Quantum mechanical investigation of enzymatic reactions

• Project/Area Number: 24550190
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Chemistry related to living body
• Research Institution: Kyushu University
• Principal Investigator: KAMACHI Takashi 九州大学, 先導物質化学研究所, 助教 (40403951)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000); Fiscal Year 2014: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2013: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2012: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: 酵素反応 / 密度汎関数法 / 遷移状態 / QM/MM法 / シトクロムP450 / 基質特異性 / 酵素化学

Outline of Final Research Achievements

In this study, reactivity and electronic structure of active species in the active site of enzymes were investigated with the Quantum Mechanical/Molecular Mechanical (QM/MM) method. QM/MM studies on fluoroacetate dehalogenase, heme oxygenase, and diol dehydratase were published.

Research Products

• [Journal Article] Selective carbon dioxide adsorption of ε-Keggin-type zincomolybdate-based purely-inorganic 3D frameworks (2015)
  • Author(s): Zhenxin Zhang, Masahiro Sadakane, Shin-ichiro Noro, Toru Murayama, Takashi Kamachi, Kazunari Yoshizawa, and Wataru Ueda
  • Journal Title: Journal of Materials Chemistry A Volume: 3 Issue: 2 Pages: 746-755
  • DOI: 10.1039/c4ta05496b
  • Peer Reviewed / Open Access
• [Journal Article] Enantioselective Alkylation by Binaphthyl Chiral Phase-Transfer Catalysts: A DFT-Based Conformational Analysis (2014)
  • Author(s): T. Kamachi and K. Yoshizawa
  • Journal Title: Org. Lett. Volume: 16 (2) Issue: 2 Pages: 472-475
  • DOI: 10.1021/ol4033545
  • Peer Reviewed
• [Journal Article] Computational Mutation Design of Diol Dehydratase: Catalytic Ability toward Glycerol beyond the Wild-Type Enzyme (2014)
  • Author(s): Doitomi, K.; Tanaka, H.; Kamachi, T.; Toraya, T.; Yoshizawa, K.
  • Journal Title: Bulletin of the Chemical Society of Japan Volume: 87 Issue: 9 Pages: 950-959
  • DOI: 10.1246/bcsj.20140115
  • NAID: 130004153315
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Molecular Motor-driven Abrupt Anisotropic Shape Change in a Single Crystal of a Ni Complex (2014)
  • Author(s): Z.-S. Yao, M. Mito, T. Kamachi, Y. Shiota, K. Yoshizawa, N. Azuma, Y. Miyazaki, K. Takahashi, K. Zhang, T. Nakanishi, S. Kang, S. Kanegawa, O. Sato
  • Journal Title: Nature Chem. Volume: 6 Issue: 12 Pages: 1079-1083
  • DOI: 10.1038/nchem.2092
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Oxidation of Silanes to Silanols on Pd Nanoparticles: H2 Desorption Accelerated by Surface Oxygen Atom (2013)
  • Author(s): T. Kamachi, K. Shimizu, D. Yoshihiro, K. Igawa, K. Tomooka, and K. Yoshizawa
  • Journal Title: J. Phys. Chem. C Volume: 117 Issue: 44 Pages: 22967-22973
  • DOI: 10.1021/jp408269s
  • Peer Reviewed
• [Journal Article] Initial Step of B12-Dependent Enzymatic Catalysis: Energetic Implications Regarding Involvement of One-electron Reduced Form of Adenosylcobalamin Cofactor (2012)
  • Author(s): P. M. Kozlowski et al
  • Journal Title: J. Biol. Inorg. Chem. Volume: 17 Issue: 2 Pages: 293-300
  • DOI: 10.1007/s00775-011-0850-3
  • Peer Reviewed
• [Journal Article] Naphthalene and Anthracene Complexes Sandwiched by Two Cp*FeI Fragments: Strong Electronic Coupling Between the FeI Centers (2012)
  • Author(s): T. Hatanaka et al
  • Journal Title: Chem. Asian J. Volume: 7 Issue: 6 Pages: 1231-1242
  • DOI: 10.1002/asia.201101037
  • Peer Reviewed
• [Journal Article] Substrate Specificity of Fluoroacetate Dehalogenase: An Insight from Crystallographic Analysis, Fluorescence Spectroscopy, and Theoretical Computations (2012)
  • Author(s): T. Nakayama et al
  • Journal Title: Chem. Eur. J. Volume: 18 Issue: 27 Pages: 8392-8402
  • DOI: 10.1002/chem.201103369
  • Peer Reviewed
• [Journal Article] Quantum mechanical/molecular mechanical study of a mechanism for heme oxidation by heme oxygenase (2012)
  • Author(s): T. Kamachi et al
  • Journal Title: Dalton Trans. Volume: 41 Issue: 38 Pages: 11642-11650
  • DOI: 10.1039/c2dt30777d
  • Peer Reviewed
• [Journal Article] Mechanism of Glycerol Dehydration by Diol Dehydratase from Combined QM/MM Calculations (2012)
  • Author(s): K. Doitomi, et al.
  • Journal Title: Biochemistry Volume: 51 Issue: 45 Pages: 9202-9210
  • DOI: 10.1021/bi300488u
  • Peer Reviewed
• [Journal Article] Surface Oxygen Atom as Cooperative Ligand in Pd Nanoparticles Catalysis for Selective Hydration of Nitriles to Amides in Water: Experimental and Theoretical Studies (2012)
  • Author(s): K. Shimizu et al
  • Journal Title: ACS Catalysis Volume: 2 Issue: 12 Pages: 2467-2474
  • DOI: 10.1021/cs3006154
  • Peer Reviewed
• [Journal Article] Hydrolytic Enantioselective Protonation of Dienyl Esters and a Racemic β-Diketone with Chiral Phase-Transfer Catalysts (2012)
  • Author(s): E. Yamamoto et al
  • Journal Title: Org. Lett. Volume: 14 Issue: 24 Pages: 6178-6181
  • DOI: 10.1021/ol3027363
  • Peer Reviewed
• [Presentation] アントラキノン法の水素化過程に関する理論的研究 (2015)
  • Author(s): 蒲池高志、緒方龍展、森英一郎、井浦克弘、奥田典和、長田昌輝、吉澤一成
  • Organizer: 日本化学会第95春季年会
  • Place of Presentation: 船橋
  • Year and Date: 2015-03-26 – 2015-03-29
• [Presentation] ビナフチル骨格をもつNスピロ型キラル相間移動触媒による不斉アルキル化反応に関する研究：密度汎関数法に基づいた配座解析 (2014)
  • Author(s): 蒲池 高志、吉澤 一成
  • Organizer: 分子科学討論会2014
  • Place of Presentation: 東広島
  • Year and Date: 2014-09-21 – 2014-09-24
• [Presentation] Quantum Mechanical/Molecular Mechanical (QM/MM)法による酵素反応解析 (2014)
  • Author(s): 蒲池高志
  • Organizer: 徳島大学 特別講演会 創薬分野への若手理論計算化学研究者のチャレンジ
  • Place of Presentation: 徳島
  • Year and Date: 2014-07-28
  • Invited
• [Presentation] Toward Rational Design of Organocataysts: DFT-Based Conformation Analysis (2014)
  • Author(s): Takashi Kamachi, Kazunari Yoshizawa
  • Organizer: ICOMC 2014 Pre-symposium in Kyoto
  • Place of Presentation: Kyoto
  • Year and Date: 2014-07-10 – 2014-07-11
  • Invited
• [Presentation] In silico design of fine-tuned phase transfer catalyst: DFT-based conformation search (2014)
  • Author(s): Takashi Kamachi, Kazunari Yoshizawa
  • Organizer: 5th French-Japanese Workshop on Computational Methods in Chemistry
  • Place of Presentation: Strasbourg
  • Year and Date: 2014-06-30 – 2014-07-01
• [Presentation] ビナフチル骨格をもつNスピロ型キラル相間移動触媒による不斉アルキル化反応に関する理論的解析 (2014)
  • Author(s): 蒲池 高志、吉澤一成
  • Organizer: 日本化学会第94春季年会
  • Place of Presentation: 名古屋
• [Presentation] 表面を酸素修飾したPd/Cによるシランの酸化反応に関する理論的研究 (2013)
  • Author(s): 蒲池 高志、清水研一、久保 隆寛、薩摩 篤、吉澤 一成
  • Organizer: 第112回触媒討論会
  • Place of Presentation: 秋田
• [Presentation] DFT計算によるPd表面上の酸素原子の触媒機能解明 (2013)
  • Author(s): 蒲池 高志、清水研一、井川和宣、友岡克彦、吉澤 一成
  • Organizer: 分子科学討論会2013
  • Place of Presentation: 京都
• [Presentation] ヘムオキシゲナーゼによるヘムの代謝機構に関するQM/MM計算 (2013)
  • Author(s): 蒲池 高志、西見智徳、吉澤一成
  • Organizer: 日本化学会第93春季年会
  • Place of Presentation: 草津
• [Presentation] Water-Assisted Oxo Mechanism for Heme Oxidation by Heme Oxygenase (2012)
  • Author(s): Takashi Kamachi, Tomonori Nishimi, Kazunari Yoshizawa
  • Organizer: AsBIC-VI
  • Place of Presentation: 香港
• [Presentation] ヘムオキシゲナーゼによるヘムの代謝機構に関する理論的研究 (2012)
  • Author(s): 蒲池 高志、西見智徳、吉澤一成
  • Organizer: 分子科学討論会2012
  • Place of Presentation: 東京
• [Presentation] フルオロ酢酸デハロゲナーゼによるC-F結合活性化機構に関する理論的研究 (2012)
  • Author(s): 蒲池 高志、中山智則、実森啓二、栗原達夫、江崎信芳、吉澤一成
  • Organizer: 第110回触媒討論会
  • Place of Presentation: 福岡