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2009 Fiscal Year Final Research Report

Free Energy Surfaces and Dynamics of Chemical Reactions in Solution

Research Project

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Project/Area Number 18066008
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Science and Engineering
Research InstitutionKyoto University

Principal Investigator

KATO Shigeki  Kyoto University, 大学院・理学研究科, 教授 (20113425)

Co-Investigator(Kenkyū-buntansha) YAMAMOTO Takeshi  京都大学, 大学院・理学研究科, 助教 (30397583)
Project Period (FY) 2006 – 2009
Keywords理論化学 / 化学反応 / ダイナミックス / 溶液 / 励起状態 / 酵素反応
Research Abstract

Method development and applications have been made for studying hemical reactions in solution and protein environments. New theoretical methods have een developed called LRFE-SCF, RISM-MP2, and QM/MM-MF methods. To elucidate the echanism of photochemical processes in condensed phase, we proposed a new omputational framework for locating minimum energy conical intersection based on on-equilibrium free energy surfaces. We also developed a new molecular mechanical force ield for proteins using charge response kernel (CRK) and applied it to the study of lectronic polarization effects on proteins and ionic liquids.

  • Research Products

    (18 results)

All 2010 2009 2008 2007 2006

All Journal Article (15 results) (of which Peer Reviewed: 14 results) Presentation (3 results)

  • [Journal Article] A wave-function based approach for polarizable charge model: Systematic comparison of polarization effects on protic, aprotic, and ionic liquids2010

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

      Journal of Chemical Physics 113

      Pages: 044106

    • Peer Reviewed
  • [Journal Article] Electronic spectra of coumarin 151 in polar solvents: Linear response free energy approach2010

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

      Chemical Physics Letters 492

      Pages: 193-197

    • Peer Reviewed
  • [Journal Article] Protein collective motion coupled to ligand migration in myoglobin2010

    • Author(s)
      Y. Nishihara, S. Hayashi, S. Kato
    • Journal Title

      Biophysical Journal 98

      Pages: 1649-1657

  • [Journal Article] Grignard reagents in solution: Theoretical study of equilibria and the reaction with a carbonyl compound in diethyl ether solvent2009

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

      Journal of Physical Chemistry A 113

      Pages: 6158-6165

    • Peer Reviewed
  • [Journal Article] Dynamic electron correlation effect on conical intersections in photochemical ring-opening reaction of cyclohexadinene: MS-CASPT2 study2009

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

      Chemical Physics Letters 476

      Pages: 97-100

    • Peer Reviewed
  • [Journal Article] Polarizable force field for protein with charge response kernel2009

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

      Journal of Chemical Theory and Computation 5

      Pages: 2809-2821

    • Peer Reviewed
  • [Journal Article] An accurate calculation of electronic contribution to static permittivity tensor for organic molecular crystals on the basis of the charge response kernel theory2009

    • Author(s)
      J. Tsutsumi, H. Yoshida, R. Murdey, S. Kato, N. Sato
    • Journal Title

      Journal of Physical Chemistry A 113

      Pages: 9207-9212

    • Peer Reviewed
  • [Journal Article] A search for ligand diffusion pathway in myoglobin using a metadynamics simulation2008

    • Author(s)
      Y. Nishihara, S. Hayashi, S. Kato
    • Journal Title

      Chemical Physics Letters 464

      Pages: 220-225

    • 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

      Journal of Chemical Physics 126,15

      Pages: 224513

    • 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

      Journal of Chemical Physics 126,10

      Pages: 144503

    • 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

      Chemical Physics Letters 437

      Pages: 293-297

    • 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

      Chemical Physics Letters 437

      Pages: 159-163

    • 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

    • 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

      Journal of Chemical Physics 126

      Pages: 054511,15

    • Peer Reviewed
  • [Journal Article] Quantum dynamics study on multichannel dissociation and isomerization reactions of formaldehyde2006

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

      Journal of Chemical Physics 125,10

      Pages: 084307

    • Peer Reviewed
  • [Presentation] Some numerical quests for accurate quantum dynamics in gas and condensed phases2010

    • Author(s)
      山本武志
    • Organizer
      The 69th Okazaki Conference on "New Frontier in Quantum Chemical Dynamics"
    • Place of Presentation
      分子科学研究所(名古屋)
    • Year and Date
      2010-02-21
  • [Presentation] QM/MM法に基づく化学反応の自由エネルギー計算と反応経路の探索2010

    • Author(s)
      山本武志
    • Organizer
      IMSスーパーコンピュータワークショップ
    • Place of Presentation
      分子科学研究所(名古屋)
    • Year and Date
      2010-01-13
  • [Presentation] Free Energy Surfaces and Dynamics of Chemical Reactions in Solution and Biological Systems2009

    • Author(s)
      加藤重樹
    • Organizer
      Theory and Applications of Computational Chemistry 2008
    • Place of Presentation
      中国・上海
    • Year and Date
      2009-09-29

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Published: 2011-06-18   Modified: 2016-04-21  

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