Applications of density functional theory
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Exposure to high-energy radiation can cause mutations in living organisms by generating lethal lesions in DNA strands. Density functional theory has been employed to study microhydration effects on formation of the anions of three pyrimidine nucleic acid bases (NABs), thymine, uracil, and cytosine, which are thought to play an important role in the radiation-induced DNA damage process, by explicitly considering various structures of complexes of the three bases with up to five water molecules at the B3LYP/DZP++ level of theory. For all three bases, both the adiabatic electron affinities (AEAs) and vertical detachment energies (VDEs) are found to increase with the number of hydrating water molecules, implying that formation of the anions of the NABs are energetically favorable, although the anions of the NABs in the gas phase are not bound or weakly bound at most. For a given hydration number, uracil is predicted to have the largest electron affinities, while cytosine has the smallest. The methyl group of thymine is found to lower the AEA by 0.04 eV, compared to the AEA of uracil. These results are qualitatively consistent with available experimental results from photodetachment-photoelectron spectroscopy studies of Schiedt et al. [Chem. Phys. 239, 511 (1998)]. The hydrogen-abstracted radicals from the adenine-uracil base pair have also been studied at the B3LYP/DZP++ level of theory. The radical arising from removal of an amino hydrogen of the adenine moiety which forms a hydrogen bond with the uracil O4 atom resulted í1in a significant decrease in the base pair dissociation energy (5.9 kcal mol). This radical is more likely to dissociate into the two isolated bases than to recover the hydrogen bond with the O4 atom through the N6-H bond rotation along the C6-N6 bond. On the contrary, removal of the uracil N3 hydrogen atom does not affect the base pair dissociation energy of the resulting radical, due to electron density transfer from the adenine N1 atom to the uracil N3 atom.