A theoretical study on the water structure for nucleic acids bases and base pairs in solution at T=300 K

Abstract

Monte Carlo simulations are presented for the bases A, C, G, T, and U enclosed in a cluster of forty water molecules and for the base pairs A–T, G–C, and A–U enclosed in a cluster of fifty water molecules. These computations are carried out at a simulated temperature of 300 K. The importance of the temperature effect is shown by carrying the MC simulation for adenine at T=100 K. The intermolecular interactions are computed with atom–atom pair potentials obtained from quantum‐mechanical calculations on the water–water and water–base complexes. The identification of the positions and orientations for the water molecules in the first hydration shell is obtained from hydrogen and oxygen atoms probability distribution maps. Relations between the water structure around the bases and base pairs and the water structure in the major and minor groove of B‐DNA double helix are preliminarily presented.