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Mechanistic Insights into metal- and enzyme-catalyzed reactions using hybrid quantum chemical and information science approaches

Research Project

Project/Area Number 21K05016
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 33010:Structural organic chemistry and physical organic chemistry-related
Research InstitutionIbaraki University

Principal Investigator

MORI SEIJI  茨城大学, 理工学研究科(理学野), 教授 (50332549)

Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2023: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2022: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2021: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Keywords触媒反応 / 酵素反応 / 密度汎関数計算 / 非共有結合性相互作用 / QM/MM法 / 反応機構 / 密度汎関数法計算 / 非共有結合相互作用 / 酵素 / MDシミュレーション / 選択性 / 量子化学計算 / 分子動力学シミュレーション / ビックデータサイエンス / クラスタリング
Outline of Research at the Start

本研究では、高精度量子化学計算と情報科学的解析を融合させることで、金属を用いた均一的触媒反応および酵素反応機構の非共有結合性相互作用、添加物の効果、立体配座によるエネルギー分布をはじめとした統計力学的効果および動力学効果の役割を明確にすることを目的とする。量子化学計算およびクラスタリングに基づいたバナジウム触媒による不斉トリフルオロメチル化を含む酸化的カップリング反応、ヒドロキシステロイドデヒドロゲナーゼ触媒によるステロイド類の還元反応の検討を通じて明らかにする。

Outline of Final Research Achievements

In this study, we aim to clarify the roles of non-covalent interactions, effects of additives, and energy distributions due to stereoconformations, as well as statistical mechanical effects and kinetic effects in homogeneous metal-catalyzed reactions that are important in synthetic chemistry, and in enzyme reaction mechanisms that are also medically significant, by integrating high-precision quantum chemical calculations with informatics analysis. As achievements over the entire period, we have (1) conducted DFT calculations on various chemically-selective or stereoselective molecular transformation reactions using metal catalysts, reported the elucidation of mechanisms and prediction of rate-determining steps in various scientific papers, and (2) examined the chemical properties of various enzymes, understanding the importance of stereoconformations while combining multiphysics methods with informatics techniques.

Academic Significance and Societal Importance of the Research Achievements

以上行った研究は、医薬の設計や高効率的・選択的反応設計に役立つであろうと考えられる。さらに、マルチフィジックス的手法や情報科学的解析方法を駆使していることから、これらの改良・開発にも指針を与えると期待される。

Report

(4 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • Research Products

    (52 results)

All 2024 2023 2022 2021 Other

All Int'l Joint Research (8 results) Journal Article (17 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 17 results,  Open Access: 3 results) Presentation (21 results) (of which Int'l Joint Research: 4 results,  Invited: 4 results) Remarks (5 results) Funded Workshop (1 results)

  • [Int'l Joint Research] ベトナム国家大学自然科学大学 ハノイ校(ベトナム)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] チェンマイ大学(タイ)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] 台湾・清華大学(その他の国・地域)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] ベトナム国家大学自然科学大学ハノイ校(ベトナム)

    • Related Report
      2022 Research-status Report
  • [Int'l Joint Research] チェンマイ大学(タイ)

    • Related Report
      2022 Research-status Report
  • [Int'l Joint Research] チェンマイ大学/BIOTEC(タイ)

    • Related Report
      2021 Research-status Report
  • [Int'l Joint Research] 台湾・国立精華大学/Fu Jen Catholic University(その他の国・地域)

    • Related Report
      2021 Research-status Report
  • [Int'l Joint Research] ANSTO(オーストラリア)

    • Related Report
      2021 Research-status Report
  • [Journal Article] Asymmetric cyclization catalyzed by a chiral phosphoric acid-gold(I) hybrid complex as a multifunctional catalyst2024

    • Author(s)
      Taniguchi Naoya、Ueda Mitsuhiro、Michigami Kenichi、Mori Seiji、Ohashi Masato
    • Journal Title

      Bulletin of the Chemical Society of Japan

      Volume: 97 Issue: 3

    • DOI

      10.1093/bulcsj/uoae026

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Incorporation of a bromine atom into DNA-related molecules changes their electronic properties2023

    • Author(s)
      Hirato Misaki、Yokoya Akinari、Baba Yuji、Mori Seiji、Fujii Kentaro、Wada Shin-ichi、Izumi Yudai、Haga Yoshinori
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 25 Issue: 21 Pages: 14836-14847

    • DOI

      10.1039/d3cp01597a

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Systematic elucidation of the second coordination sphere effect on the structure and properties of a blue copper protein, pseudoazurin2023

    • Author(s)
      Yamaguchi Takahide、Taborosi Attila、Sakai Chihiro、Akao Kohei、Mori Seiji、Kohzuma Takamitsu
    • Journal Title

      Journal of Inorganic Biochemistry

      Volume: 246 Pages: 112292-112292

    • DOI

      10.1016/j.jinorgbio.2023.112292

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical Investigations of Palladium‐Catalyzed [3+2] Annulation via Benzylic and <i>meta</i> C?H Bond Activation2023

    • Author(s)
      Yoshimoto Rie、Taborosi Attila、He Qiyuan、Ano Yusuke、Chatani Naoto、Mori Seiji
    • Journal Title

      Chemistry - An Asian Journal

      Volume: 18 Issue: 18

    • DOI

      10.1002/asia.202300531

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Asymmetric Cross Couplings of Trifluoromethyl Radical to Vinylarenes with <i>N</i>‐Hydroxy‐oxazinediones and Subsequent Aerobic Oxidative Homocoupling of 2‐Naphthols Catalysed by Chiral Vanadyl Complexes2023

    • Author(s)
      Chen Chien‐Tien、Hung Shiang‐Fu、Tsai Bang‐You、Chen Tsung‐Cheng、Lein Chien‐I、Tseng Pin‐Xuan、Chang Yu‐Chang、Chuang Chin‐Wei、Agarwal Rachit、Hsu Chan‐Wei、Shimizu Yuto、Fujii Ryoma、Mori Seiji
    • Journal Title

      Advanced Synthesis &amp; Catalysis

      Volume: 366 Issue: 2 Pages: 248-261

    • DOI

      10.1002/adsc.202300901

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Neutron crystallography and quantum chemical analysis of bilin reductase PcyA mutants reveal substrate and catalytic residue protonation states2023

    • Author(s)
      Joutsuka Tatsuya、Nanasawa Ryota、Igarashi Keisuke、Horie Kazuki、Sugishima Masakazu、Hagiwara Yoshinori、Wada Kei、Fukuyama Keiichi、Yano Naomine、Mori Seiji、Ostermann Andreas、Kusaka Katsuhiro、Unno Masaki
    • Journal Title

      Journal of Biological Chemistry

      Volume: 299 Issue: 1 Pages: 102763-102763

    • DOI

      10.1016/j.jbc.2022.102763

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Experimental and theoretical studies of the rhodium(I)-catalysed C-H oxidative alkenylation/cyclization of N-(2-(methylthio)phenyl)benzamides with maleimides2023

    • Author(s)
      Skhiri Aymen、Taborosi Attila、Ohara Nozomi、Ano Yusuke、Mori Seiji、Chatani Naoto
    • Journal Title

      Organic Chemistry Frontiers

      Volume: 10 Issue: 7 Pages: 1617-1625

    • DOI

      10.1039/d3qo00023k

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Non-innocent redox behavior of CuII-pi-dimethylaminophenolate complexes: formation and characterization of the CuI-phenoxyl radical species2022

    • Author(s)
      Shima Yuto、Suzuki Takashi、Abe Hitoshi、Yajima Tatsuo、Mori Seiji、Shimazaki Yuichi
    • Journal Title

      Chemical Communications

      Volume: 58 Issue: 44 Pages: 6401-6404

    • DOI

      10.1039/d2cc01409b

    • Related Report
      2022 Research-status Report
    • Peer Reviewed
  • [Journal Article] Iridium(III)-Catalyzed Asymmetric Site-Selective Carbene C-H Insertion during Late-Stage Transformation2022

    • Author(s)
      Yamakawa Yuki、Ikuta Takashi、Hayashi Hiroki、Hashimoto Keigo、Fujii Ryoma、Kawashima Kyohei、Mori Seiji、Uchida Tatsuya、Katsuki Tsutomu
    • Journal Title

      The Journal of Organic Chemistry

      Volume: 87 Issue: 10 Pages: 6769-6780

    • DOI

      10.1021/acs.joc.2c00470

    • Related Report
      2022 Research-status Report
    • Peer Reviewed
  • [Journal Article] Integrated Experimental and Computational Studies on the Organocatalytic Kinetic Resolution of β-Unfunctionalized Primary Alcohols Using a Chiral 1,2-Diamine: The Importance of Noncovalent Interactions2022

    • Author(s)
      Sakai Naoki、Ojima Kohei、Mori Seiji、Oriyama Takeshi
    • Journal Title

      The Journal of Organic Chemistry

      Volume: 87 Issue: 6 Pages: 4468-4475

    • DOI

      10.1021/acs.joc.1c03033

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] Reaction Path Determination of Rhodium(I)-Catalyzed C-H Alkylation of N-8-Aminoquinolinyl Aromatic Amides with Maleimides2021

    • Author(s)
      Taborosi Attila、He Qiyuan、Ano Yusuke、Chatani Naoto、Mori Seiji
    • Journal Title

      The Journal of Organic Chemistry

      Volume: 87 Issue: 1 Pages: 737-743

    • DOI

      10.1021/acs.joc.1c02737

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] Solid State Characterization of One‐ and Two‐Electron Oxidized CuII‐salen Complexes with para‐Substituents: Geometric Structure‐Magnetic Property Relationship2021

    • Author(s)
      Takeyama Tomoyuki、Suzuki Takashi、Kikuchi Misa、Kobayashi Misato、Oshita Hiromi、Kawashima Kyohei、Mori Seiji、Abe Hitoshi、Hoshino Norihisa、Iwatsuki Satoshi、Shimazaki Yuichi
    • Journal Title

      European Journal of Inorganic Chemistry

      Volume: 2021 Issue: 39 Pages: 4133-4145

    • DOI

      10.1002/ejic.202100776

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] H/D Isotope Effects in Keto-Enol Tautomerism of β-Dicarbonyl Compounds: Importance of Nuclear Quantum Effects of Hydrogen Nuclei2021

    • Author(s)
      Udagawa Taro、Murphy Rhys B.、Darwish Tamim A.、Tachikawa Masanori、Mori Seiji
    • Journal Title

      Bulletin of the Chemical Society of Japan

      Volume: 94 Issue: 7 Pages: 1954-1962

    • DOI

      10.1246/bcsj.20210083

    • NAID

      130008076866

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Calculation of CYP450 protein-ligand binding and dissociation free energy paths2021

    • Author(s)
      Su Kuan-Hsuan、Wu Chin-Teng、Lin Shang-Wei、Mori Seiji、Liu Wei-Min、Yang Hsiao-Ching
    • Journal Title

      The Journal of Chemical Physics

      Volume: 155 Issue: 2 Pages: 025101-025101

    • DOI

      10.1063/5.0046169

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Combined Computational and Experimental Studies on the Asymmetric Michael Addition of α-Aminomaleimides to β-Nitrostyrenes Using an Organocatalyst Derived from Cinchona Alkaloid2021

    • Author(s)
      Sakai Naoki、Kawashima Kyohei、Kajitani Masashi、Mori Seiji、Oriyama Takeshi
    • Journal Title

      Organic Letters

      Volume: 23 Issue: 15 Pages: 5714-5718

    • DOI

      10.1021/acs.orglett.1c01831

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] Enantioselective Radical Type, 1,2-Oxytrifluoromethylation of Olefins Catalyzed by Chiral Vanadyl Complexes: Importance of Noncovalent Interactions2021

    • Author(s)
      Chen Chien-Tien、Su Yu-Cheng、Lu Chia-Hao、Lien Chien-I、Hung Shiang-Fu、Hsu Chan-Wei、Agarwal Rachit、Modala Ramuasagar、Tseng Hung-Min、Tseng Pin-Xuan、Fujii Ryoma、Kawashima Kyohei、Mori Seiji
    • Journal Title

      ACS Catalysis

      Volume: 11 Issue: 12 Pages: 7160-7175

    • DOI

      10.1021/acscatal.1c01813

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Combined MD and QM/MM Investigations of Hydride Reduction of 5α-Dihydrotestosterone Catalyzed by Human 3α-Hydroxysteroid Dehydrogenase Type 3:Importance of Noncovalent Interactions2021

    • Author(s)
      Hiroaki Mitsuizumi, Seiji Mori
    • Journal Title

      Journal of Physical Chemistry B

      Volume: - Issue: 19 Pages: 4998-5008

    • DOI

      10.1021/acs.jpcb.1c01751

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Presentation] Importance of noncovalent interactions in homogeneous and enzymatic catalysis2024

    • Author(s)
      Seiji Mori
    • Organizer
      PACCON 2024
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Evaluation of the effects of mutations in Cp*Rh(III) complex-linked artificial metalloenzyme NitrobindinHLH-Cp*Rh(III) by MD simulation2023

    • Author(s)
      Mitsuhiro Bandai, Shunsuke Kato, Akira Onoda, Takashi Hayashi, Seiji Mori
    • Organizer
      The 5th conference of Theory and Applications of Computational Chemistry (TACC) Sapporo
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] パラジウム触媒による[3+2]環化付加反応の反応経路及び配向基効果に関する理論的研究2023

    • Author(s)
      吉元 理江、Attila Taborosi、Qiyuan He、阿野 勇介、茶谷 直人、森 聖治
    • Organizer
      第25回理論化学討論会(横浜)
    • Related Report
      2023 Annual Research Report
  • [Presentation] MDシミュレーションを用いたCp*Rh(III)錯体連結型人工金属酵素NitrobindinHLH-Cp*Rh(III)における変異の影響の評価2023

    • Author(s)
      萬代 充裕、加藤 俊介、小野田 晃、林 高史、森 聖治
    • Organizer
      錯体化学会第73回討論会
    • Related Report
      2023 Annual Research Report
  • [Presentation] モリブデン-ゲルミリン錯体による芳香族アルデヒドのヒドロホウ素化反応に関する理論的研究2023

    • Author(s)
      清水雄仁、Christof Israel Marbella Fontanilla, 長田 浩一、橋本久子、森 聖治
    • Organizer
      錯体化学会第73回討論会
    • Related Report
      2023 Annual Research Report
  • [Presentation] キラルリン酸-Au(I)複合錯体を用いた触媒的インドール縮環型七員環形成反応の不斉発現機構の解明2023

    • Author(s)
      谷口 直哉・植田 光洋・道上 健一・森 聖治・大橋 理人
    • Organizer
      錯体化学会第73回討論会
    • Related Report
      2023 Annual Research Report
  • [Presentation] キラルリン酸-Au(I)複合錯体触媒を用いたエナンチオ選択的環化反応の開発2023

    • Author(s)
      谷口 直哉・植田 光洋・道上 健一・森 聖治・大橋 理人
    • Organizer
      第49回反応と合成の進歩シンポジウム
    • Related Report
      2023 Annual Research Report
  • [Presentation] Computational Perspectives of Non-covalent Interactions in Transition Metal- and Enzyme-catalyzed Reactions2023

    • Author(s)
      Seiji Mori
    • Organizer
      TCS-2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] モリブデン-ゲルミリン錯体によるカルボニル化合物のヒドロホウ素化反応の理論的研究2023

    • Author(s)
      清水 雄仁、Christof Israel Marbella Fontanilla、長田浩一、橋本 久子、森 聖治
    • Organizer
      日本化学会第103春季年会(2023)
    • Related Report
      2022 Research-status Report
  • [Presentation] Combined DFT and experimental studies on the importance of noncovalent interactions in vanadium-catalyzed oxidative trifluoromethylation reactions of olefins2022

    • Author(s)
      Seiji Mori、Chien-Tien Chen
    • Organizer
      WATOC 2020
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] パラジウム触媒を用いたマレイミドの[3+2]環化付加反応における 2-メチルベンズアミド類の窒素上の配向基効果に関する理論的研究2022

    • Author(s)
      吉元 理江、Attila Taborosi、Qiyuan He、阿野 勇介、茶谷 直人、森 聖治
    • Organizer
      化学反応経路探索のニューフロンティア2022
    • Related Report
      2022 Research-status Report
  • [Presentation] キラルなバナジル触媒によるオレフィンのエナンチオ選択的 1,2-オキシトリフルオロメチル化反応における遷移状態の相互作用エネルギー分割解析2022

    • Author(s)
      清水雄仁、Chien-Tien Chen、森 聖治
    • Organizer
      化学反応経路探索のニューフロンティア2022
    • Related Report
      2022 Research-status Report
  • [Presentation] ニッケル触媒による脱カルボニル化を含む塩化アシルのシアノ化反応に関する理論的研究2022

    • Author(s)
      穂積 玲於、川島 恭平、西原 康師、森 聖治
    • Organizer
      錯体化学会第72回討論会
    • Related Report
      2022 Research-status Report
  • [Presentation] パラジウム触媒による[3+2]環化付加反応を含むベンジル及びメタ炭素-水素結合活性化反応に関する理論的研究2022

    • Author(s)
      吉元 理江、Attila Taborosi、Qiyuan He、阿野 勇介、茶谷 直人、森 聖治
    • Organizer
      錯体化学会第72回討論会
    • Related Report
      2022 Research-status Report
  • [Presentation] パラジウム触媒を用いた四置換ビニルシランの檜山カップリングに関する理論的研究2022

    • Author(s)
      大塚 悠斗、西原 康師、森 聖治
    • Organizer
      日本コンピュータ化学会2022年秋季年会in 長野
    • Related Report
      2022 Research-status Report
  • [Presentation] キラル1,2-ジアミン触媒を用いるβ位に官能基を有さない第一級アルコールの速度論的光学分割2022

    • Author(s)
      酒井 直樹、小島 嵩平、森 聖治、折山 剛
    • Organizer
      日本化学会 第102春季年会 (2022)
    • Related Report
      2021 Research-status Report
  • [Presentation] パラジウム触媒によるAlkenyl Carboxylatesのクロスカップリング反応の理論的研究2022

    • Author(s)
      岡本 優悟,森 聖治
    • Organizer
      日本化学会 第102春季年会 (2022)
    • Related Report
      2021 Research-status Report
  • [Presentation] キラルなバナジウム触媒を用いた酸化的1,2-トリフルオロメチル化反応の理論的研究2022

    • Author(s)
      藤井 稜馬, Bang-You Tsai, Tsung-Cheng Chen, Chien-I Lein, Yu-Chang Chang, Pin-Xuan Tseng, Chin-Wei Chuang, Rachit Agarwal, Chan-Wei Hsu, Chien-Tien Chen, 森 聖治
    • Organizer
      日本化学会 第102春季年会 (2022)
    • Related Report
      2021 Research-status Report
  • [Presentation] Theoretical Investigations of Palladium-Catalyzed Cross-Coupling of Alkenyl Carboxylates2021

    • Author(s)
      岡本 優悟,森 聖治
    • Organizer
      日本コンピュータ化学会2021秋季年会
    • Related Report
      2021 Research-status Report
  • [Presentation] Theoretical study on the asymmetric Michael addition of α-aminomaleimides to β-nitrostyrenes2021

    • Author(s)
      酒井直樹,森聖治,折山剛,川島恭平
    • Organizer
      令和3年度化学系学協会東北大会
    • Related Report
      2021 Research-status Report
  • [Presentation] Computational Perspectives of Non-covalent Interactions in Transition Metal- and Enzyme-catalyzed Reactions2021

    • Author(s)
      森 聖治
    • Organizer
      錯体化学会第71回討論会
    • Related Report
      2021 Research-status Report
    • Invited
  • [Remarks] 物理有機化学研究室(森研究室)ホームページ

    • URL

      http://smori.sci.ibaraki.ac.jp/

    • Related Report
      2023 Annual Research Report
  • [Remarks] 物理有機化学ホームページ

    • URL

      http://smori.sci.ibaraki.ac.jp/

    • Related Report
      2022 Research-status Report 2021 Research-status Report
  • [Remarks] 太陽光エネルギーの吸収が水素原子1つで変わる! (プレスリリース)

    • URL

      https://www.ibaraki.ac.jp/news/2022/12/21011834.html

    • Related Report
      2022 Research-status Report
  • [Remarks] β位に官能基を有さない第一級アルコールの速度論的光学分割法の開発に成功

    • URL

      https://www.ibaraki.ac.jp/news/2022/03/07011531.html

    • Related Report
      2021 Research-status Report
  • [Remarks] 前例のない4成分の非対称ラジカル1,4-オキシトリフルオロメチル化反応の開発に成功

    • URL

      https://www.ibaraki.ac.jp/news/2021/06/22011254.html

    • Related Report
      2021 Research-status Report
  • [Funded Workshop] 7th International Symposium of Quantum Beam Science at Ibaraki University2022

    • Related Report
      2022 Research-status Report

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Published: 2021-04-28   Modified: 2025-01-30  

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