Physics – Chemical Physics
Scientific paper
2008-07-17
Physics
Chemical Physics
revised version with small changes submitted to Chem. Phys. Lett
Scientific paper
10.1016/j.cplett.2008.09.024
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 $\NN$-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.
Krishnan Gireesh M.
Kühn Oliver
Yan Yun-an
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