Computation of Nitrile vibrations as a probe of the structure and dynamics of condensed matter systems

The use of a nitrile vibration to measure structure and dynamical properties of complex chemical and biochemical systems with sub-picosecond resolution has been investigated computationally. The nitrile functional group is an interesting candidate for use as a vibrational probe because it has a good infrared absorption coefficient, can be used to monitor hydrogen bonding environments and local electric fields, and it absorbs in an uncluttered region of the infrared spectrum. The calculation of vibrational spectra allows for a direct connection between the atomistic simulations and the observed experimental features. The nitrile stretch infrared absorption line shape was calculated for dilute acetonitrile in water and methanol using a novel optimized quantum mechanics/molecular mechanics (OQM/MM) methodology. Once the OQM/MM methodology was validated the chemical-exchange two-dimensional infrared spectra of acetonitrile in methanol were computed. These calculations provide new insights on the dynamics of hydrogen bonding in the acetonitrile/methanol mixture. Additionally, vibrational frequencies of the nitrile vibration in a cyanylated cysteine residue at a protein-protein interface have been calculated, with the intent of understanding the experimentally observed vibrational Stark shift due to the electric field of the interface.