Adiabatic Electron Affinities of the Polyhydrated Adenine−Thymine Base Pair:  A Density Functional Study

Abstract

Adiabatic electron affinities (AEAs) of the adenine-thymine (AT) base pair surrounded by 5 and 13 water molecules have been studied by density functional theory (DFT). Geometries of neutral AT x nH2O and anionic (AT x nH2O)- complexes (n = 5 and 13) were fully optimized, and vibrational frequency analysis was performed at the B3LYP/6-31+G** level of theory. The optimized structures of the neutral (AT x nH2O) and (AT x nH2O)- complexes were found to be somewhat nonplanar. Some of the water molecules are displaced away from the AT ring plane and linked with one another by hydrogen bonds. The optimized structures of the complexes are found to be in a satisfactory agreement with the observed experimental and molecular dynamics simulation results. In the optimized anionic complexes, the thymine (T) moiety was found to be puckered, whereas the adenine (A) moiety remained almost planar. Natural population analysis (NPA) performed using the B3LYP/6-31+G** method shows that the thymine moiety in the anionic (AT x nH2O)- complexes (n = 5 and 13) has most of the excess electronic charge, i.e., approximately -0.87 and approximately -0.81 (in the unit of magnitude of the electronic charge), respectively. The zero-point energy corrected adiabatic electron affinities of the hydrated AT base pair were found to be positive both for n = 5 and 13 and have the values of 0.97 and 0.92 eV, respectively, which are almost three times the AEA of the AT base pair. The results show that the presence of water molecules appreciably enhances the EA of the base pair.

Theoretical Modeling of Radiation‐Induced DNA Damage

“…Using the above-mentioned approaches, the electron affinities of DNA bases and base pairs have been studied in a number of publications in recent years. 70,[89][90][91][92][93][94][95][96][97][98] Using B3LYP/DZPþþ level of theory, Schaefer and co-workers [90][91][92] calculated the electron affinities of T, C, and U in the presence of 1-5 waters and their calculated ZPE-corrected absolute electron affinities of T, U, and C with 5 waters were calculated to be 0.65, 0.74, and 0.61 eV. [90][91][92] respectively.…”

“…In another study, AEA of the thymidine monophosphate-adenine (5 0 -dTMPH-A) pair was calculated using the PCM model and the B3LYP/DZPþþ method as 2.05 eV, 93 while the AEA of an AT base pair in the presence of 13 waters was predicted to be 0.97 eV at B3LYP/6-31þG Ã level of theory. 97 In a recent study, 98 the EA of GC base pair was also calculated using B3LYP/6-31þG…”

Hydrogen atom abstraction reactions of the sugar moiety of 2′‐deoxyguanosine with an OH radical: A quantum chemical study

“…Further, both the specific and bulk solvent effects should be combined to treat the solvent effect properly [34][35][36][37]. Here, we have included three water molecules to treat the specific solvent effect of water followed by the treatment of bulk solvent effect of water using the IEF-PCM [25].…”

Electronic‐Excited‐State Structures and Properties of Hydrated DNA Bases and Base Pairs

“…Several theoretical and experimental investigations were also performed to determine the electron affinity, ionization potential and protonation and deprotonation properties of purine and pyrimidine bases and base pairs [88][89][90][91][92][93][94][95][96][97][98][99][100][101][102][103]. Based on the experimental and theoretical data, the adiabatic valence electron affinity for pyrimidine bases has been estimated to be in the range 0-0.2 eV, while those for adenine and guanine amount to about À0.35 and À0.75 eV respectively [88].…”

“…Schaefer and coworkers [101] have recently investigated the structures and properties of deprotonated GC base pairs. Kumar et al [102,103] have recently investigated the adiabatic electron affinities of GC, AT and hypoxanthine-cytosine base pairs at the DFT level. These authors have found that polyhydration leads to significant increase in the electron affinity of the AT base pair.…”