COMPUTER SIMULATION OF ELECTRON TRANSFER REACTIONS

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Electron Transfer (ET) reactions play a major role in many biological and chemical processes. Early experimental and theoretical studies have identified the key factors in ET reactions and led to a qualitative picture using continuum solvent models. However, recent experiments have provided information at a level where the microscopic nature of the environment around donor and acceptor might be important. this is particularly relevant in studies of biological ET such as bacterial reaction centers (RC's) where the protein structure is known and the challenge is to reproduce experimental facts using this structure. The overall objective of this project is to advance the understanding of ET processes in biological and chemical systems to a microscopic level using computer simulation approaches. During the previous grant period we developed, examined and refined a wide range of simulation strategies for ET processes in proteins and solution, including a free energy perturbation/umbrella sampling method, semiclassical trajectory, dispersed polaron and density matrix approaches. These were applied to study ET processes in bacterial RC's and solution. Our studies and those of other groups demonstrated the usefulness of computer simulations. In particular, we were able to simulate ET in bacterial RC's and to examine different feasible mechanisms. In the current grant period we would like to move to a more quantitative level in the description of ET in proteins and solution. This will involve the following projects: (i) Further study of bacterial RC's. Earlier simulations yielded encouraging results but unique conclusions about the charge separation mechanism were not reached. Using longer simulations with improved long- range treatment while focussing on mutation effects is expected to give valuable information about the energetics of charge transfer states. (ii) Error range evaluation through extensive study of mutation effects on the redox potential of cytochromes and other proteins with mutants of known structure. The performance of several methods, including local reaction field augmented free energy perturbation, will be examined. (iii) Analysis of time resolved information about bacterial photosynthesis by various simulation methods. (iv) Exploration of the energetics of ET and proton transfer in the quinone sites. (v) Simulation of ET in Ru-cyt c to estimate the inherent dependence of the rate constant on the electronic coupling term, by factoring out the possible effect of protein fluctuations and reorganization energy. (vi) Simulation of ET in solution, using an explicit representation of donor and acceptor, trying to reproduce experimental results of well defined test cases.