}[\rho] \tag{12}$$

In the above equation, the first term corresponds to kinetic energy of non‐interacting electrons, the second term denotes the nuclear‐electron attraction, the third represents Coulomb electron‐ electron repulsion, and the last term is called the exchange‐correlation. In Kohn‐Sham theory, the only approximation to be made is for the exchange‐correlation functional. Different DFT methods vary in the functional form of this exchange‐correlation energy. Kohn‐Sham approach is an independent particle model, similar to the HF theory, but simpler than many‐particle (correlation) wave function methods. Once proper exchange‐correlation functional has been chosen, the next job is to determine a set of orthogonal orbitals corresponding to the minimum energy. There are different types of exchange‐correlation functionals. *Local density approxima‐ tion* (LDA) [9–13] is the simplest exchange‐correlation functional, where the density is treated as a uniform electron gas, or slowly varying function at a given point. A better approximation is the *generalized gradient approximation* (GGA) [14–16] that apart from the density itself includes the first derivative of the density as a variable. Another popular type is hybrid functional that is a combination of DFT correlation and DFT and HF exchange [17, 18].

Molecular orbitals (MOs) are generally expressed in terms of basis set. Although it requires infinite functions to represent a MO, the basis sets used are finite for practical purpose. Two common types of orbitals used to form basis set are Slater type orbitals (STOs) [19] and Gaussian type orbitals (GTOs) [20]. Another computationally less costly basis set is contracted basis set [4]. Some examples are 3‐21G, 6‐31G, 6‐311G, etc. Polarization [21] and diffuse [22] functions can be added to each of these basis sets.

## **2.4. Geometry optimization**

The first step of any quantum chemical calculation is the geometry optimization of the molecule. In general, optimization is performed on an isolated molecule, considering non‐ interacting system in the gas phase. Initial structure is either taken from the literature or obtained from *empirical force field model*. Geometry optimization starts with solving the Kohn‐ Sham equation self‐consistently on the initial geometry. Energy and force on the molecule are calculated from the solution. If the force on the molecule is not zero, a different geometry is assumed. The process of finding a local minimum in the *potential energy surface* is achieved through the *conjugate gradient* [23] method.

#### **2.5. Frequency calculations**

Once the equilibrium atomic positions of the atoms are known, the electronic structure can be calculated on the optimized structure. The interaction of the atoms is now known, which enables to calculate force constants. Force constants can be calculated by displacing each atom from their equilibrium positions and recalculating the total energy of the deformed configu‐ ration. By numerical differentiation of the total energy, force constants on each atom can be calculated. This enables to construct Hessian matrix for the vibrational modes as described earlier. The frequency needs to be calculated at the same theoretical model and with same basis set as that used in the optimization procedure.

## **3. Applications of the combined study of vibrational spectroscopy and DFT for conformational analysis**

In the above equation, the first term corresponds to kinetic energy of non‐interacting electrons, the second term denotes the nuclear‐electron attraction, the third represents Coulomb electron‐ electron repulsion, and the last term is called the exchange‐correlation. In Kohn‐Sham theory, the only approximation to be made is for the exchange‐correlation functional. Different DFT methods vary in the functional form of this exchange‐correlation energy. Kohn‐Sham approach is an independent particle model, similar to the HF theory, but simpler than many‐particle (correlation) wave function methods. Once proper exchange‐correlation functional has been chosen, the next job is to determine a set of orthogonal orbitals corresponding to the minimum energy. There are different types of exchange‐correlation functionals. *Local density approxima‐ tion* (LDA) [9–13] is the simplest exchange‐correlation functional, where the density is treated as a uniform electron gas, or slowly varying function at a given point. A better approximation is the *generalized gradient approximation* (GGA) [14–16] that apart from the density itself includes the first derivative of the density as a variable. Another popular type is hybrid functional that

Molecular orbitals (MOs) are generally expressed in terms of basis set. Although it requires infinite functions to represent a MO, the basis sets used are finite for practical purpose. Two common types of orbitals used to form basis set are Slater type orbitals (STOs) [19] and Gaussian type orbitals (GTOs) [20]. Another computationally less costly basis set is contracted basis set [4]. Some examples are 3‐21G, 6‐31G, 6‐311G, etc. Polarization [21] and diffuse [22]

The first step of any quantum chemical calculation is the geometry optimization of the molecule. In general, optimization is performed on an isolated molecule, considering non‐ interacting system in the gas phase. Initial structure is either taken from the literature or obtained from *empirical force field model*. Geometry optimization starts with solving the Kohn‐ Sham equation self‐consistently on the initial geometry. Energy and force on the molecule are calculated from the solution. If the force on the molecule is not zero, a different geometry is assumed. The process of finding a local minimum in the *potential energy surface* is achieved

Once the equilibrium atomic positions of the atoms are known, the electronic structure can be calculated on the optimized structure. The interaction of the atoms is now known, which enables to calculate force constants. Force constants can be calculated by displacing each atom from their equilibrium positions and recalculating the total energy of the deformed configu‐ ration. By numerical differentiation of the total energy, force constants on each atom can be calculated. This enables to construct Hessian matrix for the vibrational modes as described earlier. The frequency needs to be calculated at the same theoretical model and with same basis

is a combination of DFT correlation and DFT and HF exchange [17, 18].

194 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

functions can be added to each of these basis sets.

through the *conjugate gradient* [23] method.

set as that used in the optimization procedure.

**2.4. Geometry optimization**

**2.5. Frequency calculations**

Conformational analysis of molecules is very important in chemistry, biochemistry and structural biology as it determines their functions. Intra‐ and inter‐molecular interactions play important role in determining structure of a molecule. Solvent has significant effect on the structure. The effect of solvent on structure of protein was studied by Zhu et al. [24] on a model tripeptide upon micro‐solvation. Doubly terminated tripeptide Z‐Aib‐Pro‐NHMe (Z = benzyloxycarbonyl), an important structure for many natural and synthetic peptides, was studied in solvent‐free gas phase and complexed with one‐ and two‐methanol molecules. There are two competing secondary structures present in the peptide as found in the literature. In the condensed phase, it prefers β‐turn structure, whereas in gas phase, γ‐turn structure is found. In this work, authors carried out IR study combined with the theoretical study of the peptide in the gas phase and in solvent. IR absorption of amide bands [25] and fingerprint region (<1500 cm‐1) was recorded. The DFT calculation was carried out at B3LYP/6‐311++G(d, p) level for different conformers. Amide bands are sensitive to the secondary structure of the protein and can be used as marker bands. The three amide bands namely amide I, II and III were used to determine the secondary structures of the peptides. It was shown that the model tripeptide in the unsolvated form and one‐methanol cluster prefers to form γ‐turn structure, whereas in the two‐methanol cluster, because of more H‐bonding interaction with the methanol, γ‐turn structure is favourable that is similar to the condensed phase. From the shift observed in the amide bands and the comparison of experimental spectrum with the theoretical one, it was also concluded that the methanol binding sites are the head and tail part of the tripeptide (see **Figure 1**).

Biological molecules remain in zwitterionic form naturally. Conformational analysis of these molecules is important as they are highly flexible, and their conformations determine H‐ bonding networks leading to the hydrophobic and hydrophilic interactions. Moreno et al. [26] have studied two amino acids, l‐Phenylalanine (l‐Phe) and l‐Tyrosine (l‐Tyr), by IR and Raman spectroscopy in the zwitterionic form to investigate their conformational preferences. For conformational analysis study, different conformers of zwitterionic forms were found by force field method. The DFT calculation was carried out with B3LYP and MO62X functionals together with 6‐31+G(d) and 6‐311++G(d,p) basis sets. The MO62X functional was found to be better for agreement with the experiment as it describes the non‐covalent interactions present in the zwitterionic form well. It was found that the low‐frequency region (30–500 cm‐1 region) contained rich information about different conformers. Comparing the calculated spectra of different conformers and the experimental spectra, contribution on spectra from different conformers could be identified. This study might help in understanding the folding mecha‐ nism of proteins.

Conformational preferences of two tripeptides, *N*‐acetyl‐Phe‐Pro‐NH2 and *N*‐acetyl‐Pro‐Phe‐ NH2, were studied by Chin et al. [27] in the gas phase with the help of IR spectroscopy and DFT. Modification of *N* and *C* termini helps in investigating the conformational preference of each residue isolated from the neighbouring residues. Initially, the lowest energy conforma‐ tions were found out by exploring the potential energy surface. Further, geometry optimization and vibrational frequency were carried out by DFT calculation at B3LYP/6‐31+G (d) level. The NH stretch region was found to be sensitive to the conformations and used as marker bands. Together with the DFT calculation, it was concluded that most of the conformation assumed repeated γ‐turn structure; however, only one conformation of *N*‐Ac‐Phe‐Pro‐NH2 took up β‐ turn structure. It was also observed that the conformation is dependent on the neighbouring residues of the Phe. In case of *N*‐acetyl‐Phe‐NH2 or *N*‐acetyl‐Phe‐Pro‐NH2, Phe favours β conformation while in case of *N*‐acetyl‐Pro‐ Phe‐NH2, it prefers γL conformation.

**Figure 1.** Comparison between theoretical and experimental mid‐IR spectra for peptide with (a) one or (b) two metha‐ nol. Reproduced from Ref 24 with permission of The Royal Society of Chemistry.

Nicotinic acid and its derivatives are subjects of intense study because of their biological activity and versatile bonding capability. The conformational and vibrational studies (Fourier transform (FT) IR and FT‐Raman) of two derivatives of nicotinic acids, 2‐bromonicotinic acid and 6‐bromonicotinic acids, were reported by Karabacak et al. [28]. The geometrical optimi‐ zation and vibrational wave numbers were calculated by DFT method using B3LYP as a functional and the 6‐311++G(d,p) as basis set. By varying the dihedral angle, energy of different conformations was calculated, and most stable conformation was found. Vibrational assign‐ ments were made based on the total energy distribution (TED) [29]. Raman activities calculated by Gaussian program [30] were converted to relative intensity [31]. The calculated and experimental vibrational spectra were compared. Disagreement between experimental and calculated spectra was ascribed to the neglect of inter‐molecular interaction present in solid samples as well as the neglect of anharmonicity present in real system. After applying proper scaling factor, calculated spectra resembled well with the experimentally obtained spectra. Dimer structures of the two derivatives and the presence of inter‐molecular H‐bonding between the pyridine *N* atom and O‐H group were also determined.

tions were found out by exploring the potential energy surface. Further, geometry optimization and vibrational frequency were carried out by DFT calculation at B3LYP/6‐31+G (d) level. The NH stretch region was found to be sensitive to the conformations and used as marker bands. Together with the DFT calculation, it was concluded that most of the conformation assumed repeated γ‐turn structure; however, only one conformation of *N*‐Ac‐Phe‐Pro‐NH2 took up β‐ turn structure. It was also observed that the conformation is dependent on the neighbouring residues of the Phe. In case of *N*‐acetyl‐Phe‐NH2 or *N*‐acetyl‐Phe‐Pro‐NH2, Phe favours β

**Figure 1.** Comparison between theoretical and experimental mid‐IR spectra for peptide with (a) one or (b) two metha‐

Nicotinic acid and its derivatives are subjects of intense study because of their biological activity and versatile bonding capability. The conformational and vibrational studies (Fourier transform (FT) IR and FT‐Raman) of two derivatives of nicotinic acids, 2‐bromonicotinic acid and 6‐bromonicotinic acids, were reported by Karabacak et al. [28]. The geometrical optimi‐

nol. Reproduced from Ref 24 with permission of The Royal Society of Chemistry.

conformation while in case of *N*‐acetyl‐Pro‐ Phe‐NH2, it prefers γL conformation.

196 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

The room temperature ionic liquids (ILs) have gained interest over last decade due to their potential applications. They are environment friendly because of their non‐volatility. Their high thermal stability and tuneable solvent property make them ideal candidates to use as reaction media for organic synthesis or as electrolytes in solar cell. To understand the relation between structure and function of these ILs, details structural and bonding data are required. In the absence of X‐ray structural data for the liquids, vibrational spectroscopic data can be helpful in gaining insights into their structures. Several imidazolium‐based ILs were studied by Katsyuba et al. [32] by vibrational spectroscopy along with the DFT calculations. The functional chosen for calculation was B3LYP with 6‐31G\* basis set. Multiple stable structures were found placing anions at different positions. It was shown that halide anions were able to occupy all the positions around the imidazolium ring, whereas perfluorinated anions prefer forward position. Vibrations of the cations depend upon the conformation as well as the interaction with the counterions. In the complex, only imidazolium C‐H group vibrations (stretching and out‐of‐plane vibrations) and perfluoroanions stretching vibrations are affected. Thus, the study could shed some light on the relationship between the structure, vibrations and melting point of ILs.

In another study by the same group [33], combination of vibrational spectroscopy with theoretical calculation was used to quantitatively characterize the strength of H‐bonding in ILs. DFT calculation was carried out by B3LYP functional with 6‐31G\*\* basis set. Since B3LYP functional does not take into account the van der Waals dispersion forces, dispersion‐corrected energy was calculated using DFT‐D3 [34] along with Becke‐Johnson damping function [35]. It was found that various interactions affect the structure and vibrational spectra. These inter‐ actions led to the blue shift of the CH group stretching vibration. This study could help in understanding the role of H‐bonding in ILs, which would help in synthesis of ILs of desired physical and chemical properties.

The spectroscopic distinction of bis(trifluoromethanesulphonyl)imide anion (TFSI‐ ) was carried out by Herstedt et al. [36]. The TFSI‐ anion can exist in two conformational states, a tronsoid form of C2 symmetry and a cisoid form of C1 symmetry. In this work, the effect on Raman and IR spectroscopy due to conformation was investigated with the help of theoretical calculation. DFT calculations were performed at B3LYP/6‐31G\*\* level. It was shown that even the effect of conformation on the vibrational spectra was subtle, still it was possible to distinguish TFSI‐ conformational isomerism. In IR spectroscopy, the regions 130–1380 and 480–60 cm‐1 were found to be sensitive to the conformational state. It was also possible to distinguish the change due to conformational state from that due to ionic interactions. The ratio of the two conformers in solution was found by measuring IR bands at 602 or 656 (for cisoid, C1) and 618 cm‐1 (for transoid, C2). In Raman spectra, the marker bands were found at 629 (for transoid) and 653 cm‐1 (for cisoid).

**Figure 2.** Optimized geometries of the zinc complexes of 4‐MeIm in different protonation states. Reprinted with per‐ mission from The Journal of Physical Chemistry A, vol. 106, pp.3377–3390. Copyright 2012 American Chemical Society [39].

The alkaloids that are mainly found in plants, and to a lesser quantity in animals, have been studied by ATR‐IR and FT‐Raman spectroscopy for fast, reliable detection in pharmaceutical products. One such candidate in the group, morphine, was studied by Baranska and Kaczor [37]. For theoretical study, potential energy scanning (PES) was performed to find the mini‐ mum energy conformations. Subsequently, geometry optimizations and frequency calcula‐ tions were carried out on these conformers. It was found that IR spectroscopy could help in monitoring the arrangement of hydroxyl group of the morphine molecule while Raman is not very sensitive to these changes. Chemical modifications of perfluoropolymers were studied using spectroscopic method and quantum calculation by Radice et al. [38]. In the IR absorption spectra, carbonyl stretching region was found to be sensitive to the different polymer degra‐ dation pathways.

distinguish TFSI‐

[39].

629 (for transoid) and 653 cm‐1 (for cisoid).

conformational isomerism. In IR spectroscopy, the regions 130–1380 and

480–60 cm‐1 were found to be sensitive to the conformational state. It was also possible to distinguish the change due to conformational state from that due to ionic interactions. The ratio of the two conformers in solution was found by measuring IR bands at 602 or 656 (for cisoid, C1) and 618 cm‐1 (for transoid, C2). In Raman spectra, the marker bands were found at

198 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 2.** Optimized geometries of the zinc complexes of 4‐MeIm in different protonation states. Reprinted with per‐ mission from The Journal of Physical Chemistry A, vol. 106, pp.3377–3390. Copyright 2012 American Chemical Society

The alkaloids that are mainly found in plants, and to a lesser quantity in animals, have been studied by ATR‐IR and FT‐Raman spectroscopy for fast, reliable detection in pharmaceutical Metal plays an important role in determining the structure and properties of molecules. Several authors investigated metal‐molecule interactions using vibrational spectroscopy. When metal binds to the molecule, few peaks change considerably and those peaks can be used as marker bands to determine its coordination and protonation state. Hasegawa et al. [39] studied different protonated and metal‐bound forms of 4‐methylimidazole (4‐MeIm) vibrational spectroscopy in conjunction with theoretical calculations. The N‐H stretching frequencies were seen to be downshifted by ∼50 cm‐1 on complexation with Zn while CH stretching vibration showed upshifts. The CC and CN stretching showed complicated behaviour in the Zn‐bound form as these vibrations are coupled with other vibrations, and upon metal binding, some of the coupling changed. From these changes, together with theoretical study, the different metal‐ bound forms of the histidine could be identified (see **Figure 2**).

**Figure 3.** A comparison between experimental and calculated Raman spectrum. Reprinted from Journal of Molecular Structure, vol. 1102, Kundu *et al.*, Raman, IR and DFT studies of mechanism of sodium binding to urea catalyst, pp 267‐274, Copyright (2015), with permission from Elsevier [41].

A bis‐camphorsulphonyl was synthesized as a hydrogen‐bonding catalyst [40]. It was found that the enantioselectivity capability of the catalyst is poor. However, when it was complexed with sodium ion, the selectivity of the catalyst increased significantly. The X‐ray crystallo‐ graphic structure showed that the native conformation of the catalyst is unfavourable for enantioselectivity. The X‐ray data for the complex form could not be obtained as it was not soluble in most of the organic solvents, and thus crystal could not be formed. Since vibrational spectroscopy does not require crystalline samples, we were interested to probe the structure of the catalyst in its free and sodium‐bound form by vibrational spectroscopy, both experi‐ mentally and theoretically [41]. For DFT calculations, we have chosen B3LYP/6‐31G (d,p) level. To include the inter‐molecular interaction present in the solid form, we considered dimer structure of the catalyst for frequency calculation. A comparison between calculated Raman spectrum and experimentally obtained one is shown in **Figure 3**. To study the effect of sodium

**Figure 4.** Optimized structure of urea catalyst in (a) free and (b) Na‐bound form. Colour representation: white–hydro‐ gen, red–oxygen, grey–carbon, blue–nitrogen, violet–sodium, yellow–sulphur. Reprinted from Journal of Molecular Structure, vol. 1102, Kundu *et al.*, Raman, IR and DFT studies of mechanism of sodium binding to urea catalyst, pp 267‐ 274, Copyright (2015), with permission from Elsevier [41].

ion, we have compared the monomer form of the catalyst and its complex (see **Figure 4**). In our predicted structure, we considered two sodium forming bond with the oxygen atoms of the urea carbonyl and sulphonyl groups. The shift of stretching frequency of carbonyl, sulphonyl, C‐N and N‐H frequencies observed experimentally could be qualitatively repro‐ duced in the theoretical calculation. The study showed how in the absence of any X‐ray data, vibrational spectroscopy together with theoretical study was helpful in predicting the confor‐ mation of the catalyst in complex form (see **Figure 5**).

**Figure 5.** Experimental IR spectra of urea catalyst, NaBPh4 and complex showing the changes in the spectrum of cata‐ lyst upon sodium binding. Reprinted from Journal of Molecular Structure, vol. 1102, Kundu *et al.*, Raman, IR and DFT studies of mechanism of sodium binding to urea catalyst, pp 267–274, Copyright (2015), with permission from Elsevier [41].

## **4. Conclusions**

A bis‐camphorsulphonyl was synthesized as a hydrogen‐bonding catalyst [40]. It was found that the enantioselectivity capability of the catalyst is poor. However, when it was complexed with sodium ion, the selectivity of the catalyst increased significantly. The X‐ray crystallo‐ graphic structure showed that the native conformation of the catalyst is unfavourable for enantioselectivity. The X‐ray data for the complex form could not be obtained as it was not soluble in most of the organic solvents, and thus crystal could not be formed. Since vibrational spectroscopy does not require crystalline samples, we were interested to probe the structure of the catalyst in its free and sodium‐bound form by vibrational spectroscopy, both experi‐ mentally and theoretically [41]. For DFT calculations, we have chosen B3LYP/6‐31G (d,p) level. To include the inter‐molecular interaction present in the solid form, we considered dimer structure of the catalyst for frequency calculation. A comparison between calculated Raman spectrum and experimentally obtained one is shown in **Figure 3**. To study the effect of sodium

200 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 4.** Optimized structure of urea catalyst in (a) free and (b) Na‐bound form. Colour representation: white–hydro‐ gen, red–oxygen, grey–carbon, blue–nitrogen, violet–sodium, yellow–sulphur. Reprinted from Journal of Molecular Structure, vol. 1102, Kundu *et al.*, Raman, IR and DFT studies of mechanism of sodium binding to urea catalyst, pp 267‐

274, Copyright (2015), with permission from Elsevier [41].

In conclusion, in this chapter, we discuss two complementary vibrational techniques, Raman and IR. We give brief theoretical background for this technique. We also discuss about density functional theory, widely used to predict the spectrum of a molecule and help in assigning the bands. Then, we discuss the use of the combination of these two techniques in different molecular systems. We hope this will give the readers an idea of the potential of these techni‐ ques for various conformational analyses.

## **Author details**

Partha P. Kundu1 and Chandrabhas Narayana2\*

\*Address all correspondence to: cbhas@jncasr.ac.in

1 Department of Physics, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India

2 Light Scattering Laboratory, Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka, India

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Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

#### **Geometric and Electronic Properties of Porphyrin and its Derivatives Geometric and Electronic Properties of Porphyrin and its Derivatives**

Metin Aydin and Daniel L. Akins Metin Aydin and Daniel L. Akins

Additional information is available at the end of the chapter

Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/64583

#### **Abstract**

206 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

In this chapter, we discuss protonation and substitution effects on the absorption spectra of porphyrin molecules based on density functional theory (DFT) and time-dependent DFT calculations. The results of the calculations are compared with experimental data. The calculations show that protonation of core nitrogen atoms of porphyrin and *meso*substituted porphyrins produces a substantial shift in Soret and Q-absorption bands, relative to their positions in corresponding nonprotonated and nonsubstituted chromophores. A relaxed potential energy surface (RPES) scan has been utilized to calculate ground and excited state potential energy surface (PES) curves as functions of the rotation of one of the *meso*-substituted sulfonatophenyl groups about dihedral angles *θ* (corresponding to Cα─Cm─Cϕ─C) ranging from 40 to 130°, using 10° increments. The ground state RPES curve indicates that when the molecule transitions from the lowest ground state to a local state, the calculated highest potential energy barrier at the dihedral angle of 90° is only 177 cm−1. This finding suggests that the *meso*sulfonatophenyl substitution groups are able to rotate around Cm─Cϕ bond at room temperature because the thermal energy (*kBT*) at 298 K is 207.2 cm−1. Furthermore, the calculations show that the geometric structure of the porphyrin is strongly dependent on protonation and the nature of the *meso*-substituted functional groups.

**Keywords:** porphyrins, protonation, absorption, PES, DFT calculation

## **1. Introduction: overview of molecular spectroscopy and quantum calculations**

Spectroscopy is the branch of science dealing with the interaction of electromagnetic and other forms of radiated energy with matter. The earliest prospect of making spectroscopic

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

measurements came with the observation that visible light can be dispersed by an optical prism, and the concomitant recognition that matter could be intimately investigated through its response to optical radiative energy as a function of frequency, defining what is referred to as optical spectroscopy. As it turns out, optical spectroscopy is a useful approach for both qualitative and quantitative studies of physical and chemical processes involving matter in most of its states by measurement of absorption, emission, or scattering of electromagnetic radiation; moreover, optical spectroscopic measurements can be very sensitive, nondestructive, and typically require only small amounts of material for analysis.

Absorption spectra are usually acquired for analytes dissolved in nonabsorbing solvents. And, ideally the absorbance of a dissolved analyte depends linearly on concentration, thereby resulting in an absorption spectrum providing quantitative measurement of the analyte's concentration in solution, arrived at by applying the Beer-Lambert Law. In particular, since absorption spectra of molecules depend on their energy level structure, absorption spectra are not only useful for identifying isolated molecules, but also can be used to probe intermolecular interactions (e.g., effects of aggregation) that affect energy level structure.

It is to be noted that molecules that are excited to higher energy than the lowest excited state above the ground electronic state can relax to lower excited levels by a range of intrinsic processes. Included among such deactivation processes are emission of radiation, more popularly referred to as luminescence, as well as processes that are nonradiative in nature, where lower energy states can be directly populated without the emission of photons. Luminescence from such intermediate states can be defined as fluorescence or phosphorescence, where fluorescence is a process by which electronically excited molecules return to a lower electronic state of the same spin multiplicity (which is often the electronic ground state) by emitting a photon; phosphorescence, on the other hand, is the corresponding transition between states with different spin multiplicities. While fluorescence is a spin-allowed process and generally occurs rapidly, phosphorescence is spin forbidden and is typically a slower relaxation process.

Paths by which nonradiative relaxation can occur include, but are not limited to, such phenomena as collisional energy transfer, electron or proton transfer processes, change of molecular conformation, photochemistry, formation of excited state complexes (e.g., excimers or exciplexes), as well as the classic processes of internal conversion (IC) (e.g., vibrational relaxation) and intersystem crossing (ISC) (e.g., singlet-triplet conversion).

It is to be noted that transient intermediates are likely to form during IC and ISC radiationless processes, and detection of such species, if at all possible, often necessitates the use of highly sensitive ultrafast optical (or other) techniques.

The aforementioned phenomena are depicted more fully in **Figure 1** that shows a combined Perrin-Jablonski diagram illustrating the different processes involved in the interaction of a molecule with photons in the spectral region between 300 and 1500 nm. Photophysical processes for an isolated molecule would occur via transitions between the different internal energy states shown in **Figure 1**.

measurements came with the observation that visible light can be dispersed by an optical prism, and the concomitant recognition that matter could be intimately investigated through its response to optical radiative energy as a function of frequency, defining what is referred to as optical spectroscopy. As it turns out, optical spectroscopy is a useful approach for both qualitative and quantitative studies of physical and chemical processes involving matter in most of its states by measurement of absorption, emission, or scattering of electromagnetic radiation; moreover, optical spectroscopic measurements can be very sensitive, nondestruc-

Absorption spectra are usually acquired for analytes dissolved in nonabsorbing solvents. And, ideally the absorbance of a dissolved analyte depends linearly on concentration, thereby resulting in an absorption spectrum providing quantitative measurement of the analyte's concentration in solution, arrived at by applying the Beer-Lambert Law. In particular, since absorption spectra of molecules depend on their energy level structure, absorption spectra are not only useful for identifying isolated molecules, but also can be used to probe intermolecular

It is to be noted that molecules that are excited to higher energy than the lowest excited state above the ground electronic state can relax to lower excited levels by a range of intrinsic processes. Included among such deactivation processes are emission of radiation, more popularly referred to as luminescence, as well as processes that are nonradiative in nature, where lower energy states can be directly populated without the emission of photons. Luminescence from such intermediate states can be defined as fluorescence or phosphorescence, where fluorescence is a process by which electronically excited molecules return to a lower electronic state of the same spin multiplicity (which is often the electronic ground state) by emitting a photon; phosphorescence, on the other hand, is the corresponding transition between states with different spin multiplicities. While fluorescence is a spin-allowed process and generally occurs rapidly, phosphorescence is spin forbidden and is typically a slower

Paths by which nonradiative relaxation can occur include, but are not limited to, such phenomena as collisional energy transfer, electron or proton transfer processes, change of molecular conformation, photochemistry, formation of excited state complexes (e.g., excimers or exciplexes), as well as the classic processes of internal conversion (IC) (e.g., vibrational

It is to be noted that transient intermediates are likely to form during IC and ISC radiationless processes, and detection of such species, if at all possible, often necessitates the use of highly

The aforementioned phenomena are depicted more fully in **Figure 1** that shows a combined Perrin-Jablonski diagram illustrating the different processes involved in the interaction of a molecule with photons in the spectral region between 300 and 1500 nm. Photophysical processes for an isolated molecule would occur via transitions between the different internal

relaxation) and intersystem crossing (ISC) (e.g., singlet-triplet conversion).

sensitive ultrafast optical (or other) techniques.

energy states shown in **Figure 1**.

tive, and typically require only small amounts of material for analysis.

208 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

interactions (e.g., effects of aggregation) that affect energy level structure.

relaxation process.

**Figure 1.** A general Perrin-Jablonski diagram, where S and T stand for singlet and triplet electronic states, respectively. IC and ISC represent "internal conversion" and "intersystem crossing," respectively.

Using **Figure 1** for discussion, in the gaseous or solution phase at room temperature a molecular system is generally in its ground state (S0). The transition from the ground state to an upper vibroelectronic state by absorption of a photon would take place within ca. 10−15 s, which is much faster than the emission of the photon from an excited electronic state (*Sk* >1) to its ground state (ca. 10−8 s). As suggested earlier, all of the excited molecules might not directly return to their ground state by emission of radiation (*Sk* > 0 → S0 + *hν*), but some may return by internal conversion (IC). For example, when a molecule is excited to an upper vibroelectronic state (*Sk* > 1), it could undergo relaxation to the first excited singlet level S1 (in 10-12 s) by way of vibrational coupling between these states before undergoing additional vibrational relaxation and returning to the lowest singlet electronic energy level (as per Kasha's Rule). As illustrated in **Figure 1**, another possible pathway is that a molecule in the first excited singlet level *S*1 may undergo a transition to a triplet state by ISC, which can relax to the lowest triplet state (T1) via vibrational relaxation and IC processes. The molecule can then return to its ground state through phosphorescence. There is also the possibility of a transition from T1 to S1 followed by the transition to S0 by emitting a photon. This latter path is not shown in **Figure 1**.

During the past two decades, there has been very intense theoretical research on the physical and chemical properties of molecular structures. Computational chemistry is a powerful tool for investigation of molecules, surfaces, and interfaces at the electronic structure level. Various molecular properties directly comparable with experiment such as structural parameters, thermodynamic data, and vibrational spectra can be obtained by solving quantum mechanical equations. When the result of a theoretical prediction is consistent with an experimental measurement, one can more confidently interpret the experimental result. Computational studies are not only carried out in order to provide an understanding of experimental data, such as the position and source of spectroscopic peaks, but also can be used to predict the existence of unobserved molecules, intermediates, or to explore reaction mechanisms that are not readily studied experimentally.

The particular computational method chosen depends critically on the desired accuracy (qualitative vs. quantitative) sought, the size of the system, and available computational capacities. At a qualitative level, especially for large systems, molecules can be treated by classical mechanics using a class of methods called molecular mechanics. The structure of a protein containing hundreds of atoms might be calculated this way. Somewhat more quantitatively accurate are the semiempirical methods. These methods (such as PM3) use experimentally measured parameters that approximate parts of a quantum mechanical system. These latter methods can be fast, and give good results if the molecule of interest is very similar to those used to determine the parameters. However, many molecules of interest (i.e., transition metal complexes) do not have sufficiently good parameter sets to be accurately calculated using such methods. *Ab initio* methods, however, do not assume experimental parameters, but instead attempt to calculate the molecular wave functions directly using a variety of approximation techniques. These methods, such as Hartree-Fock (HF) and MP2, can be very accurate for some observable phenomena, but can also be computationally expensive. HF with a midlevel basis set will often be used as a good starting point for more accurate calculations, or as a relatively fast way of getting qualitative data.

The fourth type of computational methods are the density functional theory (DFT) methods. With a few exceptions, DFT is the most cost-effective method to achieve a given level of quantitative accuracy. It incorporates electron correlation and is computationally less expense.

In addition to choosing a method, one must also choose a basis set. A basis set is a set of functions that substitute for the "real" atomic orbitals (AOs) of a system and should approximate the real wave functions well enough to give chemically meaningful and close approximations to the correct values of measurable quantities being considered (e.g., geometry and energy). Using more complex basis sets improves results at the cost of increased computer time to make a calculation (i.e., increased computational expense). Basis sets, in order to allow electron-electron correlation to be taken into account, must incorporate polarization terms to allow distortions in orbital shapes; they must also incorporate diffuse functions (especially necessary when you have a molecule with weakly bound electrons) (as in the case of some anions and for some transition states); and they must account for relativistic effects (for heavier atoms).

In this chapter, we will discuss protonation and *meso*-substitution effects on geometric and electronic structures of the porphyrin macrocycle based on quantum chemical methods. This chapter is also a sister publication for an accompanying article in another chapter of the present book entitled "Infrared and Raman Spectroscopic Characterization of Porphyrin and its Derivatives." Details about the calculations that we have made are provided in Section 4.

## **2. Porphyrin macrocycle**

equations. When the result of a theoretical prediction is consistent with an experimental measurement, one can more confidently interpret the experimental result. Computational studies are not only carried out in order to provide an understanding of experimental data, such as the position and source of spectroscopic peaks, but also can be used to predict the existence of unobserved molecules, intermediates, or to explore reaction mechanisms that are

210 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

The particular computational method chosen depends critically on the desired accuracy (qualitative vs. quantitative) sought, the size of the system, and available computational capacities. At a qualitative level, especially for large systems, molecules can be treated by classical mechanics using a class of methods called molecular mechanics. The structure of a protein containing hundreds of atoms might be calculated this way. Somewhat more quantitatively accurate are the semiempirical methods. These methods (such as PM3) use experimentally measured parameters that approximate parts of a quantum mechanical system. These latter methods can be fast, and give good results if the molecule of interest is very similar to those used to determine the parameters. However, many molecules of interest (i.e., transition metal complexes) do not have sufficiently good parameter sets to be accurately calculated using such methods. *Ab initio* methods, however, do not assume experimental parameters, but instead attempt to calculate the molecular wave functions directly using a variety of approximation techniques. These methods, such as Hartree-Fock (HF) and MP2, can be very accurate for some observable phenomena, but can also be computationally expensive. HF with a midlevel basis set will often be used as a good starting point for more accurate calculations, or as

The fourth type of computational methods are the density functional theory (DFT) methods. With a few exceptions, DFT is the most cost-effective method to achieve a given level of quantitative accuracy. It incorporates electron correlation and is computationally less expense.

In addition to choosing a method, one must also choose a basis set. A basis set is a set of functions that substitute for the "real" atomic orbitals (AOs) of a system and should approximate the real wave functions well enough to give chemically meaningful and close approximations to the correct values of measurable quantities being considered (e.g., geometry and energy). Using more complex basis sets improves results at the cost of increased computer time to make a calculation (i.e., increased computational expense). Basis sets, in order to allow electron-electron correlation to be taken into account, must incorporate polarization terms to allow distortions in orbital shapes; they must also incorporate diffuse functions (especially necessary when you have a molecule with weakly bound electrons) (as in the case of some anions and for some transition states); and they must account for relativistic effects (for heavier

In this chapter, we will discuss protonation and *meso*-substitution effects on geometric and electronic structures of the porphyrin macrocycle based on quantum chemical methods. This chapter is also a sister publication for an accompanying article in another chapter of the present book entitled "Infrared and Raman Spectroscopic Characterization of Porphyrin and its Derivatives." Details about the calculations that we have made are provided in Section 4.

not readily studied experimentally.

a relatively fast way of getting qualitative data.

atoms).

Porphyrin and its derivatives have received extensive attention from both experimentalists and theoreticians since they have been found to have many important potential applications in a broad variety of high technology and biomedical fields. Indeed, in recent years analyses of geometric and spectroscopic properties of molecular systems incorporating porphyrins have produced a substantial body of information that has greatly expanded our knowledge of high efficiency utilization of solar energy [1–5] and the use of such synthetic molecular analogs as active agents in molecular electronic devices [6, 7]. Also, a great deal of interest has been shown for the use of porphyrin-like molecular systems as therapeutic drugs and photosensitizers in photodynamic therapy of cancer [8] and their possible use in the treatment of nonmalignant conditions such as psoriasis, treatment of blocked arteries, and for the treatment of pathological and bacterial viruses [9] and HIV [10]. The biological importance of porphyrins essentially derives from their physicochemical properties that basically determine their photophysical behavior. Additionally, aggregation and axial ligation lead to significant changes in absorption spectra as well as quantum yield, fluorescence lifetime, and triplet state lifetime [11–13]. More detailed information about porphyrins can be obtained in the *Handbook of Porphyrin Science* [14, 15].

Of particular note is the observation that optical properties of porphyrin can be altered by the protonation or metallation of nitrogen atoms in its core structure, with electronic changes as a result of structural alterations such as flattening and distortion from planarity of the macrocycle, interactions between porphyrins (aggregation), redox reactions, and solvent effects. A few porphyrins have been found to form aggregates; a requirement of being zwitterionic character upon protonation of macrocycle core nitrogen atoms. It has also been suggested that aggregation is facilitated by interaction with proteins [16, 17] and surfactants [18].

Indeed, aggregation of the anionic porphyrin *meso*-tetrakis(*p*-sulfonatophenyl)porphyrin (TSPP) has been discussed extensively [9, 19–21]. The electronic absorption spectrum of monomeric TSPP at neutral pH exhibits multiple electronic transition bands with an intense peak maximum at about 410 nm and several weak transitions in the region of 500 to 700 nm in aqueous solutions. The intense transition at 410 nm is known as Soret or B-band, and the weaker bands are termed Q-bands. In very acidic medium, the TSPP becomes protonated, and one finds that highly ordered molecular aggregates are formed. While the protonated TSPP (i.e., H4TSPP) shows a strong absorbance peak at around 430 nm (Soret band) along with the weak bands in the Q-bands region, the aggregated-H4TSPP spectrum displays a Soret band at about 490 nm [21] and difference Q-type bands at longer wavelengths.

The developments in computing facilities and the sophisticated computation programs, with increasingly efficient algorithms, especially the fundamental improvements in the treatment of electron correlation based on density-functional theory (DFT) [22], have combined to allow quantum chemical methods to routinely handle molecular systems containing hundreds of atoms. As a result, DFT has become one of the most important techniques used by theoreticians to provide deep insight into spectroscopic and structural properties, even for complex molecular systems, especially those of large sizes such as the porphyrinoids [23–28].

In this chapter, we discuss the effect of *meso*-substitution groups and protonation of the N atoms at the core (of parent-porphine or porphyrin macrocycle) of its geometric and electronic structures. The density functional theory (DFT) and time-dependent DFT (TD-DFT) have been employed to calculate the geometric structures and electronic transition energies of porphyrin and derivatives in water used as solvent. The compounds studied here are unsubstituted porphyrin (free-base porphin, FBP), *meso*-tetraphenylporphyrin (TPP), *meso*-tetrakis(*p*sulfonatophenyl)porphyrin (TSPP), protonated-FBP (H4FBP), deuterated-H4FBP (D4FBP), protonated-TPP (H4TPP or dicationic TPP), deuterated-H4TPP (D4TPP), protonated-TSPP (H4TSPP or dianionic-TSPP), deuterated-H4TSPP (D4TSPP),dicationic TSPP (H8TSPP), and deuterated-H8TSPP (D8TSPP). The possible internal conversion (IC) and intersystem crossing (ISC) processes for the porphyrin and derivatives are also discussed based on the results of the TD-DFT calculations. Furthermore, the relaxed potential energy surface scans were employed to study the minimum potential energy pathways for the ground and excited states of the TSPP molecule as a function of rotation Cm─Cϕ bond (or dihedral angle (Cα─Cm─Cϕ─C(ph)). We would like to point out that the calculated and experimental data are taken from our prior work [29].

## **3. Structures of porphyrin and its derivatives**

DFT theory at the B3LYP/6-311G(d,p) level was performed to predict the geometric parameters of the ground state of the parent porphyrin and its derivatives in water used as a solvent. The

**Figure 2.** Optimized geometric structures of unsubstituted porphyrin (FBP), *meso*-tetraphenylporphyrin (TPP), anionic *meso*-tetrakis(*p*-sulfonatophenyl)porphyrin (TSPP), and their protonated derivatives (H4FBP, H4TPP, H4TSPP, and H8TSPP) in water at the B3LYP/6-311G(d,p) level of DFT.

optimized ground state geometry of these compounds is provided in **Figure 2**. The selected bond angles and dihedral angles are given in **Table 1**. Results of the calculations show that while the *meso* substitution of porphyrin with tetraphenyl or tetrasulfonatophenyl brings about slight out-of-plane distortion from the planar structure of the macrocycle within 3–5° for both TPP and TSPP, the protonation of the porphyrin core gives rise to a substantial distortion from planarity ranging from 10 to 20° for H4FBP, H4TPP, H4TSPP, and H8TSPP, principally due to repulsive interactions between the H atoms bonded to core N atoms. Moreover, with reference to the average plane of the macrocycle (**Figure 2** and **Table 1**), the peripheral phenyl and sulfonatophenyl substituents are tilted by an angle of about 72° for the nonprotonated structures TPP and TSPP, and about 48° for protonated H4TPP, H4TSPP, and H8TSPP. Rotation of the *meso* substituents is attributed to repulsive interactions between H atoms on Cβ and C in phenyl, as well electron correlation effect.

to provide deep insight into spectroscopic and structural properties, even for complex

In this chapter, we discuss the effect of *meso*-substitution groups and protonation of the N atoms at the core (of parent-porphine or porphyrin macrocycle) of its geometric and electronic structures. The density functional theory (DFT) and time-dependent DFT (TD-DFT) have been employed to calculate the geometric structures and electronic transition energies of porphyrin and derivatives in water used as solvent. The compounds studied here are unsubstituted porphyrin (free-base porphin, FBP), *meso*-tetraphenylporphyrin (TPP), *meso*-tetrakis(*p*sulfonatophenyl)porphyrin (TSPP), protonated-FBP (H4FBP), deuterated-H4FBP (D4FBP), protonated-TPP (H4TPP or dicationic TPP), deuterated-H4TPP (D4TPP), protonated-TSPP (H4TSPP or dianionic-TSPP), deuterated-H4TSPP (D4TSPP),dicationic TSPP (H8TSPP), and deuterated-H8TSPP (D8TSPP). The possible internal conversion (IC) and intersystem crossing (ISC) processes for the porphyrin and derivatives are also discussed based on the results of the TD-DFT calculations. Furthermore, the relaxed potential energy surface scans were employed to study the minimum potential energy pathways for the ground and excited states of the TSPP molecule as a function of rotation Cm─Cϕ bond (or dihedral angle (Cα─Cm─Cϕ─C(ph)). We would like to point out that the calculated and experimental data are taken from our prior

DFT theory at the B3LYP/6-311G(d,p) level was performed to predict the geometric parameters of the ground state of the parent porphyrin and its derivatives in water used as a solvent. The

**Figure 2.** Optimized geometric structures of unsubstituted porphyrin (FBP), *meso*-tetraphenylporphyrin (TPP), anionic *meso*-tetrakis(*p*-sulfonatophenyl)porphyrin (TSPP), and their protonated derivatives (H4FBP, H4TPP, H4TSPP, and

molecular systems, especially those of large sizes such as the porphyrinoids [23–28].

212 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

work [29].

**3. Structures of porphyrin and its derivatives**

H8TSPP) in water at the B3LYP/6-311G(d,p) level of DFT.


**Table 1.** Comparison of selected dihedral angles (*D*) and bond angles (*A*) of the parent porphyrin and its derivatives: unsubstituted porphyrin (FBP), *meso*-tetraphenylporphyrin (TPP), and anionic *meso*-tetrakis(*p*-sulfonatophenyl) porphyrin (TSPP) with their protonated structures (H4FBP, H4TPP, H4TSPP and H8TSPP), calculated in water as solvent at the B3LYP/6-311G(d,p) level of DFT.

It is ascertained that the calculated bond lengths are consistent with X-ray data within ca. ± 0.01 Å. Hence, one can conclude that protonation of the porphyrin core, in addition to causing deviation from planarity of the macrocycle, also simply has an effect on the tilt angles of the phenyl and *p*-sulfonatophenyl substituent groups.

In Section 3.1, protonation and *meso* substitution of the porphyrin macrocycle is found to not only affect the geometric structure, but also, due to the change in molecular symmetry, lead to significant changes in electronic band positions as well as the number of bands.

#### **3.1. Calculated electronic spectra of porphyrin and its derivatives**

Porphyrin and its derivatives find use in a myriad of important natural and biomimetic processes, with the major focus in the latter case on processes such as conversion of solar energy into chemical energy, photodynamic therapy, and as active agents in optical sensors. The excited states of porphyrins play fundamental roles in essentially all processes involving porphyrin and its derivatives.

In this section, we discuss the *meso* substitution and protonation effects on the electronic energy levels of the porphyrin macrocycle. Up to 24 singlet and 24 triplet energy levels of porphyrins have been calculated in water used as solvent at the TD-B3LYP/6-31G(d,p) level; singlet-singlet absorption spectra have been calculated for these specific compounds and are provided in **Figure 3**.

**Figure 3.** Comparison of calculated dipole-allowed electronic transitions of the parent porphyrin (FBP), *meso*-tetraphenylporphyrin (TPP), dianionic *meso*-tetrakis(*p*-sulfonatophenyl)porphyrin (TSPP), protonated-FBP (H4FBP), protonated-TPP (H4TPP), protonated TSPP (H4TSPP), and dicationic-TSPP (H8TSPP). The calculations were carried out in water used as a solvent at the TD-B3LYP/6-31G(d,p) level of TD-DFT.

The calculations mainly produce a strong electronic absorption band in the 360–450 nm range and a few weak or very weak electronic transitions below as well as above the strong bands (**Figure 3**). The strongest band is known as the Soret band (also referred to as the B-band), and weaker bands at longer wavelength, in the range 500–750 nm, are known as Q-bands that are usually quite weak. The results of calculations indicate that (1) the electronic bands in the parent porphyrin (FBP, neutral) are slightly blue-shifted in diprotonated-FBP (H4FBP, dicationic) structure; (2) the bands in neutral TPP molecule (*meso*-phenyl substituted porphyrin) become significantly red-shifted in the dicationic or diprotonated-TPP (H4TPP)—this observation indicates that the cationic macrocycle is stabilized by *meso*-substituted phenyl rings; (3) in the case of the *meso*-sulfonatophenyl substituted porphyrin (TSPP− 4, anionic), the electronic bands in the TSPP are significantly red-shifted in both of the diprotonated porphyrin cores (H4TSPP, dianionic) and in the protonation of the N atoms and sulfonato (SO3 <sup>−</sup>) groups (H8TSPP, dicationic)—but the red shift in band positions for the H4TSPP is greater than that in H8TSPP; and (4) bands in the nonprotonated and diprotonated porphyrin are significantly more redshifted in its corresponding *meso*-phenyl/sulfonatophenyl structures. The electronic spectra of porphyrin and its derivatives studied here are discussed in more details in the next sections.

## **3.2. The electronic spectra of FBP and protonated-FBP (H4FBP)**

In Section 3.1, protonation and *meso* substitution of the porphyrin macrocycle is found to not only affect the geometric structure, but also, due to the change in molecular symmetry, lead to

Porphyrin and its derivatives find use in a myriad of important natural and biomimetic processes, with the major focus in the latter case on processes such as conversion of solar energy into chemical energy, photodynamic therapy, and as active agents in optical sensors. The excited states of porphyrins play fundamental roles in essentially all processes involving

In this section, we discuss the *meso* substitution and protonation effects on the electronic energy levels of the porphyrin macrocycle. Up to 24 singlet and 24 triplet energy levels of porphyrins have been calculated in water used as solvent at the TD-B3LYP/6-31G(d,p) level; singlet-singlet absorption spectra have been calculated for these specific compounds and are provided in

**Figure 3.** Comparison of calculated dipole-allowed electronic transitions of the parent porphyrin (FBP), *meso*-tetraphenylporphyrin (TPP), dianionic *meso*-tetrakis(*p*-sulfonatophenyl)porphyrin (TSPP), protonated-FBP (H4FBP), protonated-TPP (H4TPP), protonated TSPP (H4TSPP), and dicationic-TSPP (H8TSPP). The calculations were carried out in water

The calculations mainly produce a strong electronic absorption band in the 360–450 nm range and a few weak or very weak electronic transitions below as well as above the strong bands (**Figure 3**). The strongest band is known as the Soret band (also referred to as the B-band), and weaker bands at longer wavelength, in the range 500–750 nm, are known as Q-bands that are usually quite weak. The results of calculations indicate that (1) the electronic bands in the parent porphyrin (FBP, neutral) are slightly blue-shifted in diprotonated-FBP (H4FBP, dicationic) structure; (2) the bands in neutral TPP molecule (*meso*-phenyl substituted porphyrin) become significantly red-shifted in the dicationic or diprotonated-TPP (H4TPP)—this observation indicates that the cationic macrocycle is stabilized by *meso*-substituted phenyl rings; (3) in the case of the *meso*-sulfonatophenyl substituted porphyrin (TSPP− 4, anionic), the electronic

significant changes in electronic band positions as well as the number of bands.

214 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**3.1. Calculated electronic spectra of porphyrin and its derivatives**

porphyrin and its derivatives.

used as a solvent at the TD-B3LYP/6-31G(d,p) level of TD-DFT.

**Figure 3**.

The electronic spectrum of the FBP molecule exhibited two weak electronic bands at wavelength longer than that of the Soret band (B): one of the bands corresponds to S0 → S1 (B1u, at 540 nm with oscillator strength *f* = 0.0005) resulting from H − 1 → L + 1 (40%) and H → L (59%), where H and L represent HOMO and LUMO, respectively; the second band corresponds to S0 → S2 (B2u, at 506 nm and *f* = 0.0003) resulting from H − 1 → L + 1 (47%) and H → L + 1 (53%).

There are also two strong electronic bands in the spectral range of the Soret band (B): one of the bands corresponds to S0 → S4 (B2u, at 367 nm and *f* = 1.1911) resulting from H − 1 → L (50%) and H → L + 1 (47%); the second band corresponds to S0 → S3 (B1u, at 380 nm and *f* = 0.8144) resulting from H − 1 → L (23%), H − 1 → L + 1 (49%), and H → L (30%).

A relatively strong band at 330 nm is also calculated as existing. One of these is due to the S0 → S7 transition (B1u, at 330 nm and *f* = 0.6934), H − 3 → L (76%), H − 1 → L + 1 (12%), and H → L (12%), while the second band at ca. 330 nm is assignable to the transition S0 → S8 (B2u and *f* = 0.2479) and transition H − 3 → L + 1 (93%). It is to be noted that a few weak bands in range of 330–200 nm are also calculated as existing (see **Table 2**).

The experimental absorption spectrum of FBP [30] exhibits absorption bands at about 372 and 340 nm in the Soret-band region. In the Q-band region, bands at about 512 and 626 nm are observed. The measured bands in the FBP spectrum are in good agreement with calculated values for the B-bands at 380, 367, and 340 nm, and for the Q-bands at 540 and 506 nm, but not for the weak band at 626 nm. In these band regions, the calculation did not produce any dipoleallowed or forbidden singlet-singlet transition. Therefore, the free-base porphin (FBP) sample may contain the free-base aza-porphin(s) (as aza substitution at the *meso* position). Moreover, the calculations indicated the internal-conversion (IC) process, from the Soret band (S3/4 at 376 nm) to Q-bands (S2 at 506 nm and S1 at 540 nm), which is experimentally observed from the fluorescence spectra of sulfite reductase porphin methyl ester in chloroform, at the exciting light of 380 nm, showed two peaks at 597 and 640 nm [31]. We also calculated 24 triplet states (S0 → Tn) in the range of 249–822 nm for the FBP molecule. There are two triplet states: one T8(B3g) at 373 nm and the other T9(B2u) at 366 nm. The later one, T9(B2u) at 366 nm, closely overlaps with the strongly dipole-allowed electronic energy level S4(B2u) at 367 nm. This finding implies that there is not only the possibility of the internal-conversion (IC) process from the S3/4 (B2u at 376 nm) to S2 (B2u at 506 nm) and S1 (B1u at 540 nm), but also the possibility of the intersystem-crossing (ISC) process by way of the strong vibrational coupling between the singlet and triplet electronic states at S3/4 at 376 nm and T8/9 at 367 nm. The lowest triplet state


(S0 **→** T1(B2u)) was predicted at 822 nm resulting from H − 1 → L (21%) and H → L + 1 (79%) transitions.

**Table 2.** The selected values of the calculated singlet-singlet (**S0** → **Sn**) and singlet-triplet (**S0** → **Tn**) vertical electronic transitions with their oscillator strengths (f) for the FBP and protonated-FBP (H4FBP). The calculations were carried out in water used as a solvent at the TD-B3LYP/6-31G(d,p) level of TD-DFT. The percentages in parenthesis are the contributions from the different HOMO(H) → LUMO(L) transitions to a desired electronic transitions. The minor contributions are not given here.

The predicted electronic spectrum of protonated-FBP (H4FBP) exhibits Q- and B-bands for S0 → S1/2 (E at 538 nm with *f* = 0.0007) owing to H − 1 → L (48%) and H → L + 1 (52%) transitions; S0 → S3/4 (E at 366 nm and *f* = 1.4554) owing to H − 1/ → L + 1 (53%) and H → L (49%) transitions. In addition, a few weaker transitions exist up to 300 nm (**Table 2**).

(S0 **→** T1(B2u)) was predicted at 822 nm resulting from H − 1 → L (21%) and H → L + 1 (79%)

1 1.51 822 B2U H − 1 → L (21%),

3 2.04 608 B2U H − 1 → L (78%),

4 2.07 598 B1U H − 1 → L + 1 (94%)

9 3.15 393 AG H − 2 → L + 1 (93%)

1 1.63 763 E H − 1 → L + 1 (30%),

3 1.96 632 E H − 1 → L + 1 (69%),

7 3.23 384 B1 H − 3 → L + 1 (28%),

8 3.32 374 E H − 3 → L + 1 (44%),

9 3.37 367 E H − 5 → L + 1 (42%),

10 3.37 367 E H − 5 → L (42%),

2 1.63 763 E H − 1 → L (30%),

4 1.96 632 E H − 1 → L (69%),

2 1.82 682 B1U H → L (94%)

H → L + 1 (79%)

H → L + 1 (22%)

H → L + 2 (72%)

H − 1 → L + 2 (68%)

H → L (70%)

H → L (31%)

H → L + 1 (70%)

H → L + 1 (31%)

H − 2 → L (28%), H → L + 2 (31%)

H − 2 → L (44%)

H − 4 → L (48%)

H − 4 → L + 1 (48%)

**Sn (eV) (nm) f Sym Major contrib's T n (eV) (nm) Sym Major contrib's**

216 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

5 3.44 360 B3G H − 2 → L (98%) 7 2.90 428 B3G H − 2 → L (88%) 6 3.66 339 AG H − 2 → L + 1 (99%) 8 2.96 419 B1U H − 3 → L (86%)

8 3.76 330 0.2479 B2U H − 3 → L + 1 (93%) 11 3.33 373 B3G H − 8 → L + 1 (16%),

16 4.33 287 0.0914 B2U H − 5 → L + 1 (97%) 13 3.39 366 B2U H − 3 → L + 1 (96%) 18 4.41 281 0.1037 B1U H − 5 → L (99%) 15 3.61 343 AG H − 8 → L (26%),

23 5.22 237 0.1338 B1U H − 2 → L + 2 (98%) 16 3.64 340 B3G H − 4 → L + 1 (79%)

**Sn (eV) (nm) f Sym Major contrib's Tn (eV) (nm) Sym Major contrib's**

**FBP: S0 → Sn S0 → Tn**

H → L (59%)

H → L + 1 (53%)

H → L + 1 (47%)

H − 1 → L + 1 (12%), H → L (12%)

**H4FBP: S0 → Sn S0 → Tn**

H → L (52%)

H → L (48%)

H → L + 1 (52%)

H → L + 1 (48%)

H − 4 → L (53%)

H − 4 → L (45%)

H − 4 → L + 1 (45%)

**Table 2.** The selected values of the calculated singlet-singlet (**S0** → **Sn**) and singlet-triplet (**S0** → **Tn**) vertical electronic transitions with their oscillator strengths (f) for the FBP and protonated-FBP (H4FBP). The calculations were carried out in water used as a solvent at the TD-B3LYP/6-31G(d,p) level of TD-DFT. The percentages in parenthesis are the contributions from the different HOMO(H) → LUMO(L) transitions to a desired electronic transitions. The minor

H − 4 → L + 1 (53%)

H − 1 → L + 1 (48%), H → L (29%)

1 2.30 540 0.0005 B1U H − 1 → L + 1 (40%),

2 2.45 506 0.0003 B2U H − 1 → L (47%),

3 3.26 380 0.8144 B1U H − 3 → L (22%),

4 3.38 367 1.1911 B2U H − 1 → L (50%),

7 3.76 330 0.6934 B1U H − 3 → L (76%),

1 2.31 538 0.0007 E H − 1 → L + 1 (48%),

3 3.39 366 1.4554 E H − 1 → L + 1 (52%),

7 3.90 318 0.0597 E H − 5 → L + 1 (45%),

2 2.31 538 0.0007 E H − 1 → L (48%),

4 3.39 366 1.4554 E H − 1 → L (52%),

8 3.90 318 0.0597 E H − 5 → L (45%),

12 4.05 306 0.0695 E H − 5 → L (54%),

contributions are not given here.

11 4.05 306 0.0695 E H − 5 → L + 1 (54%),

transitions.

Comparing the electronic spectrum of FBP with that of H4FBP: in FBP three strong bands were predicted at 380, 360, and 330 nm, see **Figure 3** and **Table 2**, whereas the H4FBP spectrum exhibited only one strong band at 366 nm in the Soret-band region; in the Q-band region, H4FBP has a doubly degenerate band at 538 nm, while FBP has two very weak transitions at 540 and 506 nm. This reduction in the number of bands is due to the higher symmetry for H4FBP.

Also for FBP, the calculated electronic spectrum of diprotonated-FBP (i.e., H4FBP) molecule indicates two IC processes from the S3/4 (the strongest bands or B-band) at 366 nm (with the symmetry E) to the S1/2 (at 538 nm with symmetry E), as well as the ISC process between the S3/4 (at 366 nm) and T7/8 (at 367 nm), see **Table 2**.

**Figure 4.** Plot of calculated electron densities in the desired HOMOs (H) and LUMOs (L) of parent porphyrin (FBP), *meso*-tetraphenylporphyrin (TPP), dianionic *meso*-tetrakis(*p*-sulfonatophenyl)porphyrin (TSPP), and protonated-FBP (H4FBP), protonated-TPP (H4TPP), protonated-TSPP (H4TSPP), and dicationic-TSPP (H8TSPP) molecules.

The electron density plots of the molecular orbitals (i.e., HOMOs (H) and LUMOs (L)), as seen in **Figure 4** and **Table 3**, show that the H − m and L + m (m = 0, 1, 2, …) are not just pure π and π\* molecular orbitals (MOs), in particular cases they also include nonbinding atomic orbitals (AOs).


**Table 3.** Bond type of the highest occupied molecular orbitals (H - m) and the lowest unoccupied molecular orbitals (L + m), m = 0, 1, 2, …

#### **3.3. The electronic spectra of TPP and H4TPP**

While the calculated spectrum of the TPP molecule displayed two weak peaks at 571 (S0 → S1, *f* = 0.00337) and 535 nm (S0→ S2, *f* = 0.0359) in the region of the Q-absorption bands, the spectrum of diprotonated-TPP (H4TPP) exhibited only a double degenerate peak that is also red-shifted to 645 nm (S0 → S1/2, *f* = 0.3040). In the region of Soret band, two strong peaks were predicted at 401 and 393 nm (S0 → S3/4, *f* = 1.2834/1.6972) in the TPP absorption spectrum, and the H4TPP spectrum exhibited a doubly degenerate band at 430 nm (S0 → S3/4, *f* = 1.209). Both spectra show a few weak and very weak-allowed electronic transitions in the high energy region as seen in **Table 4** and **Figure 5**. The observed spectrum of the **TPP** in **DMF** (Dimethylformamide) exhibited a strong band at about 412 nm with a shoulder at around 400 nm in Soret-band region, and four weak bands at about 513, 548, 590, and 645 nm in Q-band region (**Figure 5**). However, as shown in **Figure 5**, the calculated electronic spectrum of the TPP does not indicate any dipole-allowed or forbidden singlet-singlet transition with wavelength longer than 571 nm, rather, a weak singlet-singlet transition was predicated at 645 nm for the diprotonated-TPP (H4TPP) molecule. This observation suggests that the TPP sample may contain a small percentage of aza-substituted TPP (at the beta or *meso* position) that produces weaker absorption peaks at around 590 and 646 nm. Another possibility might be that a small percentage of the TPP molecules in the sample might be at their local minima (instead of their ground state) due to rotation of the phenyl substitution at the *meso* position of TPP, resulting in weaker bands at around 590 and 646 nm.

Geometric and Electronic Properties of Porphyrin and its Derivatives http://dx.doi.org/10.5772/64583 219


The electron density plots of the molecular orbitals (i.e., HOMOs (H) and LUMOs (L)), as seen in **Figure 4** and **Table 3**, show that the H − m and L + m (m = 0, 1, 2, …) are not just pure π and π\* molecular orbitals (MOs), in particular cases they also include nonbinding atomic

H π(Cβ─Cβ/Cm─Cα) + n(N) H π(Cβ─Cβ/Cα─Cm─Cα) + n(N)

H − 4/H + 5 π(Cβ─Cβ) + n(N) H − 6/H − 7 π(Cβ─Cα─Cm) + n(minor, N)

L + 4/L + 5 π\*(Cβ─Cβ/Cm─Cα) + n(N/Cα/Cβ) L + 4 π(Cβ─Cβ and Cα─Cm) + n(N/Cα/Cm)

**Table 3.** Bond type of the highest occupied molecular orbitals (H - m) and the lowest unoccupied molecular orbitals (L

While the calculated spectrum of the TPP molecule displayed two weak peaks at 571 (S0 → S1, *f* = 0.00337) and 535 nm (S0→ S2, *f* = 0.0359) in the region of the Q-absorption bands, the spectrum of diprotonated-TPP (H4TPP) exhibited only a double degenerate peak that is also red-shifted to 645 nm (S0 → S1/2, *f* = 0.3040). In the region of Soret band, two strong peaks were predicted at 401 and 393 nm (S0 → S3/4, *f* = 1.2834/1.6972) in the TPP absorption spectrum, and the H4TPP spectrum exhibited a doubly degenerate band at 430 nm (S0 → S3/4, *f* = 1.209). Both spectra show a few weak and very weak-allowed electronic transitions in the high energy region as seen in **Table 4** and **Figure 5**. The observed spectrum of the **TPP** in **DMF** (Dimethylformamide) exhibited a strong band at about 412 nm with a shoulder at around 400 nm in Soret-band region, and four weak bands at about 513, 548, 590, and 645 nm in Q-band region (**Figure 5**). However, as shown in **Figure 5**, the calculated electronic spectrum of the TPP does not indicate any dipole-allowed or forbidden singlet-singlet transition with wavelength longer than 571 nm, rather, a weak singlet-singlet transition was predicated at 645 nm for the diprotonated-TPP (H4TPP) molecule. This observation suggests that the TPP sample may contain a small percentage of aza-substituted TPP (at the beta or *meso* position) that produces weaker absorption peaks at around 590 and 646 nm. Another possibility might be that a small percentage of the TPP molecules in the sample might be at their local minima (instead of their ground state) due to rotation of the phenyl substitution at the *meso* position of TPP, resulting in weaker bands

L/L + 1 π\*(Cβ─Cβ/Cβ─Cα/Cm─Cα) + n(minor; N) L/L + 1 π(Cβ─Cα) + n(minor, N) L + 2 π\*(Cβ─Cα) + n(Cm) L + 2 π(Cβ─Cα) + n(Cm) L + 3 π\*(Cβ─Cβ/Cm─Cα) + n(N/Cα) L + 3 π(Cβ─Cβ) + n(N/Cα/Cm)

orbitals (AOs).

+ m), m = 0, 1, 2, …

at around 590 and 646 nm.

**FBP H4FBP**

**3.3. The electronic spectra of TPP and H4TPP**

H − 1 π(Cβ─Cα) H − 1 π(Cα─Cβ) H − 2 π(Cα─N─Cα/Cβ─Cβ) H − 2/H − 3 π(Cα─Cβ) + n(N) H − 3 π(Cα─N─Cα/Cβ─Cβ) + n(minor, N/Cm) H − 4/H − 5 π(Cβ─Cβ) + n(N)

218 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

H − 6/H − 7 n(N) + σ(minor; Cβ─Cα) H − 8 π(Cα─Cm─Cα)

**Table 4.** Selected values of the calculated singlet-singlet (**S0**→**Sn**) and singlet-triplet (**S0**→**Tn**) vertical electronic transitions with their oscillator strength (f) for the TPP and H4TPP. The percentages in parenthesis are the contributions from the various HOMO (H) to LUMO (L) transitions to a desired electronic transitions. The minor contributions are not given here. The calculations were carried out in water as solvent at the TD-B3LYP/6-31G(d,p) level of TD-DFT.

**Figure 5.** Calculated and measured absorption spectra of TPP and calculated absorption spectrum of protonated-TPP (H4TPP).


**Table 5.** Bond type of the highest occupied molecular orbitals (H − m) and the lowest unoccupied molecular orbitals (L + m), m = 0, 1, 2, ….

Furthermore, Jiang *et al*. [32] measured absorption and EPR spectra of some porphyrins (TPP and derivatives) and metalloporphyrins compounds, and the measured absorption spectrum of TPP produced an intense electronic transition centered about 417 nm (B-band) and several Q-bands with weak intensities around 514, 550, 590, and 646 nm. The authors have also stated that both steric hindrance and electronic effects of the functional groups influenced the UV-vis absorption of the TPP, with the Soret bands of the *para*-substituted *meso*-tetraphenylporphine derivatives somewhat red-shifted (3–5 nm). This experimental observation is consistent with the result of our calculations (**Figure 5** and **Tables 2**–**5**).

Additionally, the results of the calculations for TPP (in solution/water) indicate the possibility of an IC process from S6 (B2 at 350 nm)/S4 (B1 at 393 nm)/S3 (B2 at 401 nm) to S2 (B1 at 535 nm) and S1 (B2 at 571 nm), which are verified by experimental measurements of the fluorescence spectrum of the TPP in different environments. Moreover, based on theoretical predictions, there are strong surface crossings between the singlet-triplet excited states of the TPP: S4 (B1 at 393 nm) and T8 (A2 at 393 nm), and S3 (B2 at 401 nm) and T7 (A1 at 403 nm), which may cause an ISC process in the excited state.

The results of the calculated electronic energy states of diprotonated-TPP molecule (H4TPP) indicate the existence of an IC process from the S3/4 (A′ and A"″ at 430 nm) to S1/2 (A′ and A″ at 645 nm), in addition to possibility of an ISC process between the S3/4 (A′ and A″ at 430 nm) and T7/8 (at 431 and 430 nm, with symmetry A′ and A″, respectively).

## **3.4. Calculated electronic spectra of TSPP, H4TSPP, and H8TSPP**

**Figure 5.** Calculated and measured absorption spectra of TPP and calculated absorption spectrum of protonated-TPP

m = 3–6

**Table 5.** Bond type of the highest occupied molecular orbitals (H − m) and the lowest unoccupied molecular orbitals (L

Furthermore, Jiang *et al*. [32] measured absorption and EPR spectra of some porphyrins (TPP and derivatives) and metalloporphyrins compounds, and the measured absorption spectrum of TPP produced an intense electronic transition centered about 417 nm (B-band) and several Q-bands with weak intensities around 514, 550, 590, and 646 nm. The authors have also stated that both steric hindrance and electronic effects of the functional groups influenced the UV-vis absorption of the TPP, with the Soret bands of the *para*-substituted *meso*-tetraphenylporphine derivatives somewhat red-shifted (3–5 nm). This experimental observation is consistent with

Additionally, the results of the calculations for TPP (in solution/water) indicate the possibility of an IC process from S6 (B2 at 350 nm)/S4 (B1 at 393 nm)/S3 (B2 at 401 nm) to S2 (B1 at 535 nm) and S1 (B2 at 571 nm), which are verified by experimental measurements of the fluorescence spectrum of the TPP in different environments. Moreover, based on theoretical predictions,

π\*(C─C in phenyl)

H π(Cα─Cm─Cα/Cβ─Cβ) + n(N and Cϕ) L/L + 1 π\*(Cβ─Cβ/Cβ─Cα/Cm─Cα) + n\*(N(H))

H − 1 π(Cα─Cβ) L + 2 π\*(Cα─Cm) + n\*(Cϕ)

220 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

π(Cβ─Cβ)/ π(N─Cα─Cm) L + m

the result of our calculations (**Figure 5** and **Tables 2**–**5**).

(H4TPP).

**TPP**

H − m m = 2, 3

+ m), m = 0, 1, 2, ….

In the Q-band region, while the calculations indicate the presence of two weak transitions at 573 nm (S0 → S1 with symmetry B2 and *f* = 0.0419) and at 536 nm (S0 → S2 with symmetry B1, *f* = 0.0506) in the TSPP spectrum, the calculated spectrum of H4TSPP shows two doubly degenerate peaks at 669 nm (S0 → S1/2 with symmetries B2 and B1 with *f* = 0.4223/0.4138) and at 528 nm (S0 → S4/5 with symmetries A1 and B2 and *f* = 0.0001/0.0005), in addition to a band at 518 nm (S0 → S10, B2 symmetry and *f* = 0.0001). However, the spectrum of the dicationic-TSPP (H8TSPP) indicates almost overlapping (or nearly degenerate) weak electronic transitions at 620 nm (S0 → S1 with symmetries B2, *f* = 0.2467) and at 619 nm (S0 → S2 with symmetries B1, *f* = 0.2377).

In the B-band (Soret band) region, while the calculated spectrum of the TSPP exhibited two strong bands at 403 nm (S0 → S3 with B2 symmetry and *f* = 1.4382) and at 396 nm (S0 → S4 with symmetry B1 and *f* = 1.8378), the H4TSPP spectrum contains two strong bands at 452/451 nm (S0 → S12/13, B1 and B2 symmetries, *f* = 0.7601/0.7369) and a medium intense band at 441 nm (S0 → S16, B2 symmetry and *f* = 0.5315). The calculated spectrum of the dicationic-TSPP (H8TSPP) exhibits a double degenerate strong transitions at 424 nm (S0 → S3/4, with B1 and B2 symmetries and *f* = 1.7153/1.7145, respectively). Additionally, many weak electronic transitions are predicted at longer wavelengths than these strong Soret bands (see **Table 6**). The predicted Bbands and Q-bands for the molecules studied here are compatible with the experimental data [21, 33].

Akins *et al.* [21] and Zhang *et al*. [33] have reported the UV-vis spectra of the free-base TSPP and the H4TSPP (dianionic-TSPP). While the measured absorption spectrum of the TSPP displayed an intense band (S-band, also known as B-band) at ~412 nm, and several very weak broad bands (known as Q-bands) at about 517 (± 2), 555 (± 3), 581 (± 3), and 640 (± 3) nm, the H4TSPP spectrum exhibited the B-band at 432 nm and very weak broad Q-bands at 589 (± 5) and 645 nm. However, in the Q-band region, the calculations produced only two very weak dipole-allowed electronic transitions at 536 and 573 nm for the TSPP and only one doubly degenerated band at 669 nm for the H4TSPP. The calculated absorption spectra suggest that the two of four absorption bands in TSPP and one of two bands for the H4TSPP, in the Q-region, must be due to vibrational progression such as from the lowest vibrational level in the electronic ground state to higher vibrational level in electronically excited state, S0(ν″ = 0) to SQ(ν′ ≥ 1).


Geometric and Electronic Properties of Porphyrin and its Derivatives http://dx.doi.org/10.5772/64583 223


**TSPP:S0 →Sn S0 →Tn**

H → L (67%)

H → L (28%)

H → L + 1 (36%)

H − 8 → L (69%)

H − 10 → L + 1 (11%)

**H4TSPP:S0 →Sn S0 →Tn**

H → L (87%)

H → L + 1 (87%)

H − 2 → L (53%)

H − 1 → L + 1 (47%)

H − 1 → L + 1 (53%)

H − 5 → L (15%)

H − 5 → L + 1 (12%)

H − 6 → L + 1 (16%), H − 5 → L + 1 (57%)

H − 6 → L (19%), H − 5 → L (54%)

H → L + 1 (64%)

5 2.16 573 0.0419 B2 H − 1 → L + 1 (32%),

6 2.31 536 0.0506 B1 H − 1 → L (36%),

11 3.13 396 1.8378 B1 H − 1 → L (62%),

10 3.07 403 1.4382 B2 H − 1 → L + 1 (62%),

38 3.56 348 0.0392 B1 H − 10 → L + 1 (28%),

48 3.77 329 0.0936 B1 H − 11 → L + 1 (82%),

1 1.85 669 **0.4223** B2 H − 5 → L + 1 (13%),

2 1.85 669 **0.4138** B1 H − 5 → L (13%),

5 2.35 528 **0.0005** B2 H − 4 → L (53%),

10 2.40 518 **0.0001** B2 H − 4 → L (47%),

12 2.74 452 **0.7601** B1 H − 6 → L (79%),

13 2.75 451 **0.7369** B2 H − 6 → L + 1 (83%),

16 2.81 441 **0.5315** B2 H − 9 → L (17%),

18 2.81 441 **0.5073** B1 H − 9 → L + 1 (16%),

4 2.35 528 **0.0001** A1 H − 3 → L + 1 (47%),

**Sn (eV) (nm) f Sym Major contrib's Tn (eV) (nm) Sym Major contrib's**

222 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

36 3.49 355 0.3924 B2 H − 10 → L (83%) 5 2.84 437 A2 H − 9 → L (49%),

47 3.64 341 0.2178 B2 H − 11 → L (83%) 7 3.07 404 A1 H − 9 → L + 1 (39%),

**Sn eV (nm)** f **Sym. Major contrib's Tn eV (nm) Sym Major contrib's**

1 1.40 884 B1 H − 1 → L (16%),

3 1.99 624 B1 H − 1 → L (84%),

4 2.05 604 B2 H − 1 → L + 1 (97%)

6 2.89 429 B2 H − 11 → L (36%),

8 3.14 395 A2 H → L + 2 (70%)

1 1.17 1056 B2 H → L (97%)

2 2.01 618 B1 H − 5 → L (95%)

3 2.34 530 A1 H − 3 → L + 1 (47%),

5 2.34 529 B1 H − 4 → L + 1 (47%),

9 2.39 518 A1 H − 3 → L + 1 (53%),

13 2.51 494 A2 H − 8 → L + 1 (34%),

14 2.62 474 B1 H − 6 → L (90%)

17 2.65 467 A1 H − 8 → L (46%),

18 2.69 462 A2 H − 8 → L + 1 (47%),

2 1.67 744 B2 H → L (97%)

H → L + 1 (86%)

H → L + 1 (15%)

H − 7 → L (39%)

H − 10 → L (48%)

H − 7 → L + 1 (51%)

H − 2 → L (52%)

H − 1 → L (52%)

H − 2 → L (47%)

H − 7 → L (35%), H → L + 2 (23%)

H − 7 → L + 1 (46%)

H − 7 → L (47%)

**Table 6.** The selected values of the calculated singlet-singlet (**S0**→**Sn**) and singlet-triplet (**S0**→**Tn**) vertical electronic transitions with oscillator strength (f) for the TSPP and protonated-TSPP (H4TSPP). The calculations were carried out in water used as a solvent at TD-B3LYP/6-31G(d,p) level of the TD-DFT. The percentages in the parenthesis indicate the contributions from the different HOMO(H) → LUMO(L) transitions to a desired electronic transitions. The minor contributions are not given here.

Also, Akins and coworkers have measured fluorescence spectra of free-base TSPP (pH = 12), monomeric H4TSPP (pH = 4.5), and aggregate H4TSPP in highly acidic situation. The authors reported that the fluorescence spectrum of the TSPP at 412 nm (B-band region) excitation displayed a peak at 642 nm with a red degraded shoulder at 702 nm. The spectrum of H4TSPP upon excitation at 432 nm in the B-band region exhibited similar structure, for example, a strong emission peak at 665 nm with relatively weak shoulder at about 716 nm [21]. Both fluorescence spectra of the TSPP and deprotonated-TSPP (H4TSPP) indicated that when excited in the Soret- or B-band region, initially internal conversion (IC) occurs from the B-band to the Q-bands, followed by a fluorescence from the lowest excited state(s) in Q-band region to the ground state S0 a sequence of: So + ho B‐band <sup>S</sup> Q‐band So+ h. These observations are consistent with our calculations. For instance, the predicted possible IC (internal-conversion) process may take place from the S3 (at 403 nm) to S1 (at 573 nm) and S2 (at 536 nm) for the TSPP; and from the S12/13 (at 452/451 nm)/S16 (at 441 nm) to S10 (at 518 nm)/S4/5(at 528 nm)/S1/2(at 669 nm) for the H4TSPP (diprotonated- or dianionic-TSPP).

The calculations also indicate that there might be an ISC (intersystem crossing) process between the S3 (at 403 nm)/S4 (at 396 nm) and the T7 (at 404 nm)/T8 (at 395 nm), and between the S1 (at 573 nm) and T4 (at 604nm) for TSPP (where the energy difference between S1 and T4 states is about 0.11 eV or 896 cm−1). For the H4TSPP (or dianionic-TSPP), the ISC process may occur between the S4/5 (at 528 nm) and T3,4,5,6 (at 530 and 529 nm), and S10 (at 518 nm) and T15,16,17,18 (at 518 nm), and between the S1(669 nm) and T3(618 nm) (where the energy difference between the S1(669 nm) and T3(618 nm) states is 0.15 eV or 1233 cm−1) (**Figure 6**). The results of the calculations suggest that, depending on competition between the IC and ISC processes, there can be ISC through vibrational coupling or potential energy surface (PES) touching between singlet and triplet states.

**Figure 6.** Calculated and measured absorption spectra of TSPP and protonated-TSPP (H4TSPP).

Likewise, for the H8TSPP (dicationic-TSPP molecule), the IC process may happen from the Bbands (S3/4 at 424 nm) to the Q-bands (S1/2 at 620/619 nm). Furthermore, the energy difference between the S1/2 (at 424/424 nm) and T3/4 (at 639/637 nm) is about 0.056 eV or 455 cm−1, which may lead to a strong vibrational coupling in their excited vibroelectronic states. Owing to this small energy distance between singlet and triplet states of the H8TSPP, there would likely occur ISC that may originate from B-bands (S1/2) to triplet states (T3/4).

Also, Akins and coworkers have measured fluorescence spectra of free-base TSPP (pH = 12), monomeric H4TSPP (pH = 4.5), and aggregate H4TSPP in highly acidic situation. The authors reported that the fluorescence spectrum of the TSPP at 412 nm (B-band region) excitation displayed a peak at 642 nm with a red degraded shoulder at 702 nm. The spectrum of H4TSPP upon excitation at 432 nm in the B-band region exhibited similar structure, for example, a strong emission peak at 665 nm with relatively weak shoulder at about 716 nm [21]. Both fluorescence spectra of the TSPP and deprotonated-TSPP (H4TSPP) indicated that when excited in the Soret- or B-band region, initially internal conversion (IC) occurs from the B-band to the Q-bands, followed by a fluorescence from the lowest excited state(s) in Q-band region to the ground state S0 a sequence of: So + ho B‐band <sup>S</sup> Q‐band So+ h. These observations are consistent with our calculations. For instance, the predicted possible IC (internal-conversion) process may take place from the S3 (at 403 nm) to S1 (at 573 nm) and S2 (at 536 nm) for the TSPP; and from the S12/13 (at 452/451 nm)/S16 (at 441 nm) to S10 (at 518 nm)/S4/5(at 528 nm)/S1/2(at

224 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

The calculations also indicate that there might be an ISC (intersystem crossing) process between the S3 (at 403 nm)/S4 (at 396 nm) and the T7 (at 404 nm)/T8 (at 395 nm), and between the S1 (at 573 nm) and T4 (at 604nm) for TSPP (where the energy difference between S1 and T4 states is about 0.11 eV or 896 cm−1). For the H4TSPP (or dianionic-TSPP), the ISC process may occur between the S4/5 (at 528 nm) and T3,4,5,6 (at 530 and 529 nm), and S10 (at 518 nm) and T15,16,17,18 (at 518 nm), and between the S1(669 nm) and T3(618 nm) (where the energy difference between the S1(669 nm) and T3(618 nm) states is 0.15 eV or 1233 cm−1) (**Figure 6**). The results of the calculations suggest that, depending on competition between the IC and ISC processes, there can be ISC through vibrational coupling or potential energy surface (PES) touching between

669 nm) for the H4TSPP (diprotonated- or dianionic-TSPP).

**Figure 6.** Calculated and measured absorption spectra of TSPP and protonated-TSPP (H4TSPP).

singlet and triplet states.


**Table 7.** Bond type of the highest occupied molecular orbitals (H − m) and the lowest unoccupied molecular orbitals (L + m), m = 0, 1, 2, …

Consequently, the results of calculated absorption spectra for the porphyrin molecules studied here (**Tables 2**–**7**) reveal several important points: (1) protonation of the N atoms at the porphyrin core and the *meso* substitutions of the parent porphyrin with the phenyl or sulfonatophenyl groups lead to substantial red-shifts in the spectral position of the Soret bands and Q-bands; (2) the IC process takes place from the B-band(s) to the Q-band(s) for the all porphyrin derivatives; (3) an ISC process might be possible through the surface touching and/or strong vibrational coupling, but would be dependent on the competition with IC processes and the rate constant of fluorescence; and (4) deuteration of the N atoms at the core of the macrocycle and O atoms do not produce significant change in their corresponding spectra.

#### **3.5. Relaxed potential energy surface (RPES) scan of TSPP molecule**

The relaxed potential energy surface (RPES) scan was performed to calculate the ground state PES of the TSPP molecule in water by rotating one of four dihedral angles *θ* (Cα─Cm─Cϕ─C) from 40 to 130° in 10° increments. The calculated ground state curve, S0(RPES), shows two minima at dihedral angles of ~66 and 110° (see **Figure 7(B)** and **(C)**). These two minima on the S0(RPES) curve represent the lowest ground state with C2v symmetry and an energetically stable local state with C2 symmetry, respectively. The local minima at 110° is about 106 cm−1 (0.0132 eV) above the lowest ground state at 66° as seen in **Figure 7(C)**. When the molecule goes from the lowest ground state to this local state, the predicted highest potential energy barrier at the dihedral angle of 90° is only 177 cm−1 (0.0219 eV). This finding suggests that the *meso*-substituted sulfonatophenyl groups are able to rotate around Cm─Cϕ bond at room temperature because the thermal energy (*kBT*) at 298 K is 207.2 cm−1. Consequently, since the computed potential energy barrier is small as much as 106 cm−1 at the dihedral angle of 90°, the self-assembling of the TSPP molecules in any environment might be very easily formed. It should be point out that the calculated ground state RPES was carried out only for the rotation of one of four *meso*-sulfonatophenyl groups within the TSPP molecule. If the RPES scans were performed for the rotations of all four *meso*-substitutional groups, there would be more than a few different local minima with dissimilar potential energy barriers on the ground state RPES. Thereby, a slight change in the potential energy barrier distribution of the *meso*-substituted porphyrin molecules, such as the TSPP, can be used as a scanning nanocalorimetric measurement (or for other electronic purposes) of very small variations in energy.

**Figure 7.** The calculated spectra of the TSPP as a function of the dihedral angle (Cα─Cm─Cϕ─C(ph)) rotation varying from 40 to 130° with 10° increment: (A) plot of dipole-allowed singlet electronic transitions S0 → Sn, with n = 1–24; (B) the relaxed potential energy surfaces of the ground state (S0) and upper singlet (Sn) and triplet (Tn) states, n = 1–24; (C)– (E) illustrate the RPES curves for the ground state S0, Q-bands and Soret bands at a low scale for a better view. It is noteworthy that only one of the four *meso*-sulfonatophenyl groups is rotated about the Cm─Cϕ bond and the uppercase letter S in (E) symbolizes the Soret band.

It is to be noted that the PES curves of the upper singlet (Sn) and triplet (Tn) energy states were calculated by the following Eqs. (1) and (2), respectively:

$$V\_n(\mathcal{S}\_n, \theta) = E(\theta) - E\_0 + E(\mathcal{S}\_0 \to \mathcal{S}\_n; \theta) \tag{1}$$

$$\mathbb{V}\_n(T\_n, \theta) = E(\theta) - E\_0 + E(\mathbb{S}\_0 \to T\_n; \theta) \tag{2}$$

(1) In the aforementioned equations, *E0* and *E*(*θ*) symbolize the calculated global (total SCF) energies at the lowest ground state and the relaxed potential energy at the dihedral angle *θ*(Cα─Cm─Cϕ─C1), respectively; *E*(S0 → Sn/S0 → Tn; *θ*) represents the vertical electronic transition energy from S0 to excited electronic energy levels Sn/Tn at the dihedral angle *θ*. It is to be noted that **Figure 7(A)** displays the computed dipole-allowed electronic transitions at each rotated dihedral angle, *θ*(Cα─Cm─Cϕ─C1), while **Figure 7(C)**–**(E)** shows the alteration in the calculated singlet and triplet electronic energy levels as a function of the *θ*(Cα─Cm─Cϕ─C1). The PES curves of the excited states Sn and Tn are akin to the ground state RPES, S0(RPES). Consequently, the results of the calculations indicated that the red-shift in spectral position of the Soret bands increases with increasing rotational dihedral angle in both right-handed and left-handed rotational directions around the equilibrium dihedral angle of ~66° in the ground state.

#### **4. Calculation section**

from 40 to 130° in 10° increments. The calculated ground state curve, S0(RPES), shows two minima at dihedral angles of ~66 and 110° (see **Figure 7(B)** and **(C)**). These two minima on the S0(RPES) curve represent the lowest ground state with C2v symmetry and an energetically stable local state with C2 symmetry, respectively. The local minima at 110° is about 106 cm−1 (0.0132 eV) above the lowest ground state at 66° as seen in **Figure 7(C)**. When the molecule goes from the lowest ground state to this local state, the predicted highest potential energy barrier at the dihedral angle of 90° is only 177 cm−1 (0.0219 eV). This finding suggests that the *meso*-substituted sulfonatophenyl groups are able to rotate around Cm─Cϕ bond at room temperature because the thermal energy (*kBT*) at 298 K is 207.2 cm−1. Consequently, since the computed potential energy barrier is small as much as 106 cm−1 at the dihedral angle of 90°, the self-assembling of the TSPP molecules in any environment might be very easily formed. It should be point out that the calculated ground state RPES was carried out only for the rotation of one of four *meso*-sulfonatophenyl groups within the TSPP molecule. If the RPES scans were performed for the rotations of all four *meso*-substitutional groups, there would be more than a few different local minima with dissimilar potential energy barriers on the ground state RPES. Thereby, a slight change in the potential energy barrier distribution of the *meso*-substituted porphyrin molecules, such as the TSPP, can be used as a scanning nanocalorimetric measure-

226 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

ment (or for other electronic purposes) of very small variations in energy.

case letter S in (E) symbolizes the Soret band.

calculated by the following Eqs. (1) and (2), respectively:

**Figure 7.** The calculated spectra of the TSPP as a function of the dihedral angle (Cα─Cm─Cϕ─C(ph)) rotation varying from 40 to 130° with 10° increment: (A) plot of dipole-allowed singlet electronic transitions S0 → Sn, with n = 1–24; (B) the relaxed potential energy surfaces of the ground state (S0) and upper singlet (Sn) and triplet (Tn) states, n = 1–24; (C)– (E) illustrate the RPES curves for the ground state S0, Q-bands and Soret bands at a low scale for a better view. It is noteworthy that only one of the four *meso*-sulfonatophenyl groups is rotated about the Cm─Cϕ bond and the upper-

It is to be noted that the PES curves of the upper singlet (Sn) and triplet (Tn) energy states were

(1)

The calculations were carried out in water used as solvent at the B3LYP level of the density functional theory (DFT) [34, 35] with the 6-311G(d,p) basis set [36]. The solvent effects were considered by using the self-consistent reaction field (SCRF) calculations [37] with the conductor-like polarizable continuum model [38–40] and a dielectric constant of 78.39 for water; SCRF = (CPCM, solvent = water) as implemented within the Gaussian 09 software package [41]. All compounds studied here were optimized to minima on their ground state relaxed potential energy surfaces (RPESs) that were verified by revealing the absence of imaginary frequencies in calculated vibrational spectra. Time-dependent DFT (TD-DFT) was performed to calculate the first 24 singlet-singlet (S0 → Sn) and singlet-triplet (S0 → Tn; n = 1 to 24) vertical electronic transitions in water. Finally, to investigate the dependence of the potential energy of the ground state (S0) and excited states (Sn and Tn) on the rotation of the Cm─C*ϕ* bond, we used the Gaussian keyword "Opt = ModRedundant." The calculated ground state (S0) potential energies at each optimized structure were plotted as a function of the rotated dihedral angle *θ* in the region of 40–130° with 10° increment. The potential energy surfaces of the singlet and triplet excited states were conducted by calculating the singlet-singlet, S0 → Sn, and singlet-triplet, S0 → Tn, electronic transition energies for each optimized structure at the rotated dihedral angle *θ*, including the SCF energy correction to each calculated electronic transition energy, ΔESCF = *E*(*θ*) − *E0*, where *E(0)* and *E*(*θ*) represent the calculated global energies of the ground state and energetically most stable structure at the dihedral angle *θ*, respectively.

We would like to point out that the electron densities in HOMO and LUMO molecular orbitals, and electronic spectra of the molecules studied here were plotted using GaussSum software [42].

## **Acknowledgements**

We would like to thank the following: the U.S. National Science Foundation (NSF) for support of research efforts under grant no. HRD-08-33180 and Ömer Andaç (of the Chemistry Department of Ondokuz Mayıs University) for kindly making available computing facilities and software setup. We also thank TUBITAK ULAKBIM, High Performance and Grid Computing Center (TR-Grid e-Infrastructure) for performing the calculations reported in this work.

## **Author details**

Metin Aydin1\* and Daniel L. Akins2

\*Address all correspondence to: aydn123@netscape.net

1 Department of Chemistry, Faculty of Art and Sciences, Ondokuz Mayıs University, Samsun, Turkey

2 Department of Chemistry and Biochemistry, Center for Analysis of Structures and Interfaces (CASI), The City College of the City University of New York, New York, USA

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Metin Aydin1\* and Daniel L. Akins2

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We would like to thank the following: the U.S. National Science Foundation (NSF) for support of research efforts under grant no. HRD-08-33180 and Ömer Andaç (of the Chemistry Department of Ondokuz Mayıs University) for kindly making available computing facilities and software setup. We also thank TUBITAK ULAKBIM, High Performance and Grid Computing Center (TR-Grid e-Infrastructure) for performing the calculations reported in this work.

228 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

1 Department of Chemistry, Faculty of Art and Sciences, Ondokuz Mayıs University, Samsun,

2 Department of Chemistry and Biochemistry, Center for Analysis of Structures and Interfa-

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Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Biological and Biomedical Applications of Molecular Spectroscopy**

232 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

#### **Applications of Molecular Spectroscopic Methods to the Elucidation of Lignin Structure Applications of Molecular Spectroscopic Methods to the Elucidation of Lignin Structure**

Tingting You and Feng Xu Tingting You and Feng Xu

Additional information is available at the end of the chapter Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/64581

#### **Abstract**

Lignin in plant cell wall is a complex amorphous polymer and is biosynthesized mainly from three aromatic alcohols, namely, *p-*coumaryl, coniferyl, and sinapyl alcohols. This biosynthesis process consists of mainly radical coupling reactions and creates a unique lignin polymer in each plant species. Generally, lignin mainly consists of *p*-hydroxyphenyl (H), guaiacyl (G), and syringyl (S) units and is linked by several types of carboncarbon (β-β, β-5, β-1, and 5–5) and ether bonds. Due to the structural complexity, various molecular spectroscopic methods have been applied to unravel the aromatic units and different interunit linkages in lignin from different plant species. This chapter is focused on the application of ultraviolet (UV) spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, Fourier transform Raman (FT-Raman) spectroscopy, fluorescence spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy to lignin structural elucidation.

**Keywords:** lignin, structure elucidation, 2D HSQC NMR, composition, linkages

## **1. Introduction**

Plant cell walls in higher plants are mainly consisted of cellulose, hemicelluloses, and lignin. As a major cell wall component, lignin in plants provides rigidity, internal transport of water and nutrients, and protection against attack by microorganisms [1]. It has been reported that lignin in lignified plants accounts for 16–36% by weight [2]. Due to the high content and complex structure, lignin plays a key role in pulping and other chemical conversion process of plants. Most importantly, lignin currently attracts widespread attention as a feedstock for biofuels and

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

biochemical production [3–5]. Broadening the knowledge of structural features of lignin is therefore necessary to help to effectively improve the economics of these processes.

#### **1.1. Lignin structure**

Lignin is the most abundant renewable aromatic biopolymer present in nature. To the best of current knowledge, lignin shows a heterogeneous composition and lacks a defined primary structure due to the special biosynthesis processes [6]. Lignin is generally considered to be synthesized mainly from three *p*-hydroxycinnamyl alcohols precursors, namely, *p*-coumaryl, coniferyl, and sinapyl alcohols. During the lignification process, each of these precursors gives rise to a different type of lignin unit called *p*-hydroxyphenyl (H), guaiacyl (G), and syringyl (S) units, respectively. This biosynthesis process consists of mainly radical coupling, and creates a unique lignin polymer in each plant species, even in different tissues of the same individual [7]. In general, softwood (spruce, pine, etc.) lignin consists almost entirely of G units,

**Figure 1.** Main structures of lignin, involving different side-chain linkages and aromatic units: (A) β-O-4 linkages; (A′) β-O-4 linkages with acetylated γ-carbon; (A″) β-O-4 linkages with *p*-coumaroylated γ-carbon; (B) resinol structures formed by β-β, α-O-γ and γ-O-α linkages; (C) phenylcoumarance structures formed by β-5 and α-O-4 linkages; (D) spirodienone structures formed by β-1 and α-O-α linkages; (E) α, β-diaryl ether substructures; (H) *p*-hydroxyphenyl unit; (G) guaiacyl unit; (S) syringyl unit; (I) cinnamyl alcohol end-groups; (J) cinnamyl aldehyde end-groups; (FA) ferulate; (PCA) *p*-coumarate; (T) tricin.

hardwood (beech, poplar, etc.) lignin is a mixture of G and S units, and herbaceous lignin (bamboo, reed, etc.) is composed of all the three units. These units are linked by several types of carbon-carbon (β-β, β-5, β-1, and 5–5) and ether bonds (β-O-4 and α-O-4) with various percentage. The β-O-4 linkages are the main lignin interunit linkages, accounting for more than 60% among various linkages. However, the less C─C linkages constitute some of the most difficult bonds to break [8]. In addition to lignin, the local noncovalent interaction and oxidative reactions among carbohydrates, phenolic components, and lignin render and control the formation of lignin-carbohydrate complex (LCC) during lignin biosynthesis processes [9, 10]. Other components, such as hydroxycynnamic acids and tricin, have been demonstrated to be incorporated into herbaceous lignin, apparently making the structure of lignin more complex [7]. **Figure 1** shows the structure of main components of lignin.

## **1.2. Methods for structural elucidation of lignin**

biochemical production [3–5]. Broadening the knowledge of structural features of lignin is

Lignin is the most abundant renewable aromatic biopolymer present in nature. To the best of current knowledge, lignin shows a heterogeneous composition and lacks a defined primary structure due to the special biosynthesis processes [6]. Lignin is generally considered to be synthesized mainly from three *p*-hydroxycinnamyl alcohols precursors, namely, *p*-coumaryl, coniferyl, and sinapyl alcohols. During the lignification process, each of these precursors gives rise to a different type of lignin unit called *p*-hydroxyphenyl (H), guaiacyl (G), and syringyl (S) units, respectively. This biosynthesis process consists of mainly radical coupling, and creates a unique lignin polymer in each plant species, even in different tissues of the same individual [7]. In general, softwood (spruce, pine, etc.) lignin consists almost entirely of G units,

**Figure 1.** Main structures of lignin, involving different side-chain linkages and aromatic units: (A) β-O-4 linkages; (A′) β-O-4 linkages with acetylated γ-carbon; (A″) β-O-4 linkages with *p*-coumaroylated γ-carbon; (B) resinol structures formed by β-β, α-O-γ and γ-O-α linkages; (C) phenylcoumarance structures formed by β-5 and α-O-4 linkages; (D) spirodienone structures formed by β-1 and α-O-α linkages; (E) α, β-diaryl ether substructures; (H) *p*-hydroxyphenyl unit; (G) guaiacyl unit; (S) syringyl unit; (I) cinnamyl alcohol end-groups; (J) cinnamyl aldehyde end-groups; (FA) feru-

therefore necessary to help to effectively improve the economics of these processes.

236 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**1.1. Lignin structure**

late; (PCA) *p*-coumarate; (T) tricin.

Lignin chemists have devoted their efforts to reveal the molecular details of lignin structure over the past few decades. Various wet-chemistry methods have been developed. Permanganate oxidation, nitrobenzene oxidation, GC-MS pyrolysis, thioacidolysis, and derivatization followed by reductive cleavage (DFRC) methods partially degrade lignin polymer and release diagnostic monomers, which reveals H/G/S composition in lignin. The presence of acylating groups in some herbaceous lignins is well known for a long time. A modified DFRC method (DFRC′) was developed for naturally acetylated lignin moieties determination [11]. Though significant strides have been made in elucidating the chemical structure of lignin by wetchemistry methods, they have not yet been completely elucidated. Only a fraction of lignin was analyzed and significantly different results were obtained even for the same sample by different wet-chemistry methods. Moreover, all protocols provide relative comparison in an array of samples rather than giving the absolute quantitative values.

Attempts through the years have been made to develop nondestructive and quantitative methods for w using molecular spectroscopic methods. Molecular spectra see differences in chemical structure of lignin that it is invisible for other analytical methods. Acid-soluble lignin in biomass is determined to be less than 4% by ultraviolet (UV) spectroscopy based on Beer' Law. On the other hand, the level of purity originated from different resources was easily determined by comparison of the extinction coefficients [12]. Despite some constituents can also be found from the UV spectra, further evidence is needed to confirm that. To date, natural lignin is found to contain several functional groups and chromophores which can be qualitatively determined by Fourier transform infrared (FT-IR) spectroscopy, FT-Raman spectroscopy, and fluorescence spectroscopy [13–15]. FT-IR spectroscopy is the most widely distributed as a modern and powerful analytical technique. The structural changes during physical and chemical pretreatment were monitored, which revealed the mechanism [16, 17]. However, no quantitative information about both lignin interunit linkages and S/G/H composition was achieved until the application of nuclear magnetic resonance (NMR). Development of 1D, 2D, and 3D NMR spectroscopic methods provides a powerful tool for lignin analysis. Evidence of the presence of lignin substructure dibenzodioxocine and spirodienone in lignin was first observed by the NMR spectroscopic methods [18, 19]. It is noted that more detailed structure of the whole macromolecule can be obtained by NMR spectroscopic methods. In addition to the structure details, the absolute amount of the side chain moieties and functional groups can be determined by combination of 13C NMR and 2D HSQC NMR spectroscopic methods [20].

This chapter describes the application of UV spectroscopy, fluorescence spectroscopy, FT-IR spectroscopy, FT-Raman spectroscopy, and various one-dimensional and multidimensional NMR spectroscopic methods in lignin structure determination.

## **2. UV spectroscopy**

Ultraviolet spectroscopy has been widely applied to quantitatively measure the acid-soluble lignin content, semiquantitatively determining the lignin purity, and predicting the possible lignin constituents [21–23]. The location of maximum absorption and the extinction coefficient of it are the two main factors that determine the properties of lignin.

Capitalizing on the stronger absorbance of lignin compare with carbohydrates in the UV region, the amount of acid-soluble lignin can be determined by applying Beer' Law. In 1985, a standard protocol was developed by the Technical Association of the Pulp and Paper Industry (TAPPI) to determine the amount of acid-soluble lignin and was applied widely across the world [24–26]. However, the accuracy is affected by measuring the absorbance at 200–205 nm, where carbohydrate monomers may also absorb light. Moreover, the extinction coefficient that is used varied with the type of lignin. In 2008, more accurate method of laboratory analytical procedure (LAP) of biomass was provided by the National Renewable Energy Laboratory (NREL) [27]. For the measurement, the absorbance of ASL was recorded at the recommended wavelength, which varied among plant species. Nowadays, many scientists use LAP for the determination of ASL in untreated and pretreated biomass. Our previous research applied LAP procedure to determine the content of ASL before and after ionic liquid-acid pretreatment, and an increased ASL was found [17]. Likewise, Rajan et al. used NREL methods to reveal the effect of dilute acid pretreatment on ASL of wheat straw [28].

Generally, the UV spectrum of lignin exhibits several absorption maxima at around wavelengths of 200, 240, 280, and 320 nm, which originate from the intrinsic structure [29]. Occurrence of the maximum absorption at around 200 nm in UV spectra is corresponding to the π→π\* electronic transition in the aromatic ring of lignin structure. Maxima at around 240 and 282 nm probably originate from the free and etherified hydroxyl groups. Phenolic structure and phenylpropane units (S, G) in lignin also can be detected from the UV spectra [22, 30]. It is reported that a pure syringyl lignin has an absorption maximum at 270–273 nm, whereas a red shift to 280–282 nm and three times stronger extinction coefficient are found in a pure guaiacyl lignin [22]. As for the maximum absorption at around 320 nm, it is attributed to π→π\* transitions in lignin units with Cα═Cβ linkages conjugated with aromatic ring and n→π\* transition in lignin units containing Cα═O groups. In herbaceous plants, bound hydroxycinnamic acid especially a predominance of esterified *p*-coumaric acid or etherified ferulic acid may contribute to the appearance of it [7, 31].

of the whole macromolecule can be obtained by NMR spectroscopic methods. In addition to the structure details, the absolute amount of the side chain moieties and functional groups can be determined by combination of 13C NMR and 2D HSQC NMR spectroscopic methods [20].

This chapter describes the application of UV spectroscopy, fluorescence spectroscopy, FT-IR spectroscopy, FT-Raman spectroscopy, and various one-dimensional and multidimensional

Ultraviolet spectroscopy has been widely applied to quantitatively measure the acid-soluble lignin content, semiquantitatively determining the lignin purity, and predicting the possible lignin constituents [21–23]. The location of maximum absorption and the extinction coefficient

Capitalizing on the stronger absorbance of lignin compare with carbohydrates in the UV region, the amount of acid-soluble lignin can be determined by applying Beer' Law. In 1985, a standard protocol was developed by the Technical Association of the Pulp and Paper Industry (TAPPI) to determine the amount of acid-soluble lignin and was applied widely across the world [24–26]. However, the accuracy is affected by measuring the absorbance at 200–205 nm, where carbohydrate monomers may also absorb light. Moreover, the extinction coefficient that is used varied with the type of lignin. In 2008, more accurate method of laboratory analytical procedure (LAP) of biomass was provided by the National Renewable Energy Laboratory (NREL) [27]. For the measurement, the absorbance of ASL was recorded at the recommended wavelength, which varied among plant species. Nowadays, many scientists use LAP for the determination of ASL in untreated and pretreated biomass. Our previous research applied LAP procedure to determine the content of ASL before and after ionic liquid-acid pretreatment, and an increased ASL was found [17]. Likewise, Rajan et al. used NREL methods to reveal the

Generally, the UV spectrum of lignin exhibits several absorption maxima at around wavelengths of 200, 240, 280, and 320 nm, which originate from the intrinsic structure [29]. Occurrence of the maximum absorption at around 200 nm in UV spectra is corresponding to the π→π\* electronic transition in the aromatic ring of lignin structure. Maxima at around 240 and 282 nm probably originate from the free and etherified hydroxyl groups. Phenolic structure and phenylpropane units (S, G) in lignin also can be detected from the UV spectra [22, 30]. It is reported that a pure syringyl lignin has an absorption maximum at 270–273 nm, whereas a red shift to 280–282 nm and three times stronger extinction coefficient are found in a pure guaiacyl lignin [22]. As for the maximum absorption at around 320 nm, it is attributed to π→π\* transitions in lignin units with Cα═Cβ linkages conjugated with aromatic ring and n→π\* transition in lignin units containing Cα═O groups. In herbaceous plants, bound hydroxycinnamic acid especially a predominance of esterified *p*-coumaric acid or etherified

NMR spectroscopic methods in lignin structure determination.

238 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

of it are the two main factors that determine the properties of lignin.

effect of dilute acid pretreatment on ASL of wheat straw [28].

ferulic acid may contribute to the appearance of it [7, 31].

**2. UV spectroscopy**

**Figure 2.** UV spectra of stem milled wood lignin (MWL), foliage MWL, stem alkaline lignin (AL), and foliage AL from *A. donax*. The lignin fractions were dissolved in DMSO, and scanned from 500 to 190 nm on a UV 2300 spectrophotometer (reprinted with permission from [7]. Copyright 2013 American Chemical Society).

The UV spectroscopic patterns of lignin cary among plant species. It has been demonstrated that the maximum of the absorption curve of milled wood lignin (MWL) from spruce fibers is at about 280 nm, whereas the UV spectra of acid insoluble lignin fractions from shrubs *Caligonum monogoliacum* and *Tamarix* spp. exhibits two absorption maxima at around 245 and 280 nm [22, 32]. It is noted the UV spectra of grasses are somewhat different from wood species. Apart from the first maximum absorption at 284 nm, a shoulder peak at around 320 nm is always appeared in the UV spectrum of lignin from grasses [7, 33]. For instance, esterified *p*coumaric acid is the main component if the wavelength of maximum absorption is shorter than 320 nm. In contrast, the wavelength of maximum absorption at 325 nm is indicative of rich etherified ferulic acid in lignin. **Figure 2** shows UV absorption spectra of stem MWL, foliage MWL, stem alkaline lignin (AL), and foliage AL from energy crops *Arundo donax* Linn. that reprinted from our previous article [7]. As illustrated, two maximum absorptions were found at around 284 and 310 nm in the spectra of lignin fractions. It can be inferred that the four lignin fractions may contain free and etherified hydroxyl groups, and bound *p*-coumaric acid.

UV spectroscopy has been used to semiquantitatively determine the purity of lignin with respect to the concentration. According to Beer's Law (*A* = *εcd*, where *A* = absorbance, ε = extinction coefficient, *d* = path length, *c* = concentration), the value of extinction coefficient reveals the concentration of lignin. The low extinction coefficient of lignin is due to the high amount of nonlignin materials. As aforementioned, lignin in plant tissue does not exist as an independent polymer but bonded with polysaccharides, which can be coextracted. The presence of a variety of variable abundances of lignin-carbohydrate bonds among different plant species makes it difficult to isolate lignin purely and completely. Sugar analysis of isolated cellulolytic enzyme lignin from Douglas fir, redwood, white fir, *Eucalyptus globulus* Labill., *A. donax*, and poplar wood revealed that lignin contained relatively noticeable amount (7.74–20%) of associated carbohydrates [34–36], which reduces the level of purity. Moreover, lignin fractions isolated from lignocellulosic biomass still contain other nonlignin contaminants, for instance, ash. Specifically, the ash content in technical lignins such as lignosulfonate (LS) and kraft lignin (KL) is up to 9.4 and 27.1%, respectively [37]. A certain amount of ash in lignin was demonstrated to decrease the extinction coefficient. Sun et al. found that the relatively lower absorption of lignin fractions was probable due to the higher amounts of coextracted nonlignin materials such as ash and salts [21].

**Figure 3.** Cross section of Epon embedded tracheids of black spruce earlywood photographed in ultraviolet light of wavelength 240 nm. The densitometer tracing was taken across the tracheid wall on the dotted line (reprinted with permission from [38]. Copyright 1969 Springer).

Apart from UV spectroscopy, UV microscopy has been used in a number of studies to monitor the lignin distribution among various tissues of gymnosperm and dicotyledonous angiosperm in respect to the concentration by comparison of UV absorbance. UV light transmits through ultrathin sections (0.5 μm) of wood and measure within the wavelength range 240–320 nm of lignin absorption. From the absorbance and the cell wall dimensions, the concentrations of lignin in cell wall layering structure of earlywood of black spruce (**Figure 3**) are determined to decrease in the order: the cell comers > the compound middle lamella > the secondary wall [22, 38].

## **3. Fluorescence spectroscopy**

Fluorescence spectroscopy has been used for the analysis of lignin constituents in wastewaters from pulp mills in the 1970s [14]. Subsequently, scientists focus a lot on the fluorescence properties of lignin. Lundquist et al. have investigated the fluorescence spectra of a variety of model compounds, lignin, and lignin-related products to establish a basis for the interpretation of the fluorescence results [39]. By comparing the fluorescence spectra (emission spectra and excitation spectra) of lignin with the structural elements, the possible chromophores can be determined.

Dioxane-water or water is a good solvent for the dissolution of lignin as the absorbance of these solutions is less than 0.05. This implied that the intensity of the emitted light (*Q*) can be expressed by the following equation [39, 40]: *Q* = *I0* (2.3*εcd*) *Φf* , where *(I0* = intensity of the incident light, *ε* = molar absorptivity, *c* = concentration in moles per liter, *b* = sample path length, *Φf* = quantum efficiency for fluorescence). Albinsson et al. dissolved the untreated and borohydride-reduced MWL from spruce in dioxane-water 9:1 for the fluorescence spectra collecting [14]. Lundquist et al. used either water or dioxane-water 1:1 as the solvents to explore the fluorescence properties of lignin sulfonate, MWL, and kraft lignin [39].


**Table 1.** Fluorescence properties of lignin materials.

Labill., *A. donax*, and poplar wood revealed that lignin contained relatively noticeable amount (7.74–20%) of associated carbohydrates [34–36], which reduces the level of purity. Moreover, lignin fractions isolated from lignocellulosic biomass still contain other nonlignin contaminants, for instance, ash. Specifically, the ash content in technical lignins such as lignosulfonate (LS) and kraft lignin (KL) is up to 9.4 and 27.1%, respectively [37]. A certain amount of ash in lignin was demonstrated to decrease the extinction coefficient. Sun et al. found that the relatively lower absorption of lignin fractions was probable due to the higher amounts of

240 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 3.** Cross section of Epon embedded tracheids of black spruce earlywood photographed in ultraviolet light of wavelength 240 nm. The densitometer tracing was taken across the tracheid wall on the dotted line (reprinted with

Apart from UV spectroscopy, UV microscopy has been used in a number of studies to monitor the lignin distribution among various tissues of gymnosperm and dicotyledonous angiosperm in respect to the concentration by comparison of UV absorbance. UV light transmits through ultrathin sections (0.5 μm) of wood and measure within the wavelength range 240–320 nm of lignin absorption. From the absorbance and the cell wall dimensions, the concentrations of lignin in cell wall layering structure of earlywood of black spruce (**Figure 3**) are determined to decrease in the order: the cell comers > the compound middle lamella > the secondary wall

Fluorescence spectroscopy has been used for the analysis of lignin constituents in wastewaters from pulp mills in the 1970s [14]. Subsequently, scientists focus a lot on the fluorescence properties of lignin. Lundquist et al. have investigated the fluorescence spectra of a variety of

coextracted nonlignin materials such as ash and salts [21].

permission from [38]. Copyright 1969 Springer).

**3. Fluorescence spectroscopy**

[22, 38].

Nonradiative energy transfer from lignin chromophores is excited to an acceptor and then emits the fluorescent light. Excitation spectra and emission spectra were collected on a spectrofluorimeter. Generally, the emission spectra are recorded at the wavelengths of the excitation maxima and the excitation spectra are recorded at the wavelengths of the emission maxima. **Table 1** shows the fluorescence properties of lignin materials [14, 39]. As can be seen, emission spectra of MWL from spruce exhibit a maximum at about 360 nm on excitation at different wavelengths in the range 240–320 nm. For the MWL from birch, emission spectra exhibit a maximum at 350 nm. A great difference is found for the fluorescence properties of technical lignin, such as kraft lignin or lignin sulfonate. The emission spectra of these lignins exhibit a maximum at about 400 nm on excitation at different wavelengths in the range 240– 350 nm.

Examination of the fluorescence spectra of lignin samples and model compounds suggested the possible chromophores. If the structural elements spectra closely match the emission from the lignins, it points to the possibility that the lignin fluorescence is mainly emitted from that structure of lignin. Based on these, small amounts of phenylcoumarone structures are found in lignin from pretreated acid or balling materials [14]. Reduction of carbonyl in lignin by borohydride does not change the position of emission maximum but increase the fluorescence intensity due to some "energy sink" structure in lignin. It has been determined that the "energy sink" structure could be arylconjugated carbonyl groups such as cinnamyl alcohol or phenylcoumarone type and stilbene structure.

Lignocellulosic biomass is known to be autofluorescent. Compared with holocellulose, the autofluorescent of lignin is generally much brighter [41, 42]. Laser scanning confocal fluorescence microscopy (LSCFM) allowed direct visualization of the relative amounts of lignin in different cell types on a semiquantitative basis. Based on the brightness of fluorescence images, the relative amounts of lignin in different regions of the cell wall in different cell types can be measured [43]. Donaldson et al. used confocal fluorescence microscopy (FM) to provide semiquantitative information in different regions based on lignin autofluorescence, and by staining with acriflavine [44]. The level of lignification in different plant species was then determined. FM was also used to investigate the cell wall structure changes during chemical pretreatment of biomass [45].

## **4. FT-IR and FR-Raman spectroscopy**

Fourier transform infrared and FT-Raman spectroscopic methods have been described as an efficient measurement of valuable plant components, such as lipids, fatty acids, carbohydrates, phenolic substances, and so forth [46]. Results from both FT-IR and FT-Raman spectroscopy are in general agreement and provide complimentary information. Both techniques are nondestructive, rapid, and accurate and use only microscale samples. Differed from FT-IR spectroscopy, FT-Raman spectroscopy is insensitive to water. Hence, it is more suitable to perform in situ studies of fresh plant materials that contained some moisture by FT-Raman spectroscopy. The application of these two techniques to numerous research areas has already provided useful information on lignin.

#### **4.1. FT-IR spectroscopy**

FT-IR spectroscopy is a nondestructive, noninvasive, high sensitivity, and rapid method for lignin structure investigation or wood constituent determination widely use by lignin and wood chemists as a molecular probe [13, 47, 48]. This method opens perspective to quantify lignin in samples and semiquantitative and qualitative analyses of lignin structure characteristic.

#### *4.1.1. FT-IR spectra assignment*

Much work has been published on the characterization of lignin, and a lignin FT-IR-spectrum library has been established over the past few decades. Transmission or diffuse reflectance spectra in the midinfrared (4000–200 cm−1) have been shown to provide reliable information on the chemical properties of lignin fractions or lignin in wood. Before the analysis, all of the spectra should be baseline corrected and normalized. In the region 3800–2750 cm−1, several bands are observed which are caused by the presence of alcoholic and phenolic hydroxyl groups and the methyl and methylene groups in lignin [47]. More bands are clearly discernible with deconvolution. In more detail, a wide absorption band appearing at 3580–3550 cm−1 is derived from free hydroxyl group in phenolic and alcoholic structures. Additionally, signals in the region 3000–2750 cm−1 are predominantly arising from C-H stretching in aromatic methoxyl groups and in methyl and methylene groups of the side chain. Fatty acid present in lignin undoubtedly increases the intensity of C-H stretching [49]. Demethylation or methylation affects the intensity of these bands sharply. It has been reported that the intensity of O-H stretching peak reduces dramatically upon methylation, whereas the intensity of peaks corresponding to C-H stretching increased simultaneously [50].

borohydride does not change the position of emission maximum but increase the fluorescence intensity due to some "energy sink" structure in lignin. It has been determined that the "energy sink" structure could be arylconjugated carbonyl groups such as cinnamyl alcohol or phenyl-

242 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

Lignocellulosic biomass is known to be autofluorescent. Compared with holocellulose, the autofluorescent of lignin is generally much brighter [41, 42]. Laser scanning confocal fluorescence microscopy (LSCFM) allowed direct visualization of the relative amounts of lignin in different cell types on a semiquantitative basis. Based on the brightness of fluorescence images, the relative amounts of lignin in different regions of the cell wall in different cell types can be measured [43]. Donaldson et al. used confocal fluorescence microscopy (FM) to provide semiquantitative information in different regions based on lignin autofluorescence, and by staining with acriflavine [44]. The level of lignification in different plant species was then determined. FM was also used to investigate the cell wall structure changes during chemical

Fourier transform infrared and FT-Raman spectroscopic methods have been described as an efficient measurement of valuable plant components, such as lipids, fatty acids, carbohydrates, phenolic substances, and so forth [46]. Results from both FT-IR and FT-Raman spectroscopy are in general agreement and provide complimentary information. Both techniques are nondestructive, rapid, and accurate and use only microscale samples. Differed from FT-IR spectroscopy, FT-Raman spectroscopy is insensitive to water. Hence, it is more suitable to perform in situ studies of fresh plant materials that contained some moisture by FT-Raman spectroscopy. The application of these two techniques to numerous research areas has already

FT-IR spectroscopy is a nondestructive, noninvasive, high sensitivity, and rapid method for lignin structure investigation or wood constituent determination widely use by lignin and wood chemists as a molecular probe [13, 47, 48]. This method opens perspective to quantify lignin in samples and semiquantitative and qualitative analyses of lignin structure character-

Much work has been published on the characterization of lignin, and a lignin FT-IR-spectrum library has been established over the past few decades. Transmission or diffuse reflectance spectra in the midinfrared (4000–200 cm−1) have been shown to provide reliable information on the chemical properties of lignin fractions or lignin in wood. Before the analysis, all of the spectra should be baseline corrected and normalized. In the region 3800–2750 cm−1, several bands are observed which are caused by the presence of alcoholic and phenolic hydroxyl

coumarone type and stilbene structure.

pretreatment of biomass [45].

**4. FT-IR and FR-Raman spectroscopy**

provided useful information on lignin.

**4.1. FT-IR spectroscopy**

*4.1.1. FT-IR spectra assignment*

istic.

The investigation of more complex fingerprint region is necessary to facilitate understanding of the intact lignin characteristics. Bands found at around 1735 and 1714 cm−1 are originated from unconjugated carbonyl-carboxyl stretching in ketones, carbonyls, and ester groups [13]. Esterified phenolic acids and acetyls from associated hemicelluloses are the contributors to these absorption bands. The intensity of these bands also increased when a ketone or an aldehyde structure is produced [51]. However, the occurrence of a serial of absorption peaks at range 1675–1655 cm−1 is corresponding to conjugated carbonyl-carboxyl stretching. Hergert et al. concluded that the peak at 1660 cm−1 was originated from a ketone group located at α position, whereas the peak at 1712 cm−1 was assigned to a ketone group located at β position [52]. It is noteworthy that sharp bands at 1653 cm−1 from the spectrum of oven-dried samples are probably arising from the tricin associated with lignin especially from nonwood biomass [7, 25, 53].

Every lignin FT-IR spectrum shows prominent absorptions at around 1600, 1510, and 1420 cm −1 and the C─H deformation combined with aromatic ring vibration at 1460 cm−1. The first three bands are assigned to the aromatic skeleton vibrations in lignin, which is the "core" structure of lignin. According to the classification of lignin proposed by Faix, the FT-IR spectra of lignin are divided into three categories, i.e., G type, GS type, and GSH type [13]. The spectra of type G lignins show typical feature at 1140 cm−1, which originates from aromatic C─H in-plane deformation. Structure features of G type lignin are primary found in the spectrum of softwood lignin. Generally, the spectra of lignin samples from softwood, such as pine and spruce, show absorptions at 1269 cm−1 (G ring and C═O stretch), 1140, 854, and 817 cm−1 (C─H out-of-plane vibrations at positions 2, 5, and 6 of G units). Lignin from hardwood such as poplar, birch, and beech belongs to GS type according to the IR classification criteria [13]. GS type lignin exhibites typical features at a wavenumber at around 1128 (aromatic C─H in-plane deformation), 1328 (S ring plus G ring condensed), and 834 cm−1 (C─H out-of-plane in position 2 and 6 of S). Furthermore, the spectra within the GS category are subdivided into four groups based on different intensities of each band. In the samples from *A. donax* and bamboo, the absorption band at 1167 cm−1 which is attributed to C═O in ester groups (conjugated) is additionally present compared to the spectra of GS and G type lignin [7, 54]. Hence, maxima absorption at 1167 cm−1 is typical only for GSH type lignin. Signals from lignin functional groups such as phenolic hydroxyl group can be found at 1370–1375 cm−1. As small amount of carbohydrate is apt to associate with lignin, aromatic C─H deformation at 1035 cm−1 appears as a complex vibration associated with the C─O, C─C stretching and C─OH bending in polysaccharides. For more details, see **Table 2** [7, 13, 47, 55].


**Table 2.** Main assignments of lignin in FT-IR bands.

#### *4.1.2. Qualitative and semiquantitative analysis*

FT-IR spectroscopy reflects the chemical structure of lignin. As a result, the native characteristics are uncovered and the structural changes taking place in samples are monitored. Huang et al. found that some tannin was possibly condensed with bark lignin by comparing with the FT-IR spectra discrepancy of MWLs from loblolly pine stem wood, residue, and bark [26]. Moreover, all of the three MWLs belonged to G type lignin. Differed from the softwood lignin, MWL from energy crops *A. donax* showed features of GSH type lignin. A treatment is involved in efficient utilization of lignocellulosic biomass. It is demonstrated that the "core" structure of lignin samples isolated by alkaline, ionic liquid, organic solvents, acid, and thermal treatment does not change significantly. However, the absorption frequencies correspond to the vibrational motions of the nuclei of a functional group show distinct changes when the chemical environment of the functional group is modified. Jia et al. found that a ketone structure was produced during acidic ionic liquid treatment of lignin model compound by comparing the FT-IR spectra that resulted from the cleavage of β-O-4 linkage [51]. Chen et al. have reported that the shift of 1505–1510 cm−1 accompanied with the increased intensity of the band at 1321 cm−1 identified by attenuated total reflectance (ATR)-FTIR spectra of lignin indicated the occurrence of condensed reaction during the heat treatment [56]. It should be noted that the ATR-FTIR only quantitatively determined the chemical changes in the surface of the samples. Further evidence was needed to confirm that.

Apart from the qualitative analysis, FT-IR spectroscopy has been utilized as a means of relative quantifying lignin in samples. Raiskila et al. have developed a method based on the FT-IR spectra to determine the relative amount of lignin in a large amount of samples [57]. In addition to the lignin content determination, the condensation indices (i.e., the cross-linking indexes) of lignin reflect the condensation degree of lignin, which can be expressed by the following formula [58, 59]:

> -1 -1 Sum of all minima between 1500 and 1050 cm CI= Sum of all mixima between 1600 and 1030 cm

Lignin condensation always occurred during the acid treatment or the severe ball milling. The quantitatively analysis of the CI by using FT-IR spectroscopy is extremely convenient and time saving. Furthermore, the Abs. 1742/Abs. 1768 ratio is positive in connection with the phenolic hydroxyl group in lignin [60].

## **4.2. FT-Raman spectroscopy**

**Frequency (cm−1)**

**Assignment Comments**

3000–2840 ν (C─H) C─H stretching vibrations in methyl and methylene of side chains 1738–1709 ν (C═O) C═O stretching in unconjugated ketone, carbonyl and ester;

244 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

1699–1633 ν (C═O) C═O stretching in conjugated aldehydes and carboxylic acids absorb around and

1593–1605 ν (Ar), ν(C═O) Aromatic skeletal vibrations of S and G (S > G) plus C═O Stretching; S > G and G

1167 ν (C═O) Typical for HGS type lignin; C═O stretching inconjugated ketone, ester groups

1030–1035 ν (C─H) The aromatic C─H deformation acting as a complex vibration associated with the C─O, C─C stretching and C─OH bending

834 ν (C─H) C─H out of plane in position 2 and 6 of S units, and in all positions of H units

FT-IR spectroscopy reflects the chemical structure of lignin. As a result, the native characteristics are uncovered and the structural changes taking place in samples are monitored. Huang et al. found that some tannin was possibly condensed with bark lignin by comparing with the FT-IR spectra discrepancy of MWLs from loblolly pine stem wood, residue, and bark [26]. Moreover, all of the three MWLs belonged to G type lignin. Differed from the softwood lignin, MWL from energy crops *A. donax* showed features of GSH type lignin. A treatment is involved in efficient utilization of lignocellulosic biomass. It is demonstrated that the "core" structure of lignin samples isolated by alkaline, ionic liquid, organic solvents, acid, and thermal treatment does not change significantly. However, the absorption frequencies correspond to

C─C, C─O and C═O stretching (G condensed > G etherified)

below 1700 cm−1

below 1700 cm−1

1510 ν (Ar) aromatic skeletal vibrations of S and G (G > S) 1460 ν (C─H) Asymmetric C─H deformations in ─CH3 and ─CH2

1365–1370 ν (C─H), ν (O─H) Aliphatic C─H stretching in CH3 and phenolic OH

1124 δ (C─H) Aromatic C─H bending in-plane (typical for S units)

966–990 ν (─HC═CH─) ─HC═CH- out-of-plane deformation (trans) 853–858 ν (C─H) C─H out of plane in position 2, 5, and 6 of G units

1655–1675 ν (C═O) C═O stretching in conjugated para-substitute aryl ketones

Condensed > G etherified

1420 ν (Ar) Aromatic skeletal vibrations combined with C─H in-plane deform

1684 ν (C═O) *β*-enone carbonyl stretching modes

1267 ν (Ar), ν(C═O) G ring and C═O stretching

**Table 2.** Main assignments of lignin in FT-IR bands.

*4.1.2. Qualitative and semiquantitative analysis*

1221–1230 ν (C═O), ν (C─O), ν (C─C)

C═O stretching in conjugated aldehydes and carboxylic acids absorb around and

1064 nm excited FT-Raman spectroscopy overcomes the obstacle of lignin autofluorescence, and the Raman spectra of acceptable quality for lignin or lignin-related materials can be obtained. Compared with the FT-IR spectra, more bands can be detected in the FT-Raman spectra. It has been reported that in neat state only about 60% of the bands of the total detected FT-Raman bands are detected in the FT-Raman spectra, implying that 40% of the bands could only be detected by FT-Raman [62]. In addition, fresh plants even with some extract present in them do not affect the FT-Raman spectral data. It is therefore significant to use both Raman and IR analyses to obtain the most detailed chemical information of lignin.

#### *4.2.1. FT-Raman spectra assignment*

The band assignment information in a lignin FT-Raman spectrum has been achieved primarily by Agarwal and his group [15, 61–64]. In general, the spectra are divided into three regions: 3200–2700, 1850–1350, and 1450–250 cm−1 region. In the region 3200–2700 cm−1, several bands derived from the aliphatic and aromatic C─H stretches are detected. By studying the spectra of benzene derivatives and lignin models, it is determined that band at around 3070 cm−1 is likely to be due to the aromatic C─H stretch. The bands at approximately 3007 and 2938 cm−1 are originated from the asymmetric aliphatic C─H stretch like methoxy and acetoxy groups, whereas the band at 2843 cm−1 can be assigned to the symmetric aliphatic C─H stretch. A high amount of S units and acetylation or methylation treatments give particularly more intense 2938 cm−1 band [15]. Another band at 2890 cm−1 is assigned to the C─H stretch in R3C─H structures.

The 1850–1350 cm−1 region is the most informative region for lignin. This region contains bands due to aromatic rings, ring-conjugated ethylenic C═C, α- and γ-C═O, and the *o*- and *p*quinones. Every FT-Raman spectrum of lignin exhibited a strong band at about 1600 cm−1, and can be used to normalize the spectra. This band is due to the aromatic ring stretch, and the band intensity is enhanced by the conjugation and resonance Raman effect [62]. Nonsymmetrical shape of the band suggested that two more components are included. After curve-fit treatment of the band of lignin from hardwood samples, S-marker and G-maker bands occurred. The calculation of these two bands would be a good probe to quantify the S/G ratio [65]. The band at 1660 cm−1 is assigned to ethylenic C═C bond in coniferyl alcohol units and the γ-C═O in coniferaldehyde units in lignin, whereas the band at 1630 cm−1 is found to be associated with the ring-conjugated C═C bond in coniferaldehyde units.

The 1450–250 cm−1 region reveals more details of lignin substructures. FT-Raman study of a large number of dehydrogenation polymer (DHP) lignin and hydroxycinnamic acid standard compounds is essential to establish a basis for the interpretation of FT-Raman spectra for lignin. Agarwal et al. collected and compared the spectra of G-DHP, S-DHP, and H-DHP lignin [63]. It was demonstrated that the bands at 371, 1041, 1333, and 1456 cm−1 were mainly resulted from the S type lignin, whereas the band at 1271 cm−1 was originated from G type lignin. Further investigation of softwood and hardwood MWLs confirmed these assignments. After a preliminary study of the spectra of hydroxycinnamic acid standard compounds and lignin, we recently showed that the band at 1173 cm−1 was assigned to C═O vibration form esterified or free hydroxycinnamic acid from grass *A. donax* [66]. A similar band at around 1173 cm−1 was also found in the spectra of switchgrass. Another band at about 1202 cm−1 is attributed to ring deformation and aryl-OCH3 and aryl-OH in-plane bending from H type lignin [67].

#### *4.2.2. Qualitative and semiquantitative analysis*

Similar to FT-IR spectroscopy, FT-Raman spectroscopy is useful to the rapid characterization of lignin. The basic lignin units and functional groups in different lignocellulosic biomass are easy to identify from the FT-Raman spectra according to the bands assignments aforementioned. Raman spectral changes show the modification of lignin aroused by chemical, mechanical, or biological treatment [15, 64]. The spectral data changes of lignin treated by acetylation, methylation, diimide treatment, and alkaline hydrogen peroxide bleaching are achieved [15].

Some of the bands in the Raman spectra are applied to quantify lignin content or lignin structure. It is interesting to found that the intensity (peak area) of band at 1600 cm−1 of lignin is linearly related to the kappa number of pulp (*R*<sup>2</sup> = 0.98). The residual lignin content in bleaching pulp is therefore obtained by calculating the peak area of band at 1600 cm−1. It is well known that significant variation in the S/G ratio exists among different plant species. A spectral deconvolution method based on FT-Raman spectroscopy holds significant promise in the rapid and accurate determination of S/G ratio quantitatively [65].

## **5. NMR spectroscopy**

3007 and 2938 cm−1 are originated from the asymmetric aliphatic C─H stretch like methoxy and acetoxy groups, whereas the band at 2843 cm−1 can be assigned to the symmetric aliphatic C─H stretch. A high amount of S units and acetylation or methylation treatments give particularly more intense 2938 cm−1 band [15]. Another band at 2890 cm−1 is assigned to the

The 1850–1350 cm−1 region is the most informative region for lignin. This region contains bands due to aromatic rings, ring-conjugated ethylenic C═C, α- and γ-C═O, and the *o*- and *p*quinones. Every FT-Raman spectrum of lignin exhibited a strong band at about 1600 cm−1, and can be used to normalize the spectra. This band is due to the aromatic ring stretch, and the band intensity is enhanced by the conjugation and resonance Raman effect [62]. Nonsymmetrical shape of the band suggested that two more components are included. After curve-fit treatment of the band of lignin from hardwood samples, S-marker and G-maker bands occurred. The calculation of these two bands would be a good probe to quantify the S/G ratio [65]. The band at 1660 cm−1 is assigned to ethylenic C═C bond in coniferyl alcohol units and the γ-C═O in coniferaldehyde units in lignin, whereas the band at 1630 cm−1 is found to be

The 1450–250 cm−1 region reveals more details of lignin substructures. FT-Raman study of a large number of dehydrogenation polymer (DHP) lignin and hydroxycinnamic acid standard compounds is essential to establish a basis for the interpretation of FT-Raman spectra for lignin. Agarwal et al. collected and compared the spectra of G-DHP, S-DHP, and H-DHP lignin [63]. It was demonstrated that the bands at 371, 1041, 1333, and 1456 cm−1 were mainly resulted from the S type lignin, whereas the band at 1271 cm−1 was originated from G type lignin. Further investigation of softwood and hardwood MWLs confirmed these assignments. After a preliminary study of the spectra of hydroxycinnamic acid standard compounds and lignin, we recently showed that the band at 1173 cm−1 was assigned to C═O vibration form esterified or free hydroxycinnamic acid from grass *A. donax* [66]. A similar band at around 1173 cm−1 was also found in the spectra of switchgrass. Another band at about 1202 cm−1 is attributed to ring

deformation and aryl-OCH3 and aryl-OH in-plane bending from H type lignin [67].

Similar to FT-IR spectroscopy, FT-Raman spectroscopy is useful to the rapid characterization of lignin. The basic lignin units and functional groups in different lignocellulosic biomass are easy to identify from the FT-Raman spectra according to the bands assignments aforementioned. Raman spectral changes show the modification of lignin aroused by chemical, mechanical, or biological treatment [15, 64]. The spectral data changes of lignin treated by acetylation, methylation, diimide treatment, and alkaline hydrogen peroxide bleaching are

Some of the bands in the Raman spectra are applied to quantify lignin content or lignin structure. It is interesting to found that the intensity (peak area) of band at 1600 cm−1 of lignin

bleaching pulp is therefore obtained by calculating the peak area of band at 1600 cm−1. It is well known that significant variation in the S/G ratio exists among different plant species. A spectral

= 0.98). The residual lignin content in

associated with the ring-conjugated C═C bond in coniferaldehyde units.

246 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

C─H stretch in R3C─H structures.

*4.2.2. Qualitative and semiquantitative analysis*

is linearly related to the kappa number of pulp (*R*<sup>2</sup>

achieved [15].

The structure of lignin macromolecule in plants is extreme complex. To investigate the structure of the whole lignin macromolecule, various nuclear magnetic resonance spectroscopic methods (one-dimensional and multidimensional NMR) in both solid and solution states are frequently utilized. Compare with other spectroscopic methods mentioned above, NMR spectroscopic methods have much higher resolution and enable a larger amount of information to be obtained. Solid-state 13C cross-polarization magic angle spinning (CPMAS) NMR spectroscopy allows the investigation of lignin structure in the native state and simultaneously avoids the chemical modification for sample preparation [68]. It is suitable for the analysis of lignin samples that have restricted solubility. However, due to the low resolution, only some structural features of lignin can be observed. Despite some improvements for the solid-state NMR have been made, it is still not routinely used. Solution-state NMR spectroscopy is more powerful in lignin structural elucidation. In solution, a much better resolution is obtained and a more detailed characterization of lignin aromatic and side chain is possible. Moreover, absolute quantification or relative quantification of each substructures and linkages can be unambiguously achieved [69–71]. One of the major factors that impede the application of solution-state NMR is the difficulty in dissolving lignin. In order to enhance the solubility, lignin is subjected to acetylation by anhydride/pyridine solution before the solution-state NMR spectra collection [72]. Briefly, 100 mg of lignin is dissolved in 4 mL of a solution of acetic anhydride: pyridine (1:1). After stirring for 24 h at room temperature under the exclusion of sunlight, the mixture is concentrated under reduced pressure. Then the mixture is dropped slowly into 200 mL of ice water (pH = 2.0) to induce precipitation, and the precipitate is washed with deionized water for several time. After centrifugation and freeze-drying, acetylated lignin is obtained. It is important to note that the chemical shift of lignin moieties will somewhat shift to a higher field after acetylation [69]. Recent advances in characterization of lignin polymer by solution-state NMR methodology have been reviewed [73].

## **5.1. One-dimensional NMR spectroscopy**

1D NMR spectroscopic methods including the solution-state 1 H NMR, solution- or solid-state 13C NMR, and solution-state 31P NMR have been utilized to routinely determine the amount of hydroxyl groups (aliphatic, phenolic, and carboxylic acid), interunit linkages, S units, G units, and H units in lignin. The databases of chemical shifts of these spectroscopies have been well established based on comparison with synthetic model compound data [74–78].

#### *5.1.1. 1 H NMR spectroscopy*

The 1 H NMR spectra of lignin can be obtained within a few minutes. **Table 3** lists the signal assignment of 1 H NMR data [79–82]. The integral of all signals between 6.0 and 8.0 ppm belongs to aromatic protons in G, S, and H units, whereas those between 1.60 and 2.40 ppm and from 5.76 to 6.18 ppm are due to the hydroxyl groups in lignin. Signals derived from linkages such as β-O-4 and β-1 substructures in lignin are found in the range of 2.98–3.14 and 5.76–6.18 ppm. Moreover, signals between 4.93 and 5.09 ppm are appeared in the spectrum of lignin that contained some carbohydrates. Integration of the spectra allows the quantification of some specific moieties, such as phenolic hydroxyl groups [83].


Note: \* CDCl3 was used as the solvent.

**Table 3.** Signal assignment for 1 H NMR spectroscopy of lignin\* .

#### *5.1.2. Quantitative 13C NMR spectroscopy*

Owing to the complex structure of lignin, there are many overlapping resonances on 1 H NMR spectra and only some of structure features are detected. The accuracy of calculation based on 1 H NMR spectra of lignin is relative low. To obtain the detailed molecular structures, both solidstate and solution-state 13C NMR spectroscopic methods have been applied to investigate the structural difference between lignin fractions from different plant species since 1981 [68, 84– 86]. In addition to 13C NMR spectra, the collection of distortionless enhancement by polarization transfer (DEPT) CH (*θ* = 135°) spectra of lignin has been found to have a synergetic effect [33]. 13C NMR spectroscopy allows the classification and quantification of lignin nondestructively. However, more than 24 h is needed to collect the quantitative 13C NMR spectra. To decrease the experiment time without affecting the quality of spectra, 0.01M chromium (III) triacetylacetonate (Cr(acac)3) is considered a relaxant which allows a 4-fold decrease in the experiment time. One has to take into account that the use of tetramethylsilane (TMS) as an internal reference (0.00 ppm) is significant. Additionally, it is noteworthy that differences in the location of some structures of lignin may happen due to their strong solvent dependency [19].

G units are identified by signals at 149.3 and 149.1 (C-3, G etherified), 147.8 and 147.4 (C-4, G etherified), 134.2 (C-1, G etherified), 119.0 (C-6, G), 114.8 and 114.6 (C-5, G), and 110.9 ppm (C-2, G). The S units are verified by signals at 152.0 (C-3/C-5, S), 147.8 and 147.4 (C-3/C-5, S nonetherified), 134.2 (C-1, S etherified), and 104.1 ppm (C-2/C-6 S). The H units are detected at 127.6 (C-2/C-6, H), 115.5 (C-3/C-5, H), and 159.8 ppm (C-4, H). Signals related to lignin linkages are also present. The resonance of C-β, C-α, and C-γ in β-O-4 linkages produces signals at 85.9, 72.1, and 59.5 ppm. Signals from β-β were detected at 71.3 (C-γ) and 54.1 ppm (C-β). Other C─C linkages such as signals from β-5 and 5–5 linkages are found to be 66.2 (Cγ) and 125.9 ppm (C-5), respectively. Additionally, signals from different functional (carbonyl, carboxyl, and hydroxyl) groups are also detected. Apart from signals from lignin, the carbohydrates impurity also produce signals at 100, 72.3, and 63.4 ppm. It is noted that the 13C NMR spectra of lignin is very complex and some signals can be overlapped by the impurity such as residual solvent and carbohydrates. Therefore, it is recommended that only a relative pure lignin fraction is suggested to analysis by this technique.

Estimation of lignin moieties and functional group is significant permitting more comprehensive information about the architecture and reactivity of lignin. The amount of side-chain moieties and functional groups can be estimated by integral at corresponding chemical shift in the spectra of lignin. The integral at 160–102 ppm is always set as the reference, assuming that it includes six aromatic carbons and 0.12 vinylic carbons; therefore, all moieties can be based on equivalences per aromatic ring [69]. However, signals belonging to carbon atoms of the same groups may be derived from different moieties. To calculate the amount of one of the moieties, the content of other moieties should be calculated first by other methods. For instance, signals at 50–48 ppm in the spectrum of both lignin belong to carbon atoms of phenylcoumaran and β-1 moieties [69]. Firstly, the amount of phenylcoumaran structures (0.03/Ar) was estimated from the resonance at about 87 ppm. Then, the integral at 50–48 ppm in the spectrum is calculated to be 0.05/Ar. Finally, the content of β-1 moieties can be calculated to be 0.02/Ar.

## *5.1.3. 31P NMR spectroscopy*

to aromatic protons in G, S, and H units, whereas those between 1.60 and 2.40 ppm and from 5.76 to 6.18 ppm are due to the hydroxyl groups in lignin. Signals derived from linkages such as β-O-4 and β-1 substructures in lignin are found in the range of 2.98–3.14 and 5.76–6.18 ppm. Moreover, signals between 4.93 and 5.09 ppm are appeared in the spectrum of lignin that contained some carbohydrates. Integration of the spectra allows the quantification of some

specific moieties, such as phenolic hydroxyl groups [83].

9.9–9.7 Aldehyde protons from cinnamaldehyde and benzaldehyde

248 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Signal (ppm) Assignment**

3.14–2.98 Hβ from β-1

**Table 3.** Signal assignment for 1

CDCl3 was used as the solvent.

*5.1.2. Quantitative 13C NMR spectroscopy*

Note: \*

1

[19].

7.15–6.75 Aromatic protons from G 6.75–6.25 Aromatic protons from S

6.18–5.76 Benzylic OH from β-O-4 and β-1 5.09–4.93 Protons from carbohydrates 4.00–3.33 Protons from methoxyl

2.40–2.20 Protons from acetylated phenolic OH groups

2.20–1.60 Protons from acetylated aliphatic OH groups and 5-5

H NMR spectroscopy of lignin\*

Owing to the complex structure of lignin, there are many overlapping resonances on 1

spectra and only some of structure features are detected. The accuracy of calculation based on

H NMR spectra of lignin is relative low. To obtain the detailed molecular structures, both solidstate and solution-state 13C NMR spectroscopic methods have been applied to investigate the structural difference between lignin fractions from different plant species since 1981 [68, 84– 86]. In addition to 13C NMR spectra, the collection of distortionless enhancement by polarization transfer (DEPT) CH (*θ* = 135°) spectra of lignin has been found to have a synergetic effect [33]. 13C NMR spectroscopy allows the classification and quantification of lignin nondestructively. However, more than 24 h is needed to collect the quantitative 13C NMR spectra. To decrease the experiment time without affecting the quality of spectra, 0.01M chromium (III) triacetylacetonate (Cr(acac)3) is considered a relaxant which allows a 4-fold decrease in the experiment time. One has to take into account that the use of tetramethylsilane (TMS) as an internal reference (0.00 ppm) is significant. Additionally, it is noteworthy that differences in the location of some structures of lignin may happen due to their strong solvent dependency

G units are identified by signals at 149.3 and 149.1 (C-3, G etherified), 147.8 and 147.4 (C-4, G etherified), 134.2 (C-1, G etherified), 119.0 (C-6, G), 114.8 and 114.6 (C-5, G), and 110.9 ppm

.

H NMR

Phosphitylation of hydroxyl groups in lignin followed by quantitative 31P NMR provides a valuable characterization tool for determination of the content of aliphatic hydroxyl groups, phenolic hydroxyl groups, and carboxyl group. Application of this method in lignin characterization has been reviewed by Pu et al [70]. 31P NMR spectra of MWL derivatized with 2 chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP) reproduced from our previous study are illustrated in **Figure 4**, and the signal assignments are labeled [17]. The quantitative results of these hydroxyl groups were obtained by peak integration with cyclohexanol (signals at 133.8–133.3 ppm) as internal standard (IS). Typical phosphitylating procedures are shown as follows.

Lignin sample (20 mg) was dissolved in anhydrous pyridine and deuterated chloroform (1.6:1, v/v, 500 μL) under stirring. Cyclohexanol (10.85 mg/mL, 100 μL) was added as an internal standard, followed by addition of chromium (III) acetylacetonate solution (5 mg/mL in anhydrous pyridine and deuterated chloroform 1.6:1, v/v, 100 μL) as a relaxation reagent. The mixture was reacted with TMDP (phosphitylating reagent, 100 μL) for about 10 min and placed into the NMR tube for 31P NMR analysis [7, 17].

**Figure 4.** Quantitative 31P NMR spectrum of a *A. donax* ball-milled lignin derivatized with TMDP using cyclohexanol as internal standard (reprinted with permission from [17]. Copyright 2015 American Chemical Society).

#### **5.2. Multidimensional NMR spectroscopy**

In traditional one-dimensional 1 H and 13C NMR spectra, the signals are heavily overlapped due to the very complex and heterogeneous structure of lignin and instrumental limitations [87]. In the course of time, modern solution-state two- and three-dimensional methods are developed as efficient tools to investigate the structure of lignin. Besides better resolution, the multidimensional methods provide more reliability to the assignments [88].

#### *5.2.1. Two-dimensional NMR spectroscopy*

Two-dimensional NMR spectroscopic methods such as heteronuclear multiple quantum coherence (HMQC) spectroscopy, homonuclear Hartmann-Hahn (HOHAHA) spectroscopy, total correlation (TOCSY) spectroscopy, rotating-frame Overhauser experiment (ROESY) heteronuclear single quantum coherence NMR (HSQC) spectroscopy, and heteronuclear multiple bond coherence (HMBC) have been employed in lignin structure characterization [25, 89–91]. Among these, advanced 2D HSQC NMR is the most extensively used due to its versatility in illustrating structural features and structural transformations of isolated lignin fractions. The interpretation of 2D HSQC NMR spectra of lignin has been facilitated by the application of HOHAHA, HMQC, TOCSY, and ROESY techniques. For instance, del Río et al. performed HMBC experiment to give important information about the connectivity of the ester moiety to the lignin skeleton, and ether linkages between lignin and tricin were proposed [25]. 1 H-1 H TOCSY correlation NMR analysis can further confirm the doubted assignment of crosspeak in the spectra of HMQC or HSQC [69]. The cellulolytic enzyme lignin of *A. donax* was shown in **Figure 5**, and the main substructures are depicted in **Figure 1**.

The basic composition (S, G, and H units) and various substructures linked by ether and carbon–carbon bonds (β-O-4, β–β, β-5, etc.) can be observed in the 2D HSQC spectra (**Figure 5**). In the aromatic region (*δ*C/*δ*H 150–90/8.0–6.0 ppm), S, G, and H units show prominent correlations at *δ*C/*δ*H 103.7/6.71 (S2,6), *δ*C/*δ*H 106.7/7.28 (Cα-oxidized S units S′), 110.7/6.98 (G2), 114.9/6.72 and 6.94 (G5), 118.7/6.77 (G6), 127.8/7.22 (H2,6), and 115.4/6.63 (H2,6), respectively. It is noted that some signals may be overlapped by the others. It has been reported that signals in H units that are assigned to C3,5-H3,5 at *δ*C/*δ*H 115.4/6.63 overlapped with those from G 5 position [92]. After the alkaline treatment, intensity of signals correlated to S units is sharply increased [33]. Typically, as in spectra from grasses, prominent signals corresponding to *p*coumarate (PCA) and ferulate (FA) structures are observed at *δ*C/*δ*H 115.5/6.77 (PCA3,5), 129.9/7.46 (PCA2,6), 111.0/7.32 (FA2), and 111.0/7.32 (FA6), respectively. The olefinic correlations of the cinnamyl aldehyde end-group structures (J) are observed at *δ*C/*δ*H 112.24/7.25 and 122.3/7.10. However, the aromatic cross-signals of the cinnamyl alcohol end-groups (I) are overlapped with the same signals in S and G units. In the side-chain region (*δ*C/*δ*H 90–50/6.0– 2.7 ppm), cross-signals of methoxy groups (*δ*C/*δ*H 55.9/3.73) and β-O-4 linkages are the most predominant. The Cα─Hα correlations in the β-O-4 linkages are observed at δC/δH 72/4.7 to 4.9, while the Cβ─Hβ correlations are observed at δC/δH 84/4.3 and 86/4.1 for the substructures linked to the G/acylated S and S units, respectively. The Cγ-Hγ correlations in the β-O-4 substructures are found at δC/δH 60.1/3.40 and 3.72. The presence of acylating groups in some lignin produced additional intense signals. After acylation, the intense signals corresponding to acylated *γ*-carbon in β-O-4 substructure (A′/A″) are found in the range between *δ*C/*δ*<sup>H</sup> 62.7/3.83 and *δ*C/*δ*H 62.7/4.30. C*α*─H*α* correlation of carbon-carbon linkages such as resinol ββsubstructures (B), phenylcoumaran β-5 substructures (C), spirodienone β-1 substructures (D), and *α*,*β*-diaryl ether substructures (E) are identified by the cross-peaks at δC/δH 84.8/4.66, 86.6/5.47, 81/5.01, and 79.2/5.52, respectively. In our previous research, the intensity of signals derived from β-O-4 substructures decreased during ionic liquid pretreatment suggesting the partial cleavage of this substructure [17]. With respect to signals from lignin, signals derived from carbohydrates are also found in this region and somewhat overlap with signals from Cγ-Hγ correlations in the β-O-4 substructures. For lignin-carbohydrate complex linkages investigation, the regions of *δ*C/*δ*H 90–105/3.9–5.4, 81.5–80/5.3–4.3, and 65–62/4.5–4.0 are of significance. Accordingly, benzyl ether LCC linkage could be detected in the region δC/δH 81.5– 80/5.3–4.3; intense cross-peaks of phenol glycoside LCC linkages can be observed in the area of δC/δH 102.6–101.4/5.17–4.94, whereas cross-peaks of *γ*-ester linkages can be observed at δC/ δH 65–62/4.5–4.0 [35, 93].

**Figure 4.** Quantitative 31P NMR spectrum of a *A. donax* ball-milled lignin derivatized with TMDP using cyclohexanol

due to the very complex and heterogeneous structure of lignin and instrumental limitations [87]. In the course of time, modern solution-state two- and three-dimensional methods are developed as efficient tools to investigate the structure of lignin. Besides better resolution, the

Two-dimensional NMR spectroscopic methods such as heteronuclear multiple quantum coherence (HMQC) spectroscopy, homonuclear Hartmann-Hahn (HOHAHA) spectroscopy, total correlation (TOCSY) spectroscopy, rotating-frame Overhauser experiment (ROESY) heteronuclear single quantum coherence NMR (HSQC) spectroscopy, and heteronuclear multiple bond coherence (HMBC) have been employed in lignin structure characterization [25, 89–91]. Among these, advanced 2D HSQC NMR is the most extensively used due to its versatility in illustrating structural features and structural transformations of isolated lignin fractions. The interpretation of 2D HSQC NMR spectra of lignin has been facilitated by the application of HOHAHA, HMQC, TOCSY, and ROESY techniques. For instance, del Río et al. performed HMBC experiment to give important information about the connectivity of the ester moiety to the lignin skeleton, and ether linkages between lignin and tricin were proposed [25].

H TOCSY correlation NMR analysis can further confirm the doubted assignment of crosspeak in the spectra of HMQC or HSQC [69]. The cellulolytic enzyme lignin of *A. donax* was

The basic composition (S, G, and H units) and various substructures linked by ether and carbon–carbon bonds (β-O-4, β–β, β-5, etc.) can be observed in the 2D HSQC spectra (**Figure 5**). In the aromatic region (*δ*C/*δ*H 150–90/8.0–6.0 ppm), S, G, and H units show prominent correlations at *δ*C/*δ*H 103.7/6.71 (S2,6), *δ*C/*δ*H 106.7/7.28 (Cα-oxidized S units S′), 110.7/6.98 (G2),

H and 13C NMR spectra, the signals are heavily overlapped

as internal standard (reprinted with permission from [17]. Copyright 2015 American Chemical Society).

250 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

multidimensional methods provide more reliability to the assignments [88].

shown in **Figure 5**, and the main substructures are depicted in **Figure 1**.

**5.2. Multidimensional NMR spectroscopy**

*5.2.1. Two-dimensional NMR spectroscopy*

1 H-1

In traditional one-dimensional 1

A quantitative evaluation of the lignin structure moieties has been performed successfully, and some of the quantitative methods frequently used are described. All C9 units in lignin are used as an internal standard. Integrate the G2, 0.5S2,6 + G2, and 0.5S2,6 + G2 + 0.5H2,6 signals as ISs are for softwood [91], hardwood lignin [91], and grass lignin [17, 33, 35], respectively. Based on the internal standard (all C9 units), the amount of S, G, H, and different interunit linkages could be obtained. In that way, the amount of β-O-4 linkages (% of C9 units) was determined to be 47.0–49.4 in softwood lignin, and 60.3 in beech wood lignin, and more than 50 in grass MWL [91]. Another semiquantitative strategy of interunit linkages based on the total side chains is also acceptable for directly comparison [7, 25]. The actual extent of lignin acylation can also be estimated in the similar way particularly in grass samples [94]. In addition, Zhang and Gellerstedt proposed a quantitative method by combining 13C NMR and 2D HSQC spectra, resulting in significant progress in the characterization of lignin moieties by NMR [71]. According to the method, the quantitative 13C NMR spectrum was used as a reference. Consequently, the absolute amounts of lignin substructures and even LCC moieties were quantitative calculated and expressed per 100 Ar.

**Figure 5.** HSQC spectra of cellulolytic enzyme lignin from *A. donax* a aromatic region (*δ*C/*δ*H 150–90/8.0–6.0 ppm); b side-chain region (*δ*C/*δ*H 90–50/6.0–2.7 ppm). See **Figure 1** for the main lignin structures identified (reprinted with permission from [35]. Copyright 2015 Elsevier).

#### *5.2.2. Three-dimensional NMR spectroscopy*

As discussed above, the overlapping of the lignin signals cannot be fully avoided even by 2D experiments. Thanks to the rapid advances in NMR technology, the three-dimensional HSQC-TOCSY and HMQC-HOHAHA techniques are utilized to elucidate the 1 H-1 H and 1 H-13C correlations of individual spin systems and thus indicate a certain lignin side chain structure [87, 88, 95]. The 3D spectra provide more reliability to the assignments, as the connectivity can be cross-checked from different planes of the 3D spectrum. However, long measurement time is required for the 3D experiments. As most of the structural information of lignin can be obtained by 1D and 2D NMR spectroscopic methods, the applications of 3D NMR to lignin structure characterization are still limited.

## **6. Conclusion and outlook**

Lignin is an aromatic polymer essential for defense, water and nutrient transport, and mechanical support in vascular terrestrial plants. To reveal the molecular details of lignin structure nondestructively, various molecular spectroscopic methods have been routinely utilized. It can be inferred that the extinction coefficients of UV spectra demonstrate the purity of lignin. Moreover, the functional groups and possible lignin composition can be obtained by the FT-IR, FT-Raman, and fluorescence spectroscopy spectral features, whereas more accurate composition and contents can be calculated using one-dimensional and multidimensional NMR spectroscopic methods. The combination of these molecular spectroscopic methods provides a comprehensive and systematic evaluation of lignin from different plant species. It was demonstrated that herbaceous plants and wood species displayed different structural characteristics of lignin, and structural modification was occurred during various treatment. Overall, these nondestructive techniques provide alternative safe, rapid, accurate, and nondestructive technology for lignin structure determination. The information of lignin presented by these molecular spectroscopic methods contributes to the understanding of native recalcitrance and facilitates the design of more effective strategies to produce ligninbased value-added materials, biochemicals, and biofules.

## **Acknowledgements**

Consequently, the absolute amounts of lignin substructures and even LCC moieties were

252 Applications of Molecular Spectroscopy to Current Research in the Chemical and Biological Sciences

**Figure 5.** HSQC spectra of cellulolytic enzyme lignin from *A. donax* a aromatic region (*δ*C/*δ*H 150–90/8.0–6.0 ppm); b side-chain region (*δ*C/*δ*H 90–50/6.0–2.7 ppm). See **Figure 1** for the main lignin structures identified (reprinted with per-

As discussed above, the overlapping of the lignin signals cannot be fully avoided even by 2D experiments. Thanks to the rapid advances in NMR technology, the three-dimensional HSQC-

correlations of individual spin systems and thus indicate a certain lignin side chain structure [87, 88, 95]. The 3D spectra provide more reliability to the assignments, as the connectivity can be cross-checked from different planes of the 3D spectrum. However, long measurement time is required for the 3D experiments. As most of the structural information of lignin can be obtained by 1D and 2D NMR spectroscopic methods, the applications of 3D NMR to lignin

Lignin is an aromatic polymer essential for defense, water and nutrient transport, and mechanical support in vascular terrestrial plants. To reveal the molecular details of lignin structure nondestructively, various molecular spectroscopic methods have been routinely utilized. It can be inferred that the extinction coefficients of UV spectra demonstrate the purity

H-1

H and 1

H-13C

TOCSY and HMQC-HOHAHA techniques are utilized to elucidate the 1

quantitative calculated and expressed per 100 Ar.

mission from [35]. Copyright 2015 Elsevier).

*5.2.2. Three-dimensional NMR spectroscopy*

structure characterization are still limited.

**6. Conclusion and outlook**

The authors gratefully acknowledge the financial support from National Science Foundation for Distinguished Young Scholars of China (31225005) and Chinese Ministry of Education (113014A).

## **Author details**

Tingting You1 and Feng Xu1,2\*

\*Address all correspondence to: xfx315@bjfu.edu.cn

1 Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing, China

2 Key Laboratory of Pulp and Paper Science and Technology, Ministry of Education, Qilu University of Technology, Shandong, China

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