QM/MM Lineshape Simulation of the Hydrogen-bonded Uracil NH Stretching Vibration of the Adenine:Uracil Base Pair in CDCl$_3$

TL;DR

This study uses hybrid QM/MM molecular dynamics to simulate the infrared spectrum of hydrogen-bonded uracil NH vibrations in a DNA base pair, aligning well with experimental results.

Contribution

It introduces a novel QM/MM simulation approach combined with lineshape theory to accurately predict vibrational spectra of hydrogen-bonded base pairs.

Findings

Infrared spectrum matches experimental data

Average transition frequency is accurately predicted

Spectrum width aligns with observed values

Abstract

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.