Theoretical Chemistry and Biochemistry


Most chemical reactions are carried out in solution. The solvent surroundings affect such reactions in a variety of important ways. For example, the rates of reactions between ionized molecules are often limited by the rate at which the reactants diffuse through the solvent and come into contact. Also, specific solvation effects often determine the relative free energies or stabilities of reactant, transition state, and product molecules. In our group we study such phenomena using methods from statistical mechanics. These methods range from simulation studies, in which the equations of motion of the atoms in a model system are solved on a computer, to formal studies in which we develop and solve differential or other equations.

 

We also use computer models and formal techniques to examine how protein molecules function. The proteins of interest include enzymes and ligand binding proteins such as antibody molecules. The theoretical studies show, for example, how a substrate may be attracted to the active site of an enzyme by electrostatic interactions, and how the atoms within an enzyme move to participate in catalytic transformation of a bound substrate. These methods are of practical importance in the design of new enzymes that can be synthesized by genetic engineering techniques, and in the design of new drugs that bind strongly to their receptors.

 

Our simulation studies benefit from the excellent computing facilities to which we have access. These facilities include parallel supercomputers and sophisticated computer graphics systems that allow for the visualization of the atomic dynamics in solutions or protein molecules by virtual reality methods.

 

Research in the areas outlined above provides excellent preparation for either academic or industrial employment. In the past few years, members of our group have moved on to faculty positions at the University of California, University of Michigan, Harvard University, Vanderbilt University, the ETH-Zurich, and the Technical University of Munich, among others, and to companies including Pfizer, Johnson & Johnson, and Bristol-Myers Squibb.


Research Support

The research in our group is supported in part by grants from the following agencies:

National Science Foundation, National Institutes of Health, NSF Supercomputer Centers, Burroughs Wellcome Fund, Howard Hughes Medical Institute, W.M. Keck Foundation, and the University of California.


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