In finite cluster models of proteins, one must apply constraints (<i>e.g.</i>, fixing the Cα atoms in space) in order to generate a relaxed structure starting from the crystal structure. Use of constraints can significantly slow geometry optimizations, however, and poses fundamental problems for including zero-point energy corrections to computed stationary points. In computing vibrational spectra, one must further worry whether the cluster model is sufficiently large such that fixed-atom constraints do not contaminate the normal modes of interest. We demonstrate that each of these problems can be sidestepped by application of simple harmonic confining potentials at the edges of the cluster model. This allows optimization to proceed using internal rather than Cartesian coordinates, and vibrational frequencies can be computed in a straightforward way. We demonstrate the utility of this procedure by computing zero-point corrected reaction pathway for several enzymatic reactions, and resonance Raman spectra in metalloproteins.

Novel approach to compute vibrational spectra in cluster models of enzyme active sites

2019 Spring National Meeting

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