**4.2. Sugar and phosphate group**

**Figure 3.** (a) Total ion yield as a function of electron energy for DEA process of thymine. (b) Formation of dehydrogen‐ ated anions from thymine (black curve), methylated thymine at N3 site (red curve), methylated thymine at N1 site (blue curve), and thymidine (gray area) [45]. Molecular structure of thymine with numbering and atom labeling.

At subexcitation energies, DEA leads to thymine dehydrogenation by loss of a neutral

a neutral hydrogen radical <*i* >H• < / *i* >. This dehydrogenation process depends on the site from which the H atom is removed. Experimental studies with partially deuterated thymine, in which the deuterium is at either nitrogen or carbon sites, showed that hydrogen loss occurs exclusively from the N sites. H loss from the C sites is thermodynamically accessible within this energy range, but has not been observed experimentally. Moreover, in employing methylated thymine and uracil, it has been shown that by adjusting the electron energy, the loss of H can be made even site‐selective with respect to the N1 and N3 positions. Although 1 eV electrons induce H loss at the N1 position (N1‐H), the process can be switched at 1.8 eV to N3‐H (**Figure 3b**). These results have significant consequences for the molecular mechanism of DNA strand breaks induced by LEEs. Within DNA, the N1 position of thymine is coupled with the sugar moiety and thus forms thymidine, which is one of the nucleosides. Because the shapes of the signals from thymine and the more complex thymidine resemble each other, it can be concluded that H abstraction in thymidine predominantly occurs at the thymine moiety

In addition to the detection of anions and the energies at which they are formed, much effort has been expended to matching particular types of DEA process to specific resonant peaks observed in DEA ion yields. In the case of the most abundant anion formed for all nucleobases,

–– • *<sup>H</sup> eTT T H* - +® ® + - (6)

<sup>−</sup> is the closed‐shell anion formed by the ejection of

hydrogen atom [40, 42]. This reaction can be expressed as follows:

where T<sup>−</sup> is the TMA of thymine (T) and T−<sup>H</sup>

188 Radiation Effects in Materials

and, more precisely, at the N3 position (**Figure 3b**) [45].

The high fragility of the DNA backbone with respect to the impact of LEEs with low kinetic energy was observed for 2‐deoxy‐D‐ribose and its RNA equivalent (i.e., ribose), along with their analogs [2]. In principle, the dissociation of any of P–O–C bonds in the sugar–phosphate backbone or C–C bond within the sugar could result in a DNA strand break. If such breakages were to occur via the DEA process in DNA, then DEA would represent an important pathway through which the direct interaction of LEEs could affect biologically significant damage.

The DEA to 2‐deoxy‐D‐ribose results in a strong decomposition of the sugar at electron energies near 0 eV, indicating the loss of one or more molecules of water [51]. Similar findings were observed for D‐ribose and other sugars [2], indicating that DEA at 0 eV is a common property of all monosaccharides. However, the mechanisms for DEA reactions leading to loss of neutral water are more complex in comparison to the dehydrogenation of the nucleobases, because they involve the dissociation of multiple bonds and/or atom rearrangement with simultaneous formation of new bonds. Therefore, the mechanism of DEA to sugars near 0 eV is not fully understood. It is however proposed to occur via the formation of a "shape" resonance. In a sugar molecule, the extra orbital can be a σ\* orbital of the O–H bond. As was observed for alcohols [52], the σ\* orbital of the hydroxyl group for the dehydrogenation channels appears at higher energy for simple alcohols than for cyclic alcohols. Moreover, it was found that larger numbers of hydroxyl groups present in a molecule could enhance the dissociation of an O–H bond, by decreasing the energy of the thermodynamic threshold. This mechanism has been suggested for 2‐deoxy‐D‐ribose and D‐ribose, which contain three and four hydroxyl groups, respectively [2]. In addition, experiments with the ribose analogs tetrahydrofuran and 3‐hydroxytetrahydrofuran showed that DEA cross sections were greatly enhanced by the presence of OH groups [50]. However, for alcohols, their molecular dissoci‐ ation involved simple bond cleavage, while in sugars, fragmentation of several different bonds occurs. One of the proposed models for sugar dissociation was provided from ab initio calculations of VFRs formed initially by a dipole‐bound state of sugar due to a large dipole moment [53]. Other quantum chemical calculations confirmed this model, showing that the sugar ring can convert into an open chain by intramolecular charge transfer. This mechanism can lead to dissociation by loss of a water molecule, assuming that the barrier for such a transfer is sufficiently low [54]. It was also calculated through quantum dynamics scattering theory that the formation of shape resonances for D‐ribose is excluded at low energies, but they can be formed at higher energies [55].

In the case of thymidine, in which sugar is covalently bound to thymine, the DEA study showed two resonant structures (**Figure 3b**) [45]. The one at lower energy was associated with a reaction in which the excess electron is initially localized in the sugar moiety, leading to the glycosidic bond cleavage. The second resonance was attributed to a reaction in which the excess electron was localized on the thymine moiety, resulting in the loss of a neutral H atom from the N3 site, as was mentioned for thymine. Since nucleosides can be easily decomposed due to the elevated temperatures necessary for evaporating samples, no experimental data for other gas‐phase nucleosides or nucleotides are reported, besides those for thymidine [45], cytidine [56], and 2‐deoxycytidine 5‐monophosphate [56].

Similarly, due to experimental difficulties, the phosphate group in the gas phase could not easily be investigated as an isolated compound. Its simplest analog, H3PO4 (phosphoric acid), is not easily vaporized for gas‐phase experiments or molecular deposition for thin film experiments [11]. Therefore, to understand the DEA process within the phosphate group, several compounds involving phosphoric acid derivatives, for example, dibutylphosphate and triethylphosphate [57], were examined. DEA to these compounds lead to P–O and C–O bond cleavages, which correspond to a direct single‐strand break. As for sugars, many fragmentation channels occurred close to 0 eV; however, these low‐energy channels are most likely driven by the large electron affinity of PO3 (4.95 eV). The cross sections for DEA to the sugar and phosphate group analogs were relatively small, that is, about one magnitude lower than those for nucleobases [50]. These gas‐phase results on sugars and phosphate units revealed that LEE attachment can induce single‐strand breaks by electron localization either on the sugar moiety followed by the electron transfer to the backbone or directly on the phosphate group.
