2007 Fiscal Year Final Research Report Summary
Free energy Surfaces and Dynamics of Chemical Reactions in Solutions and Biological Systems
| Project/Area Number |
17350007
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Physical chemistry
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| Research Institution | Kyoto University |
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Principal Investigator |
KATO Shigeki Kyoto University, Chemistry Department, Professor (20113425)
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| Co-Investigator(Kenkyū-buntansha) |
YAMAMOTO Takashi Kyoto University, Chemistry Department, Assistant professor (30397583)
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| Project Period (FY) |
2005 – 2007
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| Keywords | chemical reactions / free energy surfaces / dynamics / enzymatic reactions / reactions in solution / RISM-SCF method / polarizable charge model |
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| Research Abstract |
We carried out theoretical and computational studies or free energy surfaces and dynamics of chemical reactions in solution and biological systems. This project includes (1) developments of RISM-SCF method, (2) mechanisms and dynamics of chemical reactions in solution, (3) developments of computational methods tracing reaction paths on free energy surfaces based on QM/MM methodology and their applications to enzymatic reactions, and (4) molecular dynamics (MD) simulations employing a polarizable force field derived from charge response kernel (CRK) method. For the subject (1), we developed a new code for 3-dimensional RISM-SCF method by including several new algorithms or describing solute-solvent interactions and applied it to Rydberg states of pyrrle and indole in aqueous solvent. We also developed the RISM-MP2 and its free energy gradient codes and applied it to Grignard reactions in ether solvents. For the subject (2), We formulated the quantum dynamics method to treat the nonadiabatic electronic transition between free energy surfaces. For this purpose, we defined V-resolved free energy surfaces and calculated the rate constants of proton coupled electron transfer reaction between ubiquinol and phenoxy radical in aceonitrile solvent. We discussed the origin of unusual kinetic isotope effect observed for the related systems. For the subject (3), we investigated the reaction mechanism of chorismate mutase using the linear response free energy methodology developed in this project. We compared the rate constant in the enzyme with that in aqueous solvent and discussed the role of enzyme in relation to the NAC mechanism. Finally, we developed the CRK charge model based on the MP2 method and applied it to simulate the far-IR and Raman spectra of acetonitrile, methykene chloride and acetone.
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