QM/MM Simulation of the Hydrogen Bond Dynamics of an Adenine:Uracil Base Pair in Solution. Geometric Correlations and Infrared Spectrum

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dc.creatorYan, Yun-an
dc.creatorKühn, Oliver
dc.date2009-03-20
dc.date.accessioned2026-07-07T12:54:49Z
dc.date.available2026-07-07T12:54:49Z
dc.descriptionHybrid QM(DFT)/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 putting special attention to the geometric correlations of the $\NHN$ and $\NHO$ hydrogen bonds in the base pair. Further, based on empirical correlations between the hydrogen bond bond length and the fundamental NH stretching frequency its fluctuations are obtained along the trajectory. Using the time dependent frequencies the infrared lineshape is determined assuming the validity of a second order cumulant expansion. The deviations for the fundamental transition frequencies are calculated to amount to less than 2% as compared with experiment. The width of the spectrum for the $\NHN$ bond is in reasonable agreement with experiment while that for the $\NHO$ case is underestimated by the present model. Comparing the performance of different pseudopotentials it is found that the Troullier-Martins pseudopotential with a 70 Ry cut-off yields the best agreement.
dc.description10 figures
dc.identifierhttps://arxiv.org/abs/0903.3502
dc.identifierhttp://arxiv.org/abs/0903.3502
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/224065
dc.subjectChemical Physics
dc.subjectBiological Physics
dc.titleQM/MM Simulation of the Hydrogen Bond Dynamics of an Adenine:Uracil Base Pair in Solution. Geometric Correlations and Infrared Spectrum
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