Unraveling the correlated dynamics of the double hydrogen bonds of nucleic acid base pairs in solution.

ABSTRACT

Quantum mechanics/molecular mechanics hybrid simulations (CPMD/GROMOS) of nonlinear infrared spectra are performed for a modified adenine-uracil base pair in CDCl(3) solution. Employing a mapping between hydrogen bond distances and fundamental as well as overtone transition frequencies on the basis of on-the-fly snapshot potential energy curves, energy gap correlation functions are established. These correlation functions are utilized to determine pump-probe and two-dimensional photon echo spectra. Analysis of the latter yields off-diagonal peaks signifying correlated fluctuations of the N-H···N and N-H···O hydrogen bonds.