Nitrile groups as vibrational probes: calculations of the CN infrared absorption line shape of acetonitrile in water and tetrahydrofuran.

The C[TRIPLE BOND]N bond is a powerful probe of protein structure and dynamics because it absorbs in a region of the infrared spectrum apart from the other vibrations that occur naturally in proteins, and because its infrared absorption line shape is sensitive to specific characteristics of the local environment. Since the polarity experienced by the probe can differ dramatically within the protein, infrared spectroscopy of a C[TRIPLE BOND]N site-specifically labeled residue can be used to infer its local environment within the protein. It has been shown experimentally that the spectrum of acetonitrile in water is different in terms of peak position and width compared to acetonitrile in tetrahydrofuran (THF). An optimized quantum mechanics/molecular mechanics method for calculating accurate vibrational frequencies in condensed-phase was parametrized for acetonitrile in water. The transferability of the methodology to a different solvent was tested by computing the infrared line shapes of acetonitrile in both water and THF and comparing to experiment. The infrared absorption line shapes agree well with experiment in each case, and the trends observed experimentally are recovered. The accuracy of the methodology for two solvents of differing polarity indicates that this technique is suitable to study CN probes in proteins.