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2011 Fiscal Year Final Research Report

Free energy surfaces of chemical reactions in solution and protein environments

Research Project

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Project/Area Number 21350010
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

YAMAMOTO Takeshi  京都大学, 大学院・理学研究科, 助教 (30397583)

Project Period (FY) 2009 – 2011
Keywords溶液反応 / 酵素反応 / 励起状態 / 自由エネルギー / QM/MM法
Research Abstract

New methods have been developed to calculate the free energy surface of chemical reactions in solution and protein environments. Ab initio quantum chemistry and statistical mechanics have been combined to accurately evaluate the free energy of reactions at the molecular level. The obtained methods were applied to a variety of condensed-phase reactions to obtain physical insight into the environmental effects on chemical reactivity. A new method for locating conical intersection in solution have been proposed and applied to photochemical reactions in solution. Finally, the effect of electronicpolarization was studied by developing a new polarizable molecular mechanical force field of proteins. An efficient QM/MM free energy method was also developed to take into account the electronic polarization effect of solvent.

  • Research Products

    (35 results)

All 2013 2012 2011 2010 2009 Other

All Journal Article (19 results) (of which Peer Reviewed: 19 results) Presentation (15 results) Remarks (1 results)

  • [Journal Article] Accurate and Efficient Treatment of Continuous Solute Charge Density in the Mean-Field QM/MM Free Energy Calculation2013

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

      Journal of Chemical Theory and Computation

      Volume: 9 Pages: 188-203

    • DOI

      doi:dx.doi.org/10.1021/ct300831t

    • Peer Reviewed
  • [Journal Article] Including charge penetration effects into the ESP derived partial charge operator2012

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

      Chemical. Physics. Letters

      Volume: 546 Pages: 80-85

    • DOI

      doi:org/10.1016/j.cplett.2012.07.046

    • Peer Reviewed
  • [Journal Article] Variational calculation of quantum mechanical/molecular mechanical free energy with electronic polarization of solvent2012

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

      The Journal of Chemical Physics

      Volume: 136 Pages: 134107

    • DOI

      doi:10.1063/1.3699234

    • Peer Reviewed
  • [Journal Article] Proton-Coupled Electron Transfer of the Phenoxyl/Phenol Couple: Effect of Hartree-Fock Exchange on Transition Structures2011

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

      Journal of Computational Chemistry

      Volume: 32 Pages: 3081-3091

    • DOI

      DOI:10.1002/jcc.21892

    • Peer Reviewed
  • [Journal Article] Ab Initio Trajectory Study on Triplet Ketene Photodissociation via Statistical Sampling of the Crossing Seam2011

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

      Journal of Chemical Theory and Computatio

      Volume: 7 Pages: 2507-2519

    • DOI

      DOI:10.1021/ct200367y

    • Peer Reviewed
  • [Journal Article] Multireference coupled cluster calculation of the dissociation energy profile of triplet ketene2011

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

      Chemical. Physics. Letters

      Volume: 511 Pages: 28-32

    • DOI

      DOI:10.1016/j.cplett.2011.05.067

    • Peer Reviewed
  • [Journal Article] Solution reaction space Hamiltonian based on an electrostatic potential representation of solvent dynamics2011

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

      The Journal of Chemical Physics

      Volume: 134 Pages: 144108

    • DOI

      DOI:10.1063/1.3572057

    • Peer Reviewed
  • [Journal Article] A theoretical study on excited state double proton transfer reaction of a 7-azaindole dimer: an ab initio potential energy surface and its empirical valence bond model2011

    • Author(s)
      K. Ando, S. Hayashi, S. Kato
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 13 Pages: 11118-11127

    • DOI

      DOI:10.1039/c1cp20420c

    • Peer Reviewed
  • [Journal Article] Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology2010

    • Author(s)
      K.F. Wong, J.L. Sonnenberg, F. Paesani, T. Yamamoto, J. Vanicek, W. Zhang, H.B. Schlegel, D.A. Case, T.E. Cheatham, W.H. Miller, G.A. Voth
    • Journal Title

      Journal of Chemical Theory and Computation

      Volume: 6 Pages: 2566-2580

    • DOI

      DOI:10.1021/ct900579k

    • Peer Reviewed
  • [Journal Article] Quantum Mechanical Reaction Probability of Triplet Ketene at the Multireference Second-Order Perturbation Level of Theory2010

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

      Journal of Physical Chemistry A

      Volume: 114 Pages: 9981-9990

    • DOI

      DOI:10.1021/jp104089m

    • Peer Reviewed
  • [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

      The Journal of Chemical Physics

      Volume: 132 Pages: 044106

    • DOI

      DOI:10.1063/1.329887

    • 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

      Volume: 492 Pages: 193-197

    • DOI

      DOI:10.1016/j.cplett.2010.04.045

    • Peer Reviewed
  • [Journal Article] Proton Transfer in Phenol-Amine Complexes: Phenol Electronic Effects on Free Energy Profile in Solution2010

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

      Journal of Computational Chemistry

      Volume: 31 Pages: 2924-2931

    • DOI

      DOI:10.1002/jcc.21588

    • Peer Reviewed
  • [Journal Article] Conical intersections of free energy surfaces in solution: Effect of electron correlation on a protonated Schiff base in methanol solution2010

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

      The Journal of Chemical Physics

      Volume: 133 Pages: 064107

    • DOI

      DOI:10.1063/1.3472033

    • Peer Reviewed
  • [Journal Article] Protein Collective Motions Coupled to Ligand Migration in Myoglobin2010

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

      Biophysical Journal

      Volume: 98 Pages: 1649-1657

    • DOI

      DOI:10.1016/j.bpj.2009.12.4318

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

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

      Chemical Physics Letters

      Volume: 476 Pages: 97-100

    • DOI

      DOI:10.1016/j.cplett.2009.05.067

    • Peer Reviewed
  • [Journal Article] Grignard Reagents in Solution: Theoretical Study of the 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

      Volume: 113 Pages: 6158-6165

    • DOI

      DOI:10.1021/jp9009788

    • 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

      Volume: 5 Pages: 2809-2821

    • DOI

      DOI:10.1021/ct900295u

    • 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

      Volume: 113 Pages: 9207-9212

    • DOI

      DOI:10.1021/jp903420w

    • Peer Reviewed
  • [Presentation] Large tunneling effects in hydrogen transfer reaction: Antioxidant reaction of ubiquinol and vitamin E2013

    • Author(s)
      T. Inagaki and T. Yamamoto
    • Organizer
      International Symposium on "The Advent of quantum and classical dissipative theory"Institute of Molecular Science
    • Place of Presentation
      Okazaki, Japan
    • Year and Date
      2013-03-07
  • [Presentation] 溶液内水素移動反応のトンネリング効果:ユビキノール-ビタミンEの抗酸化反応2012

    • Author(s)
      稲垣泰一、山本武志
    • Organizer
      第6回分子科学討論会2012
    • Place of Presentation
      東京
    • Year and Date
      20120900
  • [Presentation] MF-QM/MM 法による化学反応の自由エネルギー計算と溶液・酵素反応への応用2012

    • Author(s)
      山本武志、中農浩史
    • Organizer
      第6回分子科学討論会2012
    • Place of Presentation
      東京
    • Year and Date
      20120900
  • [Presentation] QM/MM計算における波動関数の統計揺らぎの効果と平均場近似の妥当性の検証2012

    • Author(s)
      中農浩史、山本武志
    • Organizer
      第6回分子科学討論会2012
    • Place of Presentation
      東京
    • Year and Date
      20120900
  • [Presentation] Large tunneling effects in solution-phase H transfer reaction: Antioxidant reaction of ubiquinol and vitamin E derivative2012

    • Author(s)
      T. Inagaki, T. Yamamoto
    • Organizer
      14th International Congress of Quantum Chemistry
    • Place of Presentation
      Colorado, USA
    • Year and Date
      20120600
  • [Presentation] 平均場QM/MM法のより正確な計算手法の開発2011

    • Author(s)
      中農浩史、山本武志
    • Organizer
      第5回分子科学討論会2011
    • Place of Presentation
      札幌
    • Year and Date
      20110900
  • [Presentation] 溶液内におけるフェノール誘導体の電子・プロトン移動反応の理論的研究2011

    • Author(s)
      稲垣泰一、山本武志
    • Organizer
      第5回分子科学討論会2011
    • Place of Presentation
      札幌
    • Year and Date
      20110900
  • [Presentation] MS-CASPT2法を用いたピリジンの超高速緩和過程についての理論的研究2011

    • Author(s)
      中野勝博、森俊文、林重彦、加藤重樹
    • Organizer
      第5回分子科学討論会2011
    • Place of Presentation
      札幌
    • Year and Date
      20110900
  • [Presentation] Free energy profile for the hydrogen transfer reaction of ubiquinol complex in ethanol2011

    • Author(s)
      T. Inagaki, T. Yamamoto
    • Organizer
      2011 KAIST-Kyoto University Chemistry Symposium
    • Place of Presentation
      Korea
    • Year and Date
      20110000
  • [Presentation] 分極可能力場と組み合わせた平均場QM/MM法による化学反応の自由エネルギー計算2010

    • Author(s)
      中農浩史、山本武志
    • Organizer
      第4回分子科学討論会2010
    • Place of Presentation
      大阪
    • Year and Date
      20100900
  • [Presentation] ユビキノール-トコフェロール間における水素移動反応の理論的研究2010

    • Author(s)
      稲垣泰一、山本武志、加藤重樹
    • Organizer
      第4回分子科学討論会2010
    • Place of Presentation
      大阪
    • Year and Date
      20100900
  • [Presentation] 7-アザインドール二量体の励起状態ダブルプロトン移動反応における反応ダイナミクスの量子動力学法を用いた解析2010

    • Author(s)
      安藤耕平、加藤重樹
    • Organizer
      第4回分子科学討論会2010
    • Place of Presentation
      大阪
    • Year and Date
      20100900
  • [Presentation] 気相中におけるピリジンの超高速緩和過程についての理論的研究2010

    • Author(s)
      中野勝博、森俊文、加藤重樹
    • Organizer
      第4回分子科学討論会2010
    • Place of Presentation
      大阪
    • Year and Date
      20100900
  • [Presentation] 分極可能力場と組み合わせた平均場QM/MM法による化学反応の自由エネルギー計算2010

    • Author(s)
      中農浩史、山本武志
    • Organizer
      第13回理論化学討論会
    • Place of Presentation
      北海道
    • Year and Date
      20100000
  • [Presentation] Construction of The Potential Function for The Excited State Double Proton Transfer Reaction in 7-Azaindole Dimer2009

    • Author(s)
      K. Ando, S. Kato
    • Organizer
      XIIIth International Congress of Quantum Chemistry
    • Place of Presentation
      Helsinki
    • Year and Date
      20090600
  • [Remarks]

    • URL

      http://kuchem.kyoto-u.ac.jp/riron/

URL: 

Published: 2014-08-29  

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