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2007 Fiscal Year Final Research Report Summary

Free energy Surfaces and Dynamics of Chemical Reactions in Solutions and Biological Systems

Research Project

Project/Area Number 17350007
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Physical chemistry
Research InstitutionKyoto University

Principal Investigator

KATO Shigeki  Kyoto University, Chemistry Department, Professor (20113425)

Co-Investigator(Kenkyū-buntansha) YAMAMOTO Takashi  Kyoto University, Chemistry Department, Assistant professor (30397583)
Project Period (FY) 2005 – 2007
Keywordschemical reactions / free energy surfaces / dynamics / enzymatic reactions / reactions in solution / RISM-SCF method / polarizable charge model
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.

  • Research Products

    (20 results)

All 2007 2006 2005

All Journal Article (20 results) (of which Peer Reviewed: 13 results)

  • [Journal Article] An efficient implementation of three-dimensional reference interaction site model self-consistent-field method : Application to solvatochromic shift calculations2007

    • Author(s)
      N. Minezawa, S. Kato
    • Journal Title

      J. Chem. Phys. 126

      Pages: 054511-054525

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] Solvent effect on conical intersections in excited state 9H-adenine : Radiationless decay mechanism in polar solvent2007

    • Author(s)
      S. Yamazaki, S. Kato
    • Journal Title

      J. Am. Chem. Soc. 129

      Pages: 2901-2909

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] Analytical RISM-MP2 free energy gradient method : Application to the Schlenk equilibrium of Grignard reagent2007

    • Author(s)
      T. Mori, S. Kato
    • Journal Title

      Chem. Phys. Lett. 437

      Pages: 159-163

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] Transition state determination of enzyme reaction on free energy surface : Application to chorismate mutase2007

    • Author(s)
      M. Higashi, S. Hayashi, S. Kato
    • Journal Title

      Chem. Phys. Lett. 437

      Pages: 293-297

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] Geometry optimization based on linear response free energy with quantum mechanical/molecular mechanical method : Applications to Menshutkin-type and Claisen rearrangement reactions in aqueous solution2007

    • Author(s)
      M. Higashi, S. Hayashi, S. Kato
    • Journal Title

      J. Chem. Phys. 126

      Pages: 144503-144512

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] Ab initio calculation of proton-coupled electron transfer rates in the external-potential representation : A ubiquinol complex in solution2007

    • Author(s)
      T. Yamamoto, S. Kato
    • Journal Title

      J. Chem. Phys. 126

      Pages: 224514-224528

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] Electronic polarization effect on low-frequency infrared and Raman spectra of aprotic solvent : Molecular dynamics simulation study with charge response kernel by second order Moller-Plesset perturbation method2007

    • Author(s)
      M. Isegawa, S. Kato
    • Journal Title

      J. Chem. Phys. 127

      Pages: 244502-244512

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] An efficient implementation of three-dimensional reference interaction site model self-consistent-field method : Application to solvatochromic shift calculations2007

    • Author(s)
      N. Minezawa, S. Kato
    • Journal Title

      J. Chem. Phys. 216

      Pages: 054511-054525

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Solvent effect on conical intersections in excited state 9H-adenine: Radiationless decay mechanism in polar solvent2007

    • Author(s)
      S. Yamazaki, S. Kato
    • Journal Title

      J. Am. Chem. Soc. 129

      Pages: 2901-2909

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Electronic polarization effect on low-frequency infrared and Raman spectra of aprotic solvent'- Molecular dynamics simulation study with charge response kernel by second order Moller-Plesset perturbation method2007

    • Author(s)
      M. Isegawa, S. Kato
    • Journal Title

      J. Chem. Phys. 127

      Pages: 244502-244512

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Quantum dynamics study on multichannel dissociation and isomerization reactions of formaldehyde2006

    • Author(s)
      T. Yonehara, S. Kato
    • Journal Title

      J. Chem. Phys. 125

      Pages: 084307-084316

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] Intramolecular Charge Transfer State Formation of 4-(N, N-Dimethylainino) benzonitrile in Acetonitrile Solution : RISM-SCF Study2005

    • Author(s)
      N. Minezawa, S. Kato
    • Journal Title

      J. Phys. Chem. A 109

      Pages: 5445-5453

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] Electronic relaxation dynamics of Ni^<2+> ion aqueous solution : Molecular dynamics simulation2005

    • Author(s)
      S. Iuchi, A. Morita, S. Kato
    • Journal Title

      J. Chem. Phys. 123

      Pages: 024505-024515

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] Locating the lowest free-energy point on conical intersection in polar solvent : Reference interaction site self-consistent field study of ethylene and CH_2NH_2^+2005

    • Author(s)
      S. Yamazaki, S. Kato
    • Journal Title

      J. Chem. Phys. 123

      Pages: 114510-114522

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] Mechanism of color tuning in retinal protein : SAC-CI and QM/MM study2005

    • Author(s)
      K. Fujimoto, JY. Hasegawa, S. Hayashi, S. Kato, H. Nakatsuji
    • Journal Title

      Chem. Phys. Lett. 414

      Pages: 239-242

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] Theoretical Study on Electronic and Spin Structures of [Fe_2S_2]^<2+, +> Cluster : RISM-SCF and MRMP Approach2005

    • Author(s)
      M. Higashi, S. Kato
    • Journal Title

      J. Phys. Chem. A 1092

      Pages: 9867-9874

    • Description
      「研究成果報告書概要(和文)」より
    • Peer Reviewed
  • [Journal Article] Intramolecular Charge Transfer State Formation of 4-(N, N-Dimethylamino)benzonitrile in Acetonitrile Solution : RISMSCF Study2005

    • Author(s)
      N. Minezawa, S. Kato
    • Journal Title

      J. Phys. Chem. A 109

      Pages: 5445-5453

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Electronic relaxation dynamics of Ni^<2+> ion aqueous solution : Molecular dynamics simulation2005

    • Author(s)
      S. Iuchi, A. Morita, S. Kato
    • Journal Title

      J. Phys. Chem. 123

      Pages: 024505-024515

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Mechanism of color tuning in retinal protein : SAOCI and QM/MM Study2005

    • Author(s)
      K. Fujimoto, JY. Hasegawa, S. Hayashi, S. Kato, H. Nakatsuji
    • Journal Title

      Chem. Phys. Lett. 414

      Pages: 239-242

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Theoretical Study on Electronic and Spin Structures of [Fe_2S_2]^<2+,+> Cluster : RISM-SCF and MRMP Approach2005

    • Author(s)
      M. Higashi, S. Kato
    • Journal Title

      J. Phys. Chem. A 1092

      Pages: 9867-9874

    • Description
      「研究成果報告書概要(欧文)」より

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Published: 2010-06-09  

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