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Theoretical study on reactivity and dynamical structural changes of metalloproteins

Research Project

Project/Area Number 16K17856
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Physical chemistry
Research InstitutionHiroshima City University

Principal Investigator

Saito Toru  広島市立大学, 情報科学研究科, 講師 (80747494)

Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2018: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2017: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2016: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Keywords半経験的分子軌道法 / 開殻分子 / 金属酵素 / QM/MM MD / 計算化学 / 生物無機化学 / 擬縮退電子系 / 量子化学 / 分子動力学
Outline of Final Research Achievements

Further reduction of computational cost would achieve a rational design of catalysts on the basis of computational findings. To this end, we proposed a reparameterization variant of PM6 , namely rPM6, aiming at improving the accuracy for quasi-degenerate (open-shell) systems without degrading its accuracy for general-purpose applications. We showed its applicability to transition state search for C-H and C=C bond oxidation reactions. Quantitative assessments of rPM6 were also presented concerning magnetic exchange coupling constants and thermochemical properties (bond dissociation energies, barrier heights and reaction energies). Thus, it per se might be used as an initial screening method in predicting site of metabolism.

Academic Significance and Societal Importance of the Research Achievements

遷移金属を含む酵素(金属酵素)の特異な触媒反応を理解し、新物質・材料の開発に応用することは大変意義深い。計算化学は実験的手法の相補的な方法論として用いられてきたが、反応活性と動的構造変化の影響を調べるための有効な手だてがなかった。本研究では既存の半経験的分子軌道法のたパラメータセットを改善することにより、計算精度を損なわずに計算時間の大幅な短縮を実現できた。この計算は汎用プログラムGaussian, Mopacのインプットファイルを書き換えるだけで実行できる。高度なプログラミング技術を必要としないことから、理論、実験を問わず大きな波及効果が期待される。

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (32 results)

All 2019 2018 2017 2016 Other

All Journal Article (9 results) (of which Peer Reviewed: 9 results,  Open Access: 6 results,  Acknowledgement Compliant: 1 results) Presentation (18 results) (of which Int'l Joint Research: 7 results,  Invited: 4 results) Book (1 results) Remarks (4 results)

  • [Journal Article] Development of approximate spin projection method and its application for elucidation of electronic structures, molecular structures and physical properties of polynuclear metal complexes2018

    • Author(s)
      Kitagawa Yasutaka、Saito Toru、Yamaguchi Kizashi
    • Journal Title

      Bulletin of Japan Society of Coordination Chemistry

      Volume: 71 Issue: 0 Pages: 57-68

    • DOI

      10.4019/bjscc.71.57

    • NAID

      130007438867

    • ISSN
      1882-6954, 1883-1737
    • Year and Date
      2018-05-31
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Transition State Search Using rPM6: Iron- and Manganese-Catalyzed Oxidation Reactions as a Test Case2018

    • Author(s)
      Saito Toru、Takano Yu
    • Journal Title

      Bulletin of the Chemical Society of Japan

      Volume: 91 Issue: 9 Pages: 1377-1389

    • DOI

      10.1246/bcsj.20180119

    • NAID

      130007484202

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Quantitative Assessment of rPM6 for Fluorine- and Chlorine-Containing Metal Complexes: Comparison with Experimental, First-Principles, and Other Semiempirical Results2018

    • Author(s)
      *T. Saito, M. Fujiwara, Y. Takano
    • Journal Title

      Molecules

      Volume: 23 Issue: 12 Pages: 3332-3332

    • DOI

      10.3390/molecules23123332

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] UNO DMRG CAS CI calculations of binuclear manganese complex Mn(IV) 2 O 2 (NHCHCO 2 ) 4 : Scope and applicability of Heisenberg model2018

    • Author(s)
      Kawakami Takashi、Miyagawa Koichi、Sharma Sandeep、Saito Toru、Shoji Mitsuo、Yamada Satoru、Yamanaka Shusuke、Okumura Mitsutaka、Nakajima Takahito、Yamaguchi Kizashi
    • Journal Title

      Journal of Computational Chemistry

      Volume: 40 Issue: 2 Pages: 333-341

    • DOI

      10.1002/jcc.25602

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] rPM6 parameters for phosphorous and sulphur-containing open-shell molecules2018

    • Author(s)
      Toru Saito, Yu Takano
    • Journal Title

      Molecular Physics

      Volume: 116 Issue: 5-6 Pages: 602-610

    • DOI

      10.1080/00268976.2017.1377849

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] A Bis(mu‐oxido)dinickel(III) Complex with a Triplet Ground State2018

    • Author(s)
      Yuma Morimoto, Yusaku Takagi, Toru Saito, Takehiro Ohta, Takashi Ogura, Norimitsu Tohnai, Motohiro Nakano, Shinobu Itoh
    • Journal Title

      Angewandte Chemie International Edition

      Volume: 印刷中 Issue: 26 Pages: 7640-7643

    • DOI

      10.1002/anie.201802779

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] rPM6 parameters for manganese and application to transition state search for oxidation reactions of cyclohexene by manganese(IV)-oxo species2017

    • Author(s)
      *T. Saito, Y. Takano
    • Journal Title

      Chemistry Letters

      Volume: 46 Issue: 10 Pages: 1567-1569

    • DOI

      10.1246/cl.170687

    • NAID

      130006140026

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Assessment of semi-empirical molecular orbital calculations for describing magnetic interactions2017

    • Author(s)
      T. Saito, T. Kitagawa, T. Kawakami, S. Yamanaka, M. Okumura, Y. Takano
    • Journal Title

      Polyhedron

      Volume: 印刷中 Pages: 52-57

    • DOI

      10.1016/j.poly.2017.02.029

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] Reparameterization of PM6 applied to organic diradical molecules2016

    • Author(s)
      *T. Saito, Y. Kitagawa, Y. Takano
    • Journal Title

      J. Phys. Chem. A,

      Volume: 120 Issue: 43 Pages: 8750-8760

    • DOI

      10.1021/acs.jpca.6b08530

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Quantitative Assessment of Reparameterized PM6 (rPM6) for Hydrogen Atom Transfer Reactions2019

    • Author(s)
      Toru Saito, Hiroki Kambara, Yu Takano
    • Organizer
      The 59th Sanibel Symposium
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 計算化学による金属酵素と生体模倣触媒の研究2019

    • Author(s)
      齋藤徹
    • Organizer
      2018年度日本生物物理学会北海道支部例会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 半経験的分子軌道法の定量性の検証2019

    • Author(s)
      齋藤徹、鷹野優
    • Organizer
      日本化学会 第99春季年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Semiempirical Quantum Chemical Calculations on Quasi-Degenerate Systems2019

    • Author(s)
      Toru Saito
    • Organizer
      Symposium on Electronic Structure and Dynamics of Complex Systems
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Transition State Search Using rPM6 Method: Applications to Oxidation Reactions Catalyzed by Transition Metal Complexes2018

    • Author(s)
      Toru Saito, Yu Takano
    • Organizer
      The 43rd International Conference on Coordination Chemistry (ICCC2018)
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 計算化学による含フッ素医薬品の設計2018

    • Author(s)
      齋藤徹、鷹野優
    • Organizer
      フルオラス科学研究会第11回シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] Applications of rPM6 to Catalytic Oxidation Reactions2018

    • Author(s)
      Toru Saito
    • Organizer
      International Congress on Pure & Applied Chemistry Langkawi
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 半経験的分子軌道法rPM6の複核遷移金属錯体への適用2018

    • Author(s)
      齋藤徹、鷹野優
    • Organizer
      日本コンピュータ化学会2018秋季年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 半経験的分子軌道法による遷移金属錯体の計算2018

    • Author(s)
      齋藤徹、鷹野優
    • Organizer
      2018年日本化学会中国四国支部大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Applications of the Semi-empirical rPM6 Method to Chemical Reactions Catalyzed by Transition Metal Containing Complexes2018

    • Author(s)
      Toru Saito, Yu Takano
    • Organizer
      日本化学会 第98春季年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Modification of Semiempirical Molecular Orbital Theory for Computing Diradical Species2017

    • Author(s)
      Toru Saito, Yu Takano
    • Organizer
      日本化学会第97春季年会
    • Place of Presentation
      慶應義塾大学日吉キャンパス
    • Year and Date
      2017-03-16
    • Related Report
      2016 Research-status Report
  • [Presentation] Reparameterization of PM6 Applied to Through-bond and Through-space Magnetic Interactions2017

    • Author(s)
      Toru Saito, Yu Takano
    • Organizer
      The 57th Sanibel Symposium
    • Place of Presentation
      The King and Prince Beach and Golf Resort
    • Year and Date
      2017-02-20
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] 半経験的分子軌道法を用いた生体模倣金属錯体の計算2017

    • Author(s)
      齋藤徹、鷹野優
    • Organizer
      錯体化学会 第67回討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] 開殻分子系の高効率な遷移状態探索と酸化反応への適用2017

    • Author(s)
      齋藤徹、鷹野優
    • Organizer
      第50回 酸化反応討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] Reparameterization of PM6 Parameters for Manganese and Applications to Binuclear Manganese Complexes2017

    • Author(s)
      Toru Saito, Yu Takano
    • Organizer
      The 11th Triennial Congress of the World Association of Theoretical and Computational Chemists
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Development and Applications of Theoretical Method for Chemical Reactions Involving Open-shell Molecules2016

    • Author(s)
      Toru Saito, Yu Takano
    • Organizer
      2016年日本化学会中国四国支部大会香川大会
    • Place of Presentation
      香川大学
    • Year and Date
      2016-11-06
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] 開殻分子に対する半経験的分子軌道法の評価と改善2016

    • Author(s)
      齋藤徹, 北河康隆, 鷹野優
    • Organizer
      第10回分子科学討論会
    • Place of Presentation
      神戸ファッションマート
    • Year and Date
      2016-09-14
    • Related Report
      2016 Research-status Report
  • [Presentation] Assessment and Modification of Semi-empirical Molecular Orbital Theory for Describing Organic Radical Systems2016

    • Author(s)
      Toru Saito, Yasutaka Kitagawa, Takahiro Numata, Takashi Kawakami, Shusuke Yamanaka, Mitsutaka Okumura
    • Organizer
      ICMM 2016
    • Place of Presentation
      Sendai International Center
    • Year and Date
      2016-09-06
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Book] Approximate spin projection for broken-symmetry method and its application iin Symmetry (Group Theory) and Mathematical Treatment in Chemistry2018

    • Author(s)
      Yasutaka Kitagawa, Toru Saito, Kizashi Yamaguchi
    • Total Pages
      186
    • Publisher
      IntechOpen
    • ISBN
      9781789233155
    • Related Report
      2018 Annual Research Report
  • [Remarks] 広島市立大学 教員総覧

    • URL

      http://rsw.office.hiroshima-cu.ac.jp/Profiles/14/0001323/profile.html

    • Related Report
      2018 Annual Research Report
  • [Remarks] 広島市立大学大学院情報科学研究科医用情報科学専攻 バイオ情報学研究室ホームページ

    • URL

      http://www.bio.info.hiroshima-cu.ac.jp/

    • Related Report
      2018 Annual Research Report
  • [Remarks]

    • URL

      http://www.bio.info.hiroshima-cu.ac.jp/

    • Related Report
      2016 Research-status Report
  • [Remarks]

    • URL

      https://sites.google.com/site/tsaitosstartseite/home

    • Related Report
      2016 Research-status Report

URL: 

Published: 2016-04-21   Modified: 2020-03-30  

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