Molecular dynamics investigations of protein volumetric properties and electronic dynamics

Several theoretical and molecular dynamics investigations. of chemical and biological processes in solution are described. First, a statistical mechanical methodology is developed for evaluating excess volumetric properties of solvation. This methodology makes it possible to analyze volumetric properties in terms of the hydration shell model of solvation. The usefulness of the maximum entropy method for dealing with simulations with which significant statistical error is associated is explored. Second, this methodology is used to isolate additive contributions to the partial molar compressibilities of alcohols in aqueous solution. The magnitude of methyl and hydroxyl group contributions for methanol and ethanol are found to be the same for both solutes within statistical error. Further, the effect of each functional group on the solvent is found to be localized in the vicinity of that functional group, explaining the apparent independence of functional group contributions observed experimentally by other workers. For the potential functions employed, compressibilities calculated via classical molecular dynamics simulations are in best agreement with experiments performed at temperatures higher than those at which the simulations are performed. Finally , the effect of electronic decoherence on electron transfer rates in blue copper proteins is investigated. Electronic decoherence occurs as nuclear trajectories corresponding to alternative electronic states diverge from one another, and higher decoherence rates correspond to reduced direct electron transfer rates. A very short characteristic decoherence time of 2.4 fs is obtained for direct electron transfer between metal centers in ruthenated azurin. Protons in the aqueous solvent molecules have a large effect on the decoherence rate, underscoring the importance of treating the solvent molecules explicitly.