**3.2 Paired interaction model in DFT calculation for liquids**

The study of the formation mechanism and structure of organic liquids needs to involve the models and approximations to simulate molecular interactions. One of them can be defined as a model of paired bonds, which is based on a few reasonable assumptions. Firstly, the specific interaction in a liquid is a non-covalent interaction between molecules [41–44]. Secondly, for the definition of the pair, we can choose the strongest molecular interaction in the system. Thirdly, the liquid structure is formed by the paired molecules. Fourth, the nature of this interaction is a set of the different hydrogen bond types.

Sometime, halogen bond [45] and dihydrogen bond [46] provide a non-covalent binding, but it appears quite seldom, basically, between oppositely charged hydrogen or halogen atoms and in a solid state.

Hydrogen bond can exist in many organic and inorganic species and plays a crucial role in fields of chemistry and biology. It has been considered in many reviews; in this section, we analyze only a few recent ones [47–51]. Since the hydrogen bond existence is considered as a main aspect of the condensed phase formation theory, we would like to make a few comments regarding our conception presented in this section. Arising of the hydrogen bond presumes the occurring of an interacted pair – a hydrogen donor and a hydrogen acceptor. This type of binding is known not only in the condensed phase, but also for gases. The energy of hydrogen bond changes in the interval of 8–60 kJ/mol and more, in some cases, while its length is 2–3,5 Å.

Many authors that studied the organic liquids with a hydrogen bond in their structure, draw the statement that this bond provides the stability of liquids and the high mobility as well. This concept is quite satisfactory, because the hydrogen bond theory can be considered as a universal approach to the structure of liquid organics: amines, acids, alcohols, and related compounds; many bioactive systems can also assign to this system. Besides, it is known that some species of organic liquids can turn into a shape with a mobile proton, ex. nitro-substituted hydrocarbons, aldehydes, and ketones – they can form the hydrogen-bonded liquid system as well.

At the same time, the hydrogen-bonded pair has a linear binding, where the mobile proton is bound simultaneously with its own molecule and with a neighboring one, although to a greater extent with its own. This feature of binding allows to imagine the system, in which the initial structure of molecules remains in the combination with a thermodynamic stable molecular bulk. Therefore, the hydrogen bond is the suitable instrument to simulate the formation mechanism in a liquid phase.

Besides, it is well known that the organic matter contains of water impurities that cannot be completely removed [23, 52]. Water forms the clusters with the organic molecules due to the strong hydrogen bonds. The presence of water molecules can be considered as a variant of the mechanism for the formation of a stable organic liquid (see Section 3.3). This mechanism is valid for bioactive systems as well.

The prediction of benzene dimer formation is essential for this work because the high stable liquid in this case exists without the intermolecular hydrogen bond. The DFT calculations of the binding mechanism in the benzene dimer predicts four most stable shapes of the self-association: two variants of π-shaped and two variants of T-shaped structures [53–55].

The pair interactions' model is the most common viewpoint on the mechanism formation of organic liquids. However, this concept has a few disadvantages. Firstly, *The Formation Mechanism and Structure of Organic Liquids in the DFT Challenges DOI: http://dx.doi.org/10.5772/intechopen.100429*

this model cannot explain, why there are many organics that exist without hydrogen bond while their stability (with the vaporization enthalpy as a criterium) is higher than in a system with hydrogen bond [7]. Secondly, this model cannot reproduce the formation mechanism of the spatial structure in organic liquids. Thirdly, the benzene dimer is one of the few examples where the DFT calculations can explain the formation of associates without involving a hydrogen bond, but they cannot explain the high stability of benzene, since the energy of the intermolecular interactions in it does not exceed 0,301 kJ/mol. The mechanism of water complex formation in organic liquids combined with the hydrogen atom transfer theory (HATT) is a positive step to clarify this problem, as it is presented in the next section.

### **3.3 Hydrogen atom transfer model for organic liquids**

The hydrogen atom transfer theory (HATT) and the results of calculations obtained in terms of this model for gases and the condensed phase exhibit a wide area of investigations. The main data and the approaches referring to this theory are presented and reviewed in [56–60]. For our consideration, we have chosen the essential aspects of this concepts, applied for the formation mechanism and the structure of organic liquids.

The hydrogen atom transfer term is used to define the proton, hydrogen and hydride ion transfer which occur in many organic liquids. Two energy minima with a maximum between them arise in the system, determining the process of transfer.

The barrier of transfer changes considerably for different organics and can vary from 10 to 12 up to 100–200 kJ/mol [57]. The nature of these interactions is either activation, such as heating and irradiation of a substance, or a tunneling process. The last one is caused by the decrease of X–H bond energy under the hydrogen atom coupling with the Y-atom of the proton acceptor in the linear chain (X–H‧‧‧Y) and the hydrogen atom vibrations with a large amplitude.

The main value of this theory for the considered problem is related to the description of the spatial arrangement formation. Presuming that the hydrogen atom transfer between the donor and the acceptor of the protons (in other words between the Bronsted acid A and the several molecules of basic B1, B2) occurs in a liquid phase like: (AH + B1 → A− + B1H+ +B2 → A− + B2H+ +B1).

It means that in contrast with the dimer approach, the hydrogen atom transfer model predicts the multidirectional movement of hydrogen atom in a liquid space. These transformations can provide the spatial arrangement in the system. Besides, the HAT model gives a perspective idea that the molecular tautomerism involving different hydrogen atom transfers can be taken as a basic element of the liquid formation mechanism (see the next Section).

Another approach to hydrogen atom transfer mechanism can be formulated if organic liquid contains of the water molecules. As it was mentioned above, water often inserts in a liquid matter and then the hydrogen atom transfer can occur between the water molecules with hydronium ion formation [23, 32]. The water complexes with organics, where the interaction can be assisted with the hydrogen atom transfer, was confirmed by IR experiments [52].

The DFT calculations in the different parametrizations show that in CH3NO2 and CH3CN complexes with water molecules several binding variants can be realized: first of them is the interaction of the hydrogen atom of methyl group with the oxygen atom of water, and the second one is the coupling of the hydrogen atom of water with the nitrogen atom of CN group or the oxygen atom of NO2 group (**Figure 6**, the bonds' distances are given in Å).

The calculations predict the hydrogen atom transfer between the water molecules with the barrier about 10–12 kJ/mol and stabilizing of the hydronium cluster structure

**Figure 6.**

*The interaction model of water complex with CH3NO2 and CH3CN molecules.*

(**Figure 7**). In the hydronium ion, all hydrogen atoms are equal in their interaction with the organic molecules, and within the associates they can shift in all three-dimensional space, realizing the 'relay race' mechanism and forming the equilibrium spatial structure of the liquid. Thus, we can resume that in the liquid organics the water molecule can be a bonding agent in the formation mechanism of phase states.

The similar model was predicted by the DFT calculations for the aromatic substance – hexafluoride of benzene (**Figure 8**). In this complex, the barrier of the hydrogen atom transfer is even less than the one for CH3X (X = CN, NO2) systems (about 6 kJ/mol).

**Figure 7.** *The interaction model of hydronium ion interaction with CH3NO2 and CH3CN molecules.*

**Figure 8.** *The interaction model of water molecule and hydronium ion interaction with C6F6 molecule.*

### **3.4 Transformations' model in DFT calculation**

None of the described experimental and theoretical models can explain the formation mechanism and the structure of organic liquids completely, although they present some useful data to insight this problem. All of them proceed from the fact that the geometry of the gas phase, or, in other words, of a single molecule, is preserved in the liquid phase as well. Although it is assumed that the values of bond lengths and angles shift to some extent under the condensation, these changes *The Formation Mechanism and Structure of Organic Liquids in the DFT Challenges DOI: http://dx.doi.org/10.5772/intechopen.100429*

are considered insignificant, without profound transformations of the molecular structure. At the same time, as it was shown above, the IR data source indicates the possibility of the symmetry vibrations violation caused by the structural factors. In this section we consider as an example the interpretation of IR findings for two classes of organic liquids, which are often-used solvents and initial products for many organic syntheses – methane halides and benzene – in terms of the DFT calculations in the B3LYP variant with the 6–311++G(2d, 2p) basis set.

### *3.4.1 Methane halides*

For the interpretation of IR spectral effects, we have applied the symmetry point groups theory. In tetrachloromethane IR spectrum there should be one active C–Cl stretching band corresponding to the Td symmetry. However, two approximately equal band intensities in 750–850 cm−1 region are observed (see Section 2.4). The appearance of two bands in the IR spectra can be assigned to the pyramidal C3V and the biplanar D2h or D2V symmetry groups.

The DFT calculation predicts the transformation (**Figure 9**) of the isomer (1) into biplanar (2) and pyramidal (3) isomers. The energy barriers ΔE1 and ΔE2 are close to each other and relatively low: ΔE varies in 4–12 kJ/mol range. The calculated frequencies of C–Cl stretching vibrations (776, 713 cm−1) are agreed with the experimental ones (786, 761 cm−1) as far as it can be expected in such a calculation. Formally, the structures (1)–(3) do not differ so much, however, the distribution of charges in them changes in such a way that not only the interaction between a positively charged carbon and a negatively charged chlorine in the neighboring molecules is allowed, but also the interaction in the other direction, between two oppositely charged chlorine atoms. The calculations have shown that the atoms' charges depend on the value of (CClC) angles and not on the bond lengths. The suggested scheme sufficiently describes both spectral observation and formation mechanism of the spatial structure in liquid.

For trichloromethane, the DFT calculations were carried out for the chloroform and bromoform molecules. The obtained data predict the small barrier of transformation from a pyramidal C3V isomer to a biplanar isomer not exceeding 10 kJ/mol (**Figure 10**). As is known, such energies are not sufficient obstacles for the transformation even in the gas phase and a fortiori for the liquid state.

**Figure 9.** *The tautomeric isomers of CCl4, predicted in the DFT calculations.*

**Figure 10.** *The tautomeric isomers of CHCl3, predicted in the DFT calculations.*


#### **Table 1.**

*The charge distribution in chloroform and bromoform molecules.*

The calculations reveal a few directions of the intermolecular binding: one of them is the hydrogen bond between a positive charged hydrogen atom and a negative charged carbon or chlorine atom. At the same time, the obtained results allow the intermolecular binding between the oppositely charged chlorine atoms reminding the interaction in tetrachloromethane molecule. The different types of binding can provide the spatial structure of the liquid phase.

For chloroform and bromoform, the detected charge distribution is similar (**Table 1**), but the atomic charges for the bromoform molecule in the C3V isomer are considerably larger than in the chloroform molecule. In the biplanar configuration of bromoform, the atomic charges are significantly less, closer to the values of chloroform. This effect means that the basic interaction in bromoform is the hydrogen bond (C–H‧‧‧C) with the hydrogen atom transfer in the C3V isomer, in accordance with the IR spectra interpretation (see Section 2.4). Besides, the charge growing (along with the heavier molecular mass) can lead to a stronger intermolecular binding in bromoform and, as a result, to a higher vaporization enthalpy [61].

DFT calculation predict four directions of the tautomeric transformations for dihalogenomethane. In this case, the total energies of (1)–initial biplanar isomer {(CClCl) and (CHH)}, (2)–biplanar {two CHCl planes}, (3)–non-symmetrical pyramid with (HClCl) base and (4)–non-symmetrical pyramid with (HHCl) base (**Figure 11**) are close; ΔE1, ΔE2, and ΔE3 are about 20 kJ/mol. Therefore, we conclude that the intermolecular binding can be realized in all these directions, including the hydrogen bond (C–H‧‧‧Cl) and the interaction of two chlorine atoms.

**Figure 11.** *The tautomeric isomers of CH2Cl2, predicted in the DFT calculations.*


*The Formation Mechanism and Structure of Organic Liquids in the DFT Challenges DOI: http://dx.doi.org/10.5772/intechopen.100429*

**Table 2.**

*The charge distribution in CH2X2 molecules.*


#### **Table 3.**

*The charge distribution in CH3I molecule.*

For CH2Br2 and CH2I2 molecules, ΔE2 and ΔE3 energies are considerably higher than ΔE1. In this molecules, the transformation into isomers (3) and (4) is less expected than the C–H‧‧‧X hydrogen bond in isomer (2). Since the charge distributions for all these molecules are similar (**Table 2**), the direction of the transformation is determined by the energy factor.

For CH3I molecule, the calculated charge distribution in the initial C3V specie pyramidal isomer allows the interaction between the iodide atom and the carbon atom in the chains of neighboring molecules, while the charge distribution in molecule can provide the hydrogen bond between the iodide and the hydrogen atom of the methyl group in the neighboring molecules as well (**Table 3**). Thus, the different binding variants in liquid CH3I can provide the formation of the stable spatial arrangement.

#### *3.4.2 Benzene*

The structural element that determinates the molecular arrangement in a benzene liquid phase, was presented in the quoted literature as a set of dimers that have several geometry configurations (see Section 3.2). Unlike this approach, we have considered the trimers as a formed element in the 'stack model' of the benzene liquid phase. The conducted DFT calculations with different transformations of initial molecular geometry predict that the most optimal configuration is the stack with a 'chair' shape of the central ring and two planar rings (**Figure 12**). The trimers are bonded in a spatial structure by the hydrogen bridges. This concept can explain the IR data outside the scope of traditional assignment (see Section 2.4). In the trimer spectrum, one CH stretching band assigning to both planar rings should be observed, while the CH stretching in the central ring have to exhibit two bands: the first of them assigns to a pair of equivalent (C1–H1) and (C4–H4) bonds, and the second one – to a quartet – (Ci–Hi), i = 2.3, 5.6 (**Figure 12**). The stretching bands of the hydrogen bridges

**Figure 12.** *The fragment of the benzene spatial arrangement in a liquid phase.*

should shift in the middle IR region due to the mixing of the CH and CC stretching. Therefore, the pair of bands at 1800–2000 cm−1 corresponds to the stretching of two bridging C–H bonds in the stacks bound in two mutually perpendicular plains.
