Ab initio studies on the H-bonding of hypoxanthine and DNA bases

Abstract

Novel and interesting points are underlined by ab initio (QM) calculations of H-bonding of all the six nucleobase dimers of hypoxanthine and DNA bases, namely Hyp^anti⋯A^syn, Hyp^anti⋯A^anti, Hyp^syn⋯G^anti, Hyp^anti⋯G^syn, Hyp^anti⋯T^anti, Hyp^anti⋯C^anti. HF, DFT (Becke) and B3LYP (hybrid-DFT) methods were applied with and without polarisation functions. The H-bonding preference of hypoxanthine to natural DNA bases is G^syn > C^anti > A^anti > A^syn > T^anti ≈ G^anti. Becke and B3LYP give buckle and propeller arrangements for Hoogsteen dimers, but the use of an auxillary basis set overestimates the angles. Hartree–Fock optimised structures are almost planar and this method does not find the local minima of Hoogsteen pairs. Among the methods giving reliable geometries the Becke calculation needs the least computational resources.