Modeling the vibrational spectroscopy of carbonmonoxymyoglobin using DFT and molecular dynamics

Abstract

Ultrafast vibrational spectroscopy can be used as a tool to examine dynamics on the sub-picosecond timescale. These experiments have been performed probing carbonmonoxymyoglobin. Classical molecular dynamics simulations can aid in the interpretation of these experiments, but one must first develop a model by which the quantized vibrational frequency may be obtained from the classical simulation. In this paper, we use a classical simulation to provide a sampling of the atomic coordinates within the dynamic environment and using those coordinates we perform density functional theory calculations to obtain these frequencies. The frequency calculations are then mapped onto quantities that are readily available within the classical simulation allowing us to limit the number of the more expensive DFT calculations. Finally, we use these results to calculate the absorption lineshape which is in qualitative agreement with the experiment and examine how important the various contributions to the fluctuating frequency are to spectroscopic observables.