Ultrafast infrared spectroscopy can be used to investigate molecular dynamics on short timescales, but cannot give an atomistic view on its own or assign dephasing dynamics to particular atomic motions. Computational techniques such as molecular dynamics can complement ultrafast studies by providing an atomic level of detail of protein motions. Mixed quantum mechanical/molecular mechanical calculations were done on carbonmonoxy myoglobin (MbCO). Although quantum mechanical methods can require days to weeks of computational time, a less computationally demanding method was developed herein, which requires only a few seconds to complete. The coordinates, contributions to the electric field, and normal modes of several key atoms were correlated to the CO stretch frequency with a correlation coefficient of 0.87. Previous calculations on the Nδ-H tautomer of MbCO resulted in a distribution of CO stretch frequencies that was too narrow and offset by ~200 cm-1 from the experimentally observed spectrum. The current work on the Nε-H tautomer greatly improves upon the broadening, although problems remain with the center line frequency.
Hansen, Eric; Schooley, Nicholas; Marr, James; and Lawrence, Christopher, "Carbonmonoxy Myoglobin Dynamics: Computational Simulations" (2012). Honors Projects. 179.