Theoretical investigation of hydrogen bonding in Watson–Crick, Hoogestein and their reversed and other models: comparison and analysis for configurations of adenine–thymine base pairs in 9 models

Abstract

Hydrogen bonding in Watson–Crick, reversed Watson–Crick, Hoogestein, reversed Hoogestein and other configurations of adenine–thymine base pairs have been studied with theoretical methods. In order to determine the optimized geometries, energies, dipole moments, atomic charges, thermo chemical analysis and other properties of hydrogen bonding in A–T base pairs, we have performed quantum chemical ab initio and density functional calculations at HF/6-31G (d,p), B3LYP/6-31G (d) and B3LYP/6-31G (d,p) levels in gas phase and solution. The solvent effect is taken into account via the self-consistent reaction field (SCRF) method. We optimized the geometries of A–T base pairs in various solvents (water, methanol, ethanol and acetone) with Polarized Continuum Model (PCM). Best agreement with available gas phase experimental A–T bond enthalpies (−12.1 kcal mol −1) is obtained at the B3LYP/6-31G (d,p) level, which (for 298 K) yields −12.44 kcal mol −1, deviating by as little as −0.34 kcal mol −1 from experimental. Bond enthalpies of A–T (1) base pair in various solvents at the B3LYP/6-31G (d) level are −2.30, −2.64, −3.03 and −8.06 kcal mol −1 in water, methanol, ethanol and acetone, respectively, these results show that with increasing dielectric constant of solvent the bond enthalpies of A–T base pairs decrease. The bond enthalpy of A–T (9) model is larger than other models in gas phase and various solvents. In addition for further correction about interaction energies between A and T, the basis set super position error (BSSE), has been computed. In Watson–Crick base pair, A–T (1), the distances for (N 2⋯H 23–N 19), (N 8–H 13⋯O 24) and (C 1⋯O 18) obtained from B3LYP/6-31G (d,p) level are 2.84, 2.94 and 3.63 Å, respectively, in agreement with experimental results (2.82, 2.98 and 3.52 Å). Also, we use natural bond orbital (NBO) method to identify principle delocalizing acceptor orbital associated with each donor NBO and their topological relationship to this NBO and donor–acceptor interaction perturbation theory energy analysis, for different configurations of A–T base pairs in gas phase and solution. The effect of solvent on charge distribution of acceptor and donor atoms show that with decreasing of dielectric constant of solvent, the acceptor atom charges decreasing and for proton atoms charges increase further. In acetone, changes in distance of N–H and C O bonds in different orientations of A–T base pairs are further than other solvents. This means that with decreasing dielectric constant of solvent, hydrogen bond to be stronger. To identify any artifacts in the Mulliken population analysis, a natural bond orbital (NBO) was examined.