| Budget Amount *help |
¥18,500,000 (Direct Cost: ¥18,500,000)
Fiscal Year 2009: ¥3,400,000 (Direct Cost: ¥3,400,000)
Fiscal Year 2008: ¥5,700,000 (Direct Cost: ¥5,700,000)
Fiscal Year 2007: ¥5,700,000 (Direct Cost: ¥5,700,000)
Fiscal Year 2006: ¥3,700,000 (Direct Cost: ¥3,700,000)
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| Research Abstract |
The free-energy calculation by perturbation theory based on a mixed-Hamiltonian model (QM/MM) combined with Monte Carlo sampling of the solvent configurations was used to obtain the changes in solvation free energy. We devised a special procedure to analyze the two-dimensional free-energy surfaces to gain unique insight into the differences in the reaction mechanisms between the two systems. Two-dimensional free-energy surfaces are calculated for alkyl chloride/chloride exchange/inversion reactions surrounded by one hundred H_2O molecules as a model of solvent.
The NVT ensemble of water cluster is divided into the configurational subsets, which correspond to the topology-distinct H-bond patterns, and the relative molar Helmholtz energies of the H-bond patterns are evaluated. The method is based on the combination of standard Monte Carlo techniques with defined H-bond patterns.
We derived and implemented the ONIOM-molecular dynamics method for biochemical applications. The implementation allows the characterization of the functions of the real enzymes taking account of their thermal motion.
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