2009 Fiscal Year Final Research Report
QM/MM-MC and QM/MM-MD simulations for reactions in solution
| Project/Area Number |
18066012
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| Research Category |
Grant-in-Aid for Scientific Research on Priority Areas
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| Allocation Type | Single-year Grants |
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| Review Section |
Science and Engineering
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| Research Institution | Hiroshima University |
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Principal Investigator |
AIDA Misako Hiroshima University, 大学院・理学研究科, 教授 (90175159)
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| Co-Investigator(Kenkyū-buntansha) |
MATSUBARA Toshiaki 広島大学, 大学院・理学研究科, 特任准教授 (60239069)
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| Project Period (FY) |
2006 – 2009
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| Keywords | ab initio MO / MD / MC / シミュレーション / QM / MM / ONIOM / 溶媒効果 |
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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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