Structure and electronic properties of the Watson-Crick base pairs: role of hydrogen bonding

Abstract

The hydrogen bonding patterns in the adenine-thymine (A-T) and guanine-cytosine (G-C) base pairs for B-DNA has been studied using the density functional theory. The H-bond for the crystal geometry is found to differ considerably from the geometry optimized structures for the free base pairs with larger deviation for the G-C pair compared to the A-T pair. Furthermore, the H-bonding patterns are found to be highly non-local and co-operative. For the N···H—N bond in the G-C pair, the proton hops in between two symmetric double-well potentials localized on the donor and the acceptor, due to cancellation of the local polarizations of the top and down N—H···O and O···H—N bonds, respectively. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) gap (HOMO-LUMO gap) for the free bases decreases with increase in the strength of the H-bonds in between the base pairs with larger decrease for the G-C pair. The adiabatic electron affinity (AEA) for the free bases which are found to be all negative become positive on the formation of the H-bonds and more so for the G-C pair.