Free energy surfaces of chemical reactions in solution and protein environments

• Project/Area Number: 21350010
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Physical chemistry
• Research Institution: Kyoto University
• Principal Investigator: YAMAMOTO Takeshi (2010-2011) 京都大学, 大学院・理学研究科, 助教 (30397583); 加藤 重樹 (2009) Kyoto University, 大学院・理学研究科, 教授 (20113425)
• Co-Investigator(Kenkyū-buntansha): 山本 武志 京都大学, 大学院・理学研究科, 助教 (30397583)
• Project Period (FY): 2009 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥18,850,000 (Direct Cost: ¥14,500,000、Indirect Cost: ¥4,350,000); Fiscal Year 2011: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2010: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000); Fiscal Year 2009: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000)
• Keywords: 溶液反応 / 酵素反応 / 励起状態 / 自由エネルギー / QM/MM法 / 化学反応 / 量子化学 / 統計力学 / 溶媒効果 / タンパク質 / QM/MM / QM・MM法 / 触媒 / 溶媒内反応 / QM / MM法 / 溶液内反応

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

• [Journal Article] Accurate and Efficient Treatment of Continuous Solute Charge Density in the Mean-Field QM/MM Free Energy Calculation (2013)
  • Author(s): H. Nakano, T. Yamamoto
  • Journal Title: Journal of Chemical Theory and Computation Volume: 9 Issue: 1 Pages: 188-203
  • DOI: 10.1021/ct300831t
  • Peer Reviewed
• [Journal Article] Including charge penetration effects into the ESP derived partial charge operator (2012)
  • Author(s): H. Nakano, T. Yamamoto
  • Journal Title: Chemical. Physics. Letters Volume: 546 Pages: 80-85
  • DOI: 10.1016/j.cplett.2012.07.046
  • Peer Reviewed
• [Journal Article] Variational calculation of quantum mechanical/molecular mechanical free energy with electronic polarization of solvent (2012)
  • Author(s): H. Nakano, T. Yamamoto
  • Journal Title: The Journal of Chemical Physics Volume: 136 Issue: 13 Pages: 134107-134107
  • DOI: 10.1063/1.3699234
  • NAID: 120005439722
  • Peer Reviewed
• [Journal Article] Proton-Coupled Electron Transfer of the Phenoxyl/Phenol Couple: Effect of Hartree-Fock Exchange on Transition Structures (2011)
  • Author(s): T. Inagaki, T. Yamamoto, S. Kato
  • Journal Title: Journal of Computational Chemistry Volume: 32 Issue: 14 Pages: 3081-3091
  • DOI: 10.1002/jcc.21892
  • Peer Reviewed
• [Journal Article] Ab Initio Trajectory Study on Triplet Ketene Photodissociation via Statistical Sampling of the Crossing Seam (2011)
  • Author(s): Y. Ogihara, T. Yamamoto, S. Kato
  • Journal Title: Journal of Chemical Theory and Computatio Volume: 7 Issue: 8 Pages: 2507-2519
  • DOI: 10.1021/ct200367y
  • Peer Reviewed
• [Journal Article] Multireference coupled cluster calculation of the dissociation energy profile of triplet ketene (2011)
  • Author(s): Y. Ogihara, T. Yamamoto, S. Kato
  • Journal Title: Chemical. Physics. Letters Volume: 511 Issue: 1-3 Pages: 28-32
  • DOI: 10.1016/j.cplett.2011.05.067
  • Peer Reviewed
• [Journal Article] Solution reaction space Hamiltonian based on an electrostatic potential representation of solvent dynamics (2011)
  • Author(s): S. Aono, T. Yamamoto, S. Kato
  • Journal Title: The Journal of Chemical Physics Volume: 134 Issue: 14 Pages: 144108-144108
  • 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 model (2011)
  • Author(s): K. Ando, S. Hayashi, S. Kato
  • Journal Title: Physical Chemistry Chemical Physics Volume: 13 Issue: 23 Pages: 11118-11127
  • DOI: 10.1039/c1cp20420c
  • Peer Reviewed
• [Journal Article] Solution reaction space Hamiltonian based on an electrostatic potential representation of solvent dynamics (2011)
  • Author(s): S.Aono, T.Yamamoto, S.Kato
  • Journal Title: Journal of Chemical Physics Volume: 134
  • 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 model (2011)
  • Author(s): K.Ando, S.Hayashi, S.Kato
  • Journal Title: Physical Chemistry Chemical Physics Volume: 13 Pages: 11118-11127
  • Peer Reviewed
• [Journal Article] Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology (2010)
  • 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 Issue: 9 Pages: 2566-2580
  • DOI: 10.1021/ct900579k
  • Peer Reviewed
• [Journal Article] Quantum Mechanical Reaction Probability of Triplet Ketene at the Multireference Second-Order Perturbation Level of Theory (2010)
  • Author(s): Y. Ogihara, T. Yamamoto, S. Kato
  • Journal Title: Journal of Physical Chemistry A Volume: 114 Issue: 37 Pages: 9981-9990
  • 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 liquids (2010)
  • Author(s): H. Nakano T. Yamamoto, S. Kato
  • Journal Title: The Journal of Chemical Physics Volume: 132 Issue: 7 Pages: 44106-44106
  • DOI: 10.1063/1.329887
  • Peer Reviewed
• [Journal Article] Electronic spectra of coumarin-151 in polar solvents: Linear response free energy approach (2010)
  • Author(s): S. Aono, N. Minezawa, S. Kato
  • Journal Title: Chemical Physics Letters Volume: 492 Issue: 1-3 Pages: 193-197
  • 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 Solution (2010)
  • Author(s): S. Aono, S. Kato
  • Journal Title: Journal of Computational Chemistry Volume: 31 Issue: 16 Pages: 2924-2931
  • 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 solution (2010)
  • Author(s): T. Mori, K. Nakano, S. Kato
  • Journal Title: The Journal of Chemical Physics Volume: 133 Issue: 6 Pages: 64107-64107
  • DOI: 10.1063/1.3472033
  • Peer Reviewed
• [Journal Article] Protein Collective Motions Coupled to Ligand Migration in Myoglobin (2010)
  • Author(s): Y. Nishihara, S. Kato, S. Hayashi
  • Journal Title: Biophysical Journal Volume: 98 Issue: 8 Pages: 1649-1657
  • DOI: 10.1016/j.bpj.2009.12.4318
  • Peer Reviewed
• [Journal Article] Protein collective motions coupled to ligand migration in myoglobin (2010)
  • Author(s): Y.Nishihara, S.Kato, S.Hayashi
  • Journal Title: Biophysical Journal Volume: 98 Pages: 1649-1657
  • Peer Reviewed
• [Journal Article] A wavefunction based approach for polarizable charge model : Systematic comparison of polarization effects on protic, aprotic, and ionic liquids (2010)
  • Author(s): H.Nakano, T.Yamamoto, S.Kato
  • Journal Title: Journal of Chemical Physics Volume: 132
  • Peer Reviewed
• [Journal Article] Proton transfer studied using a combined ab initio reactive potential energy surface with quantum path integral methodology (2010)
  • Author(s): K.F.Wong, J.L.Sonnenberg, F.Paesani, T.Yamamoto, et al
  • Journal Title: Journal of Chemical Theory and Computation Volume: 6 Pages: 2566-2580
  • Peer Reviewed
• [Journal Article] Quantum mechanical reaction probability of triplet ketene at the multireference second-order perturbation level of theory (2010)
  • Author(s): Y.Ogihara, T.Yamamoto, S.Kato
  • Journal Title: Journal of Physical Chemistry A Volume: 114 Pages: 9981-9990
  • Peer Reviewed
• [Journal Article] Conical intersections of free energy surfaces in solution : Effect of electron correlation on a protonated Schiff base in methanol solution (2010)
  • Author(s): T.Mori, K.Nakano, S.Kato
  • Journal Title: Journal of Chemical Physics Volume: 133
  • Peer Reviewed
• [Journal Article] Electronic spectra of coumarin-151 in polar solvents : Linear response free energy approach (2010)
  • Author(s): S.Aono, N.Minezawa, S.Kato
  • Journal Title: Chemical Physics Letters Volume: 492 Pages: 193-197
  • Peer Reviewed
• [Journal Article] Proton transfer in phenol-amine complexes : phenol electronic effects on free energy profile in solution (2010)
  • Author(s): S.Aono, S.Kato
  • Journal Title: Journal of Computational Chemistry Volume: 31 Pages: 2924-2931
  • Peer Reviewed
• [Journal Article] A wave-function based approach for polarizable charge model : Systematic comparison of polarization effects on protic, aprotic, and ionic liquids (2010)
  • Author(s): H.Nakano, T.Yamamoto, S.Kato
  • Journal Title: Journal of Chemical Physics 132 Pages: 44106-44106
  • Peer Reviewed
• [Journal Article] Dynamic electron correlation effect on conical intersections in photochemical ring-opening reaction of cyclohexadiene: MS-CASPT2 study (2009)
  • Author(s): T. Mori, S. Kato
  • Journal Title: Chemical Physics Letters Volume: 476 Issue: 1-3 Pages: 97-100
  • 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 Solvent (2009)
  • Author(s): T. Mori, S. Kato
  • Journal Title: Journal of Physical Chemistry A Volume: 113 Issue: 21 Pages: 6158-6165
  • DOI: 10.1021/jp9009788
  • Peer Reviewed
• [Journal Article] Polarizable Force Field for Protein with Charge Response Kernel (2009)
  • Author(s): M. Isegawa, S. Kato
  • Journal Title: Journal of Chemical Theory and Computation Volume: 5 Issue: 10 Pages: 2809-2821
  • 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 Theory (2009)
  • Author(s): J. Tsutsumi, H. Yoshida, R. Murdey,S. Kato, N. Sato
  • Journal Title: Journal of Physical Chemistry A Volume: 113 Issue: 32 Pages: 9207-9212
  • DOI: 10.1021/jp903420w
  • Peer Reviewed
• [Journal Article] Grignard reagents in solution : Theoretical study of equilibria and the reaction with a carbonyl compound in diethyl ether solvent (2009)
  • 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 study (2009)
  • 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 kernel (2009)
  • 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 theory (2009)
  • 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
• [Presentation] Large tunneling effects in hydrogen transfer reaction: Antioxidant reaction of ubiquinol and vitamin E (2013)
  • 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
• [Presentation] Large tunneling effects in solution-phase H transfer reaction: Antioxidant reaction of ubiquinol and vitamin E derivative (2012)
  • Author(s): T. Inagaki, T. Yamamoto
  • Organizer: 14th International Congress of Quantum Chemistry
  • Place of Presentation: Colorado, USA
• [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
• [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
• [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
  • Organizer: 分子科学討論会
  • Place of Presentation: 東京大学
• [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
  • Organizer: 分子科学討論会
  • Place of Presentation: 東京大学
• [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
  • Organizer: 分子科学討論会
  • Place of Presentation: 東京大学
• [Presentation] 平均場QM/MM法による溶液・酵素反応の自由エネルギー計算 (2012)
  • Author(s): 中農浩史
  • Organizer: 溶液化学シンポジウム
  • Place of Presentation: 早稲田大学
• [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
• [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
• [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
• [Presentation] Free energy profile for the hydrogen transfer reaction of ubiquinol complex in ethanol (2011)
  • Author(s): T. Inagaki, T. Yamamoto
  • Organizer: 2011 KAIST-Kyoto University Chemistry Symposium
  • Place of Presentation: Korea
• [Presentation] 溶液中ATP加水分解エネルギーの分子論的解釈 (2010)
  • Author(s): 山本武志
  • Organizer: 日本生物物理学会年会
  • Place of Presentation: 東北大学(仙台)(招待)
  • Year and Date: 2010-09-21
• [Presentation] Some numerical quests for accurate quantum dynamics in gas and condensed phases (2010)
  • 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] Some numerical quests for accurate quantum molecular dynamics (2010)
  • Author(s): 山本武志
  • Organizer: 第69回岡崎カンファレンス"New frontier in Quanturn Chemical Dynamics"
  • Place of Presentation: 分子科学研究所(名古屋)(招待)
  • Year and Date: 2010-02-18
• [Presentation] QM/MM法による反応自由エネルギーの計算と反応経路の探索 (2010)
  • Author(s): 山本武志
  • Organizer: スーパーコンピュータワークショップ2010
  • Place of Presentation: 分子科学研究所(名古屋)(招待)
  • Year and Date: 2010-01-13
• [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] 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
• [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
• [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
• [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
• [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
• [Presentation] Construction of The Potential Function for The Excited State Double Proton Transfer Reaction in 7-Azaindole Dimer (2009)
  • Author(s): K. Ando, S. Kato
  • Organizer: XIIIth International Congress of Quantum Chemistry
  • Place of Presentation: Helsinki
• [Remarks]
  • URL: http://kuchem.kyoto-u.ac.jp/riron/