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

TL;DR

This study uses hybrid QM/MM molecular dynamics to analyze hydrogen bond dynamics and infrared spectra of an adenine:uracil base pair in solution, providing insights into geometric correlations and spectral features.

Contribution

It presents a detailed QM/MM simulation approach to study hydrogen bond fluctuations and infrared spectra of nucleic acid base pairs in solution, with improved accuracy in spectral predictions.

Findings

Deviations in fundamental NH stretching frequencies are less than 2% compared to experiment.

Infrared spectrum width for NHN bond matches experiment; NHO bond is underestimated.

Troullier-Martins pseudopotential with 70 Ry cutoff yields best spectral agreement.

Abstract

Hybrid 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.