New Development of Bioinorganic Chemistry from Quantum Chemical Calculations

• Project/Area Number: 18350088
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Chemistry related to living body
• Research Institution: Kyushu University
• Principal Investigator: YOSHIZAWA Kazunari Kyushu University, 先導物質化学研究所, 教授 (30273486)
• Co-Investigator(Kenkyū-buntansha): SHIOTA Yoshihito 九州大学, 先導物質化学研究所, 助教 (70335991) ; 蒲池 高志 九州大学, 先導物質化学研究所, 学術研究員 (40403951)
• Co-Investigator(Renkei-kenkyūsha): KAMACHI Takashi 九州大学, 先導物質化学研究所, 学術研究員 (40403951)
• Project Period (FY): 2006 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥17,030,000 (Direct Cost: ¥14,900,000、Indirect Cost: ¥2,130,000); Fiscal Year 2008: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000); Fiscal Year 2007: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000); Fiscal Year 2006: ¥7,800,000 (Direct Cost: ¥7,800,000)
• Keywords: 量子化学 / 生物無機化学 / 金属酵素 / 反応機構 / 密度汎関数法 / チロシナーゼ / 密度汎関数 / 酵素反応 / 生体分子 / 分子力学 / 電子輸送

Research Abstract

量子化学計算により金属酵素の構造と反応性について研究を行った。とくに、量子力学と分子力学を組み合わせた、いわゆるQM/MM法により、チロシナーゼやB12関連酵素、ビオチンカーボキシラーゼの全原子計算を行い、これらの酵素の反応機構を解明した。さらに、人工錯体による窒素分子の活性化の機構について研究を行い、これを明らかにした。

Research Products

• [Journal Article] Comparison of the Reactivity of Bis(μ-oxo)Cu^<II>Cu^<III> and Cu^<III>Cu^<III> Species to Methane (2009)
  • Author(s): Y. Shiota and K. Yoshizawa
  • Journal Title: Inorganic Chemistry 48 Pages: 838-845
• [Journal Article] Photochemical Reversibility of Ring-Closing and Ring-Opening Reactions in Diarylperfluorocyclopentenes (2009)
  • Author(s): A. Staykov and K. Yoshizawa
  • Journal Title: Journal of Physical Chemistry C 113 Pages: 3826-3834
• [Journal Article] Orbital View Concept Applied on Photoswitching Systems (2009)
  • Author(s): Y. Tsuji, A. Staykov, and K. Yoshizawa
  • Journal Title: Thin Solid Films (in press)
• [Journal Article] DFT Study on the Mechanism of N-N Bond Cleavage by a Bis(μ-hydrido)diniobium Complex (2009)
  • Author(s): H. Tanaka, Y. Shiota, T. Matsuo, H. Kawaguchi, and K. Yoshizawa
  • Journal Title: Inorganic Chemistry 48 Pages: 3875-3881
• [Journal Article] What is the Identity of the Metal Ions in the Active Sites of Coenzyme B12-Dependent Diol Dehydratase? A Computational Mutation Analysis (2009)
  • Author(s): T. Kamachi, M. Takahata, T. Toraya, and K. Yoshizawa
  • Journal Title: T. Kamachi, M. Takahata, T. Toraya, and K. Journal of Physical Chemistry B 113(in press)
• [Journal Article] Bistability of Magnetization without Spin-Transition in a High-Spin Cobalt(II)Complex due to Angular Momentum Quenching (2009)
  • Author(s): G. Juhasz, R. Matsuda, S. Kanegawa, K. Inoue, O. Sato, and K. Yoshizawa
  • Journal Title: Journal of the American Chemical Society 131 Pages: 4560-4561
• [Journal Article] Catalytic Mechanism of Fluoroacetate Dehalogenase : Computational Exploration of the Biological Dehalogenation (2009)
  • Author(s): T. Kamachi, T. Nakayama, O. Shitamichi, K. Jitsumori, T. Kurihara, N. Esaki, and K. Yoshizawa
  • Journal Title: Chemistry-A European Journal (in press)
• [Journal Article] Comparison of the Reactivity of Bis(μ-oxo)Cu^<II>Cu^<III> and Cu^<III>Cu^<III> Species to Methane (2009)
  • Author(s): Y. Shiota, et al.
  • Journal Title: Inorganic Chemistry 48 Pages: 838-845
  • Peer Reviewed
• [Journal Article] Photochemical Reversibility of Ring-Closing and Ring-Opening Reactions in Diarylperfluorocyclopentenes (2009)
  • Author(s): A. Staykov, et al.
  • Journal Title: Journal of Physical Chemistry C 113(in press)
  • Peer Reviewed
• [Journal Article] Orbital View Concept Applied on Photoswitching Systems (2009)
  • Author(s): Y. Tsuji, et al.
  • Journal Title: Thin Solid films (in press)
  • Peer Reviewed
• [Journal Article] DFT Study on the Mechanism of N≡N Bond Cleavage by a Bis(μ-hydrido)diniobium Comples (2009)
  • Author(s): H. Tanaka, et al.
  • Journal Title: Inorganic Chemistry 48(in press)
  • Peer Reviewed
• [Journal Article] What is the Identity of the Metal Ions in the Active Sites of Coenzyme B_<12>-Dependent Diol Dehydratase? A Computational Mutation Analysis (2009)
  • Author(s): T. Kamachi, et al.
  • Journal Title: Journal of Physical Chemistry B 113(in press)
  • Peer Reviewed
• [Journal Article] Bistability of Magnetization of Hgh-Spin Cobalt(II)Complex Controlled by Quenching Angular Momentum (2009)
  • Author(s): G. Juhasz, et al.
  • Journal Title: Journal of the American Chemical Society (in press)
  • Peer Reviewed
• [Journal Article] Theoretical Analysis of the Reaction Mechanism of Biotin Carboxylase (2008)
  • Author(s): Y. Ito, H. Kondo, Y. Shiota, and K. Yoshizawa
  • Journal Title: Journal of Chemical Theory and Computation 4 Pages: 366-374
• [Journal Article] Synthesis and Characterization of Novel Ferrocene-Containing Pyridylamine Ligand and Their Ruthenium(II) Complexes : Electronic Communication through Hydrogen-bonded Amide Linkage (2008)
  • Author(s): T. Kojima, D. Noguchi, T. Nakayama, Y. Inagaki, Y. Shiota, K. Yoshizawa, K. Ohkubo, and S. Fukuzumi
  • Journal Title: Inorganic Chemistry 47 Pages: 886-895
• [Journal Article] Silicon-Carbon Unsaturated Compounds. 74. Thermal Behavior of 1-Silacyclobut-3-enes Generated from the Reaction of Acylpolysilanes with tert-Butylacetylene (2008)
  • Author(s): A. Naka, S. Motoike, N. Senbu, J. Ohshita, A. Kunai, K. Yoshizawa, and M. Ishikawa
  • Journal Title: Organometallics 27 Pages: 2750-2755
• [Journal Article] DFT Study on Chemical N2 Fixation by Using a Cubane-Type RuIr_3S_4 Cluster : Energy Profile for Binding and Reduction of N_2 to Ammonia via Ru-N-NH_x (x=1-3) Intermediates with Unique Structures (2008)
  • Author(s): H. Tanaka, H. Mori, H. Seino, M. Hidai, Y. Mizobe, and K. Yoshizawa
  • Journal Title: Journal of the American Chemical Society 130 Pages: 9037-9047
• [Journal Article] Rutenium-Catalyzed Selective and Efficient Oxygenation of Hydrocarbons with Water as an Oxygen Source (2008)
  • Author(s): Y. Hirata, T. Kojima, Y. Mizutani, Y. Shiota, K. Yoshizawa, and S. Fukuzumi
  • Journal Title: Angewandte Chemie International Edition 47 Pages: 5772-5776
• [Journal Article] Orbital Views of the Electron Transport in Molecular Devices (2008)
  • Author(s): K. Yoshizawa, T. Tada, and A. Staykov
  • Journal Title: Journal of the American Chemical Society 130 Pages: 9406-9413
• [Journal Article] Mechanism and Kinetics of Cyanide Decomposition by Ferrate (2008)
  • Author(s): T. Kamachi, T. Nakayama, and K. Yoshizawa
  • Journal Title: Bulletin of the Chemical Society of Japan 81 Pages: 1212-1218
  • NAID: 10024330607
• [Journal Article] Theoretical Study of Long-Range Electron Transport in Molecular Junctions (2008)
  • Author(s): D. Nozaki, Y. Girard, and K. Yoshizawa
  • Journal Title: Journal of Physical Chemistry C 112 Pages: 17408-17415
• [Journal Article] Combined Experimental and Theoretical Approach to Understand the Reactivity of a Mononuclear Cu(II)-Hydroperoxo Complex in Oxygenation Reactions (2008)
  • Author(s): T. Kamachi, Y. -M. Lee, T. Nishimi, J. Cho, K. Yoshizawa, and W. Nam
  • Journal Title: Journal of Physical Chemistry A 112 Pages: 13102-13108
• [Journal Article] Quantum Chemical Approach to the Mechanism for the Biological Conversion of Tyrosine to Dopaquinone (2008)
  • Author(s): T. Inoue, Y. Shiota, and K. Yoshizawa
  • Journal Title: Journal of the American Chemical Society 130 Pages: 16890-16897
• [Journal Article] Theoretical Study of the Direct Synthesis of H_2O_2 on Pd and Pd/Au Surfaces (2008)
  • Author(s): A. Staykov, T. Kamachi, T. Ishihara, and K. Yoshizawa
  • Journal Title: Journal of Physical Chemistry C 112 Pages: 19501-19505
• [Journal Article] 人工変異酵素の設計と機能制御を目指して (2008)
  • Author(s): 吉澤一成
  • Journal Title: 触媒 50(7) Pages: 608-613
• [Journal Article] Theoretical Analysis of the Reaction Mechanism of Biotin Carboxylase (2008)
  • Author(s): Y. Ito, et al.
  • Journal Title: Journal of Chemical Theory and Computation 4 Pages: 366-374
  • Peer Reviewed
• [Journal Article] Synthesis and Characterization of Novel Ferrocene-Containing Pyridylamine Ligand and Their Ruthenium(II)Complexes : Electronic Communication through Hydrogen-bonded Amide Linkage (2008)
  • Author(s): T. Kojima, et al.
  • Journal Title: Inorganic Chemistry 47 Pages: 886-895
  • Peer Reviewed
• [Journal Article] Silicon-Carbon Unsaturated Compounds. 74. Thermal Behavior of 1-Silacyclobut-3-enes Generated from the Reaction of Acylpolysilanes with tert-Butylacetylene (2008)
  • Author(s): A. Naka, et al.
  • Journal Title: Organometallics 27 Pages: 2750-2755
  • Peer Reviewed
• [Journal Article] DFT Study on Chemical N_2 Fixation by Using a Cubane-Type RuIr_3S_4 Cluster : Energy Profile for Binding and Reduction of N_2 to Ammonia via Ru-N-NH_x (x = 1-3) Intermediates with Unique Structures (2008)
  • Author(s): H. Tanaka, et al.
  • Journal Title: Journal of the American Chemical Society 130 Pages: 9037-9047
  • Peer Reviewed
• [Journal Article] Rutenium-Catalyzed Selective and Efficient Oxygenation of Hydrocarbons with Water as an Oxygen Source (2008)
  • Author(s): Y. Hirata, et al.
  • Journal Title: Angewandte Chemie International Edition 47 Pages: 5772-5776
  • Peer Reviewed
• [Journal Article] Orbital Views of the Electron Transport in Molecular Devices (2008)
  • Author(s): K. Yoshizawa, et al.
  • Journal Title: Journal of the American Chemical Society 130 Pages: 9406-9413
  • Peer Reviewed
• [Journal Article] Mechanism and Kinetics of Cyanide Destruction by Ferrate (2008)
  • Author(s): T. Kamachi, et al.
  • Journal Title: Bulletin of the Chemical Society of Japan 81 Pages: 1212-1218
  • Peer Reviewed
• [Journal Article] Theoretical Study of Long-Ranged Electron Transport in Molecular Junctions (2008)
  • Author(s): D. Nozaki, et al.
  • Journal Title: Journal of Physical Chemistry C 112 Pages: 17408-17415
  • Peer Reviewed
• [Journal Article] Combined Experimental and Theoretical Approach to Understand the Reactivity of a Mononuclear Cu(II)-Hydroperoxo Complex in Oxgenation Reactions (2008)
  • Author(s): T. Kamachi, et al.
  • Journal Title: Journal of Physical Chemistry A 112 Pages: 13102-13108
  • Peer Reviewed
• [Journal Article] Quantum Chemical Approach to the Mechanism for the Biological Conversion of Tyrosine to Dopaquinone (2008)
  • Author(s): T. Inoue, et al.
  • Journal Title: Journal of the American Chemical Society 130 Pages: 16890-16897
  • Peer Reviewed
• [Journal Article] Theoretical Study of the Direct Synthesis of H_2O_2 on Pd and Pd/Au Surfaces (2008)
  • Author(s): A. Staykov, et al.
  • Journal Title: Journal of Physical Chemistry B 112 Pages: 19501-19595
  • Peer Reviewed
• [Journal Article] Theoretical Analysis of the Reaction Mechanism of Biotin Carboxylase (2008)
  • Author(s): Y.Ito
  • Journal Title: Journal of Chemical Theory and Computation 4 Pages: 366-374
  • Peer Reviewed
• [Journal Article] Synthesis and Characterization of Novel Ferrocene-Containing Pyridylamine Ligand and Their Ruthenium(II) Complexes: Electronic Communication through Hydrogen-bonded Amide Linkage (2008)
  • Author(s): T.Kojima
  • Journal Title: Inorganic Chemistry 47 Pages: 886-895
  • Peer Reviewed
• [Journal Article] Does Cob(II)alamin Act as a Conductor in Coenzyme B_<12> Dependent Mutases? (2007)
  • Author(s): P.M.Kozlowski
  • Journal Title: Angewandte Chemie International Edition 46 Pages: 980-983
  • Peer Reviewed
• [Journal Article] Vibronic Interaction in MetaHoporphyrin π-Anion Radicals (2007)
  • Author(s): K.Yoshizawa
  • Journal Title: Journal of Physical Chemistry A 111 Pages: 852-857
  • Peer Reviewed
• [Journal Article] Photoswitching of Conductivity through a Diarylperfluorocyclopentene Nanowire (2007)
  • Author(s): A.Staykov
  • Journal Title: Journal of Physical Chemistry C 111 Pages: 3517-3521
  • Peer Reviewed
• [Journal Article] Combined Experimental and Theoretical Evidence or NonhemeIron(III)-Alkylperoxo Species as a Sluggish Oxidantin Oxygenation Reactions (2007)
  • Author(s): M.S.Sea
  • Journal Title: Angewandte Chemie International Edition 46 Pages: 2291-2294
  • Peer Reviewed
• [Journal Article] Theoretical Study of Donor-π-Bridge-Acceptor Unimolecular Rectifier (2007)
  • Author(s): A.Staykov
  • Journal Title: Journal of Physical Chemistry C 111 Pages: 11699-11705
  • Peer Reviewed
• [Journal Article] Computational Mutation Analysis of Coenzyme B_<12>-Dependent Diol Dehydratase (2007)
  • Author(s): T.Kamachi
  • Journal Title: Chemistry-A European Journal 13 Pages: 7864-7873
  • Peer Reviewed
• [Journal Article] DFT Analysis of Cubane-Type Felr_3S_4 Clusters.Dinitrogen Binding and Activation at the Tetrahedral Fe Site (2007)
  • Author(s): P.M.Kozlowski
  • Journal Title: Bullet in of the Chemical Society of Japan 80 Pages: 2323-2328
  • Peer Reviewed
• [Journal Article] Does Cob(II)alamin Act as a Conductor in Coenzyme B_1_2 Dependent Mutases? (2007)
  • Author(s): P.M.Kozlowski et al.
  • Journal Title: Angew. Chem. Int. Ed. 46 Pages: 852-857
• [Journal Article] Combined Experimental and Theoretical Evidence for Nonheme Iron(III)-Alkylperoxo Species as a Sluggish Oxidant in Oxygenation Reactions (2007)
  • Author(s): M.S.Seo et al.
  • Journal Title: Angew. Chem. Int. Ed. 46 Pages: 2291-2294
• [Journal Article] Vibronic Interaction in Metalloporphyrin π-Anion Radicals (2007)
  • Author(s): K.Yoshizawa et al.
  • Journal Title: J. Phys. Chem. A 111 Pages: 852-857
• [Journal Article] Photoswitching of Conductivity through a Diarylperfluorocyclopentene Nanowire (2007)
  • Author(s): A.Staykov et al.
  • Journal Title: J. Phys. Chem. C 111 Pages: 3517-3521
• [Journal Article] Non-Radical Mechanism for Methane Hydroxylation by Iron-Oxo Complexes (2006)
  • Author(s): K.Yoshizawa et al.
  • Journal Title: Acc. Chem. Res. 39 Pages: 375-382
• [Journal Article] Catalytic Mechanism of Dopamine β-Monooxygenase Mediated by Cu(III)-Oxo (2006)
  • Author(s): K.Yoshizawa et al.
  • Journal Title: Inorg. Chem. 45 Pages: 3034-3041
• [Journal Article] Conversion of Methane to Methanol at the Mononuclear and Dinuclear Copper Sites of Particulate Methane Monooxygenase(pMMO) : A DFT and QM/MM Study (2006)
  • Author(s): K.Yoshizawa et al.
  • Journal Title: J. Am. Chem. Soc. 128 Pages: 9873-9881
• [Journal Article] QM/MM Study on the Catalytic Mechanism of Benzene Hydroxylation over Fe-ZSM-5 (2006)
  • Author(s): Y.Shiota et al.
  • Journal Title: Organometallics 25 Pages: 3118-3123
• [Journal Article] How Axial Ligands Control the Reactivity of High-Valent Iron(IV)-Oxo Porphyrin π-Cation Radicals in Alkane Hydroxylation : A Computational Study (2006)
  • Author(s): T.Kamachi et al.
  • Journal Title: J. Inorg. Biochem. 100 Pages: 751-754
• [Journal Article] Theoretical Study of a Neutral, Doubly Protonated, and Doubly Deprotonated Porphyrine Dithiolate used as a Molecular Switch (2006)
  • Author(s): Y.Girard et al.
  • Journal Title: Chem. Phys. 327 Pages: 77-84
• [Journal Article] Quantum Size Effect of Finite-Length Carbon Nanotubes (2006)
  • Author(s): T.Yumura et al.
  • Journal Title: Roy. Soc. Chem. Annu. Rep. Prog. Chem. Sect. C 102 Pages: 71-91
• [Journal Article] DFT Calculations of the Cubane-Type Mo_2Ru_2S_4 Clusters. Stability of the Possible Dinitrogen Cluster and the Isolable Acetonitrile Cluster (2006)
  • Author(s): K.Yoshizawa et al.
  • Journal Title: Bull. Chem. Soc. Jpn 79 Pages: 53-58
  • NAID: 10017169883
• [Presentation] QM/MM Study of Tyrosinase : Structure and Catalytic Mechanism (2009)
  • Organizer: International Symposium of Chemistry of Reductases II
  • Place of Presentation: Nagoya University, Japan
• [Presentation] 量子輸送現象における軌道理論 (2009)
  • Organizer: 大学間連携事業シンポジウム
  • Place of Presentation: 名古屋大学
• [Presentation] 量子化学計算による酵素化学反応へのアプローチ (2008)
  • Organizer: 九州大学情報基盤センターセミナー
  • Place of Presentation: 福岡
  • Year and Date: 2008-04-25
• [Presentation] Quantum Chemical Approach to Bioinorganic Chemistry : Structure-Reactivity Relationship in Enzymatic Reactions (2008)
  • Organizer: The 2nd International Symposium on "Molecular Theory for Real Systems"
  • Place of Presentation: Okazaki, Japan
• [Presentation] Computational Mutation Analysis of Coenzyme B_<12>-Dependent Diol Dehydratase (2008)
  • Organizer: The Eighth Triennial Congress of the World Association of Theoretical and Computational Chemists (WATOC 2008)
  • Place of Presentation: Sydney, Australia
• [Presentation] 量子輸送現象における軌道理論 (2008)
  • Organizer: 分子科学討論会
  • Place of Presentation: 福岡
• [Presentation] QM/MM Study of the Catalytic Mechanism of Tyrosinase (2008)
  • Organizer: The Fourth Asian Biological Inorganic Chemistry Conference (AsBIC IV)
  • Place of Presentation: Jeju, Korea
• [Presentation] Quantum Chemical Study on the Biological Conversion of Tyrosine to Dopaquinone (2008)
  • Organizer: The IUMRS International Conference in Asia 2008
  • Place of Presentation: Nagoya, Japan
• [Presentation] Computational approach to catalytic mechanism for alkane hydroxylation by metalloenzymes (2007)
  • Author(s): K.Yoshizawa
  • Organizer: The 13th International Conference on Biological Inorganic Chemistry(ICBICI3)
  • Place of Presentation: ウィーン、オーストリア
• [Presentation] Methane hydroxylation by transition-metal oxides and metalloenzymes (2007)
  • Author(s): K.Yoshizawa
  • Organizer: The Third Asisn Pacific Conference on Theoretical & Computational Chemistry(APCTC3)
  • Place of Presentation: 北京、中国
• [Book] Methane Hydroxylation by First Row Transition Metal Oxides, Computational Modeling of Principles and Mechanisms of Transition Metal-Based Homogeneous Catalytic Processes(Morokuma, K. ; Musaev, D. G. Ed.;) (2008)
  • Author(s): Yoshizawa, K.
  • Publisher: Wiley-VCH
• [Book] Yoshizawa, K. Methane Hydroxylation by First Row Transition Metal Oxides Morokuma, K.; Musaev, D.G.Ed.;Computational Modeling of Principles and Mechanisms of Transition Metal-Based Homogeneous Catalytic Processes; (2007)
  • Author(s): K.Yoshizawa
  • Total Pages: 18
  • Publisher: Wiley-VCH
• [Book] 分子の物理化学 (2006)
  • Author(s): 吉澤一成
  • Total Pages: 191
  • Publisher: 朝倉書店
• [Remarks]
  • URL: http://trout.scc.kyushu-u.ac.jp/yoshizawaJ/index.html
• [Remarks]
  • URL: http://trout.scc.kyushu-u.ac.jp/yoshizawaJ/index.htm