1. Ultrafast Infrared Spectroscopy as a Probe of Molecular Dynamics: A Molecular Modeling Study
Christopher P. Lawrence, Department of Chemistry, Grand Valley State University
As the neighboring atoms within the protein move in time, the frequency of the CO molecule evolves, providing a probe of molecular dynamics. Experiments have determined that this evolution occurs on two timescales: on the order of 100 fs and the ps scale.
The question then becomes: what motion within the protein occurs on these timescales?
Carbonmonoxymyoglobin
Before answering this question using classical molecular dynamics, first we need a way to obtain the vibrational frequency from the atomic coordinates. A previous study assumed a correlation between this frequency and the electric field on the CO. However, we have found this to be a poor assumption based on electronic structure calculations. Instead, we have found a very strong correlation between this frequency and a combination of bond distances, angles, and the field. We confirmed that this relationship had predictive value with additional electronic structure calculations. Using this correlation, we find that the calculated absorption line width is similar to that of the experiment, although narrower.