Geometric correlations and infrared spectrum of adenine–uracil hydrogen bonds in CDCl3 solution

Abstract

Hybrid QM/MM molecular dynamics simulations have been carried out for the Watson-Crick base pair of 9-ethyl-8-phenyladenine and 1-cyclohexyluracil in deuterochloroform solution at room temperature. Trajectories are analyzed paying special attention to the geometric correlations within the N-HN and N-HO hydrogen bonds in the base pair. Even though the two hydrogen bonds are only approximately linear and the heterocycles are tilted with respect to each other, hydrogen bond and N-H lengths follow a simple empirical correlation based on Pauling's valence bond order model. In order to describe the IR line shape of the two NH-stretching vibrations, the correlation between their fundamental transition frequencies and the hydrogen bond lengths is exploited. This facilitates efficient evaluation of the fluctuating transition frequencies along the QM/MM trajectory which allows the determination of the line shape function.