QM/MM lineshape simulation of the hydrogen-bonded uracil NH stretching vibration of the adenine:uracil base pair in

A hybrid Car–Parrinello QM/MM molecular dynamics simulation has been carried out for the Watson–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 are in reasonable agreement with recent experimental data.