QM/MM Lineshape Simulation of the Hydrogen-bonded Uracil NH Stretching Vibration of the Adenine:Uracil Base Pair in CDCl3

A hybrid Car-Parrinello QM/MM molecular dynamics simulation has been carried out for theWatson-Crick base pair of 9-ethyl-8-phenyladenine and 1-cyclohexyluracil in deuterochloroform solution at room temperature. The resulting trajectory is analyzed putting emphasis on the N-H· · ·N Hydrogen bond geometry. Using an empirical correlation between the N · · ·N-distance and the fundamental NH-stretching frequency, the time-dependence of this energy gap along the trajectory is obtained. From the gap-correlation function we determine the infrared absorption spectrum using lineshape theory in combination with a multimode oscillator model. The obtained average transition frequency and the width of the spectrum is in reasonable agreement with recent experimental data.