Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: a case study of a glutamate molecule in water solution and in a protein-bound form.

ABSTRACT: We propose a hierarchical approach to model vibrational frequencies of a ligand in a strongly fluctuating inhomogeneous environment such as a liquid solution or when bound to a macromolecule, e.g., a protein. Vibrational frequencies typically measured experimentally are ensemble averaged quantities which result (in part) from the influence of the strongly fluctuating solvent. Solvent fluctuations can be sampled effectively by a classical molecular simulation, which in our model serves as the first, low level of the hierarchy. At the second high level of the hierarchy a small subset of system coordinates is used to construct a patch of the potential surface (ab initio) relevant to the vibration in question. This subset of coordinates is under the influence of an instantaneous external force

SUBMITTER: Speranskiy K 

PROVIDER: S-EPMC4492463 | biostudies-literature | 2004 Jul

REPOSITORIES: biostudies-literature