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Analysis of the dynamic factors promoting the chemical reaction by combining the quantum mechanical and the molecular dynamics methods

Research Project

Project/Area Number 17K05766
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Physical chemistry
Research InstitutionKanagawa University

Principal Investigator

Matsubara Toshiaki  神奈川大学, 理学部, 教授 (60239069)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2019: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2018: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2017: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Keywords量子力学的手法 / 分子動力学法 / SN2反応 / 動的因子 / 溶媒効果 / 化学反応 / 量子力学計算 / 分子動力学計算
Outline of Final Research Achievements

We analyzed how the chemical reaction starts and how the substrate goes over the energy barrier from a dynamic point of view by combining the quantum mechanical and the molecular dynamics methods. We selected the SN2 reaction of 2-chlorobutane with OH- as a model reaction and performed the QM- and the ONIOM-MD simulations in the gas phase and the water solvent, respectively. As a result, it was found that the kinetic energy concentrates on the atoms participating in the reaction just before the reaction, and the substrate climbs up and down the energy barrier only when the velocity vector of those atoms satisfies a certain pattern. The pattern of the velocity vector changes in the water solvent due to the dynamic effects of the water solvent molecules on the substrate.

Academic Significance and Societal Importance of the Research Achievements

量子力学的手法は今や分子設計、反応設計の強力な手段となっているが、エネルギープロフィールの平衡構造や遷移状態の停留点、あるいは固有反応座標に関する情報は与えてくれるものの、ダイナミックな情報は与えてくれない。どのようにして化学反応が始まり、どのようにエネルギー障壁を越えていくのか、といった問題は非常に興味深い。化学反応が起こる瞬間に何が起こっているのかは依然未知の課題と言える。量子力学的手法を分子動力学法と組み合わせることで、本研究で得られた化学反応を推進する動的因子の知見は、今後の化学反応理論の発展への貢献が期待される。

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (15 results)

All 2020 2019 2018 2017

All Journal Article (6 results) (of which Peer Reviewed: 6 results,  Open Access: 2 results) Presentation (9 results) (of which Int'l Joint Research: 6 results,  Invited: 6 results)

  • [Journal Article] QM- and ONIOM-Molecular Dynamics Studies of the S<sub>N</sub>2 Reaction. How Does the Rare Event Take Place?2020

    • Author(s)
      T. Matsubara
    • Journal Title

      Journal of Computer Chemistry, Japan -International Edition

      Volume: 6 Issue: 0 Pages: n/a

    • DOI

      10.2477/jccjie.2019-0006

    • NAID

      130007822331

    • ISSN
      2189-048X
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Molecular Dynamics Study of the S<sub>N</sub>2 Reaction. How Does the Rare Event Take Place?2019

    • Author(s)
      松原世明
    • Journal Title

      Journal of Computer Chemistry, Japan

      Volume: 18 Issue: 3 Pages: 145-146

    • DOI

      10.2477/jccj.2019-0011

    • NAID

      130007744483

    • ISSN
      1347-1767, 1347-3824
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Highly active, homogeneous catalysis by polyoxometalate-assisted N-heterocyclic carbene gold(I) complexes for hydration of diphenylacetylene2019

    • Author(s)
      Kenji Nomiya, Yuichi Murara, Yuta Iwasaki, Hidekazu Arai, Takuya Yoshida, Noriko Chikaraishi Kasuga, Toshiaki Matsubara
    • Journal Title

      Molecular Catalysis

      Volume: 469 Pages: 144-154

    • DOI

      10.1016/j.mcat.2019.02.014

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] B≡B Triple Bond of Newly Synthesized Diboryne Can Take a Different Mechanism for the σ Bond Activation of Polar and Nonpolar Molecules. A Quantum Mechanical Study2018

    • Author(s)
      T. Matsubara, R. Yamasaki, T. Hori, M. Morikubo
    • Journal Title

      Bull. Chem. Soc. Jpn.

      Volume: 91 Issue: 12 Pages: 1683-1690

    • DOI

      10.1246/bcsj.20180190

    • NAID

      130007531089

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Polyoxometalate-Assisted, One-Pot Synthesis of A Pentakis{(triphenylphosphane)gold}ammonium(2+) Cation Containing Regular Trigonal Bipyramidal Geometries of Five Bonds to Nitrogen2018

    • Author(s)
      1) Kenji Nomiya, Kohei Endo, Yuichi Murata, Shinya Sato, Sho Shimazaki, Shogo Horie, Eri Nagashima, Yuta Yasuda, Takuya Yoshida, Satoshi, Matsunaga, and Toshiaki Matsubara
    • Journal Title

      Inorg. Chem.

      Volume: 57 Issue: 3 Pages: 1504-1516

    • DOI

      10.1021/acs.inorgchem.7b02795

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Theoretical Study of the Heterolytic σ Bond Cleavage on the Ge=O Bond of Germanone. An Insight into the Driving Force from both Electronic and Dynamical Aspects.2017

    • Author(s)
      Toshiaki Matsubara and Tomoyoshi Ito
    • Journal Title

      J. Phys. Chem. A

      Volume: 121 Issue: 8 Pages: 1768-1778

    • DOI

      10.1021/acs.jpca.6b12478

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Presentation] Insight into the Chemical Reactions from the Molecular Dynamics Simulation. How Does the Rare Event Take Place?2019

    • Author(s)
      Toshiaki Matsubara
    • Organizer
      International Symposium 50 years of Quantum Chemistry in Strasbourg
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Insight into the Chemical Reactions from the Molecular Dynamics Simulation2019

    • Author(s)
      Toshiaki Matsubara
    • Organizer
      Ninth Conference of the Asia-Pacific Association of Theoretical and Computational Chemists
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 分子動力学法によるSN2反応の理論研究ー化学反応はいかにして起こるかー2019

    • Author(s)
      松原世明
    • Organizer
      日本コンピュータ化学会2019春季年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] SN2反応の分子動力学的考察ー化学反応はいかにして起こるかー2019

    • Author(s)
      松原世明
    • Organizer
      第22回理論化学討論会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 新規に合成されたジボリンのB≡B三重結合の反応性とその反応機構の予測2018

    • Author(s)
      山崎龍河、堀智紀、森久保真菜、松原世明
    • Organizer
      第12回分子科学討論会
    • Related Report
      2018 Research-status Report
  • [Presentation] An Insight into the Driving Force of the σ Bond Cleavage on the Ge=O Bond of Germanone by the Combination of the Quantum Mechanical and Molecular Dynamics Methods2017

    • Author(s)
      Toshiaki Matsubara
    • Organizer
      3rd Intl Symp. on New and Advanced Materials and Technologies for Energy, Environment and Sustainable Development
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] An Insight into the Driving Force of the Chemical Reactions by the Combination of the Quantum Mechanical and Molecular Dynamics Methods2017

    • Author(s)
      Toshiaki Matsubara
    • Organizer
      BIT’s 1st Annual Conference of Quantum World - 2017
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Theoretical Study of the Chemical Reactions by the Combination of Quantum Mechanical and Molecular Dynamics Methods2017

    • Author(s)
      Toshiaki Matsubara
    • Organizer
      4th International Conference on Physical and Theoretical Chemistry
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] An Insight into the Mechanism of the Electron-Transfer Induced Repair of the (6-4) T-T Photoproduct of DNA by the Photolyase. A Computational Study2017

    • Author(s)
      Toshiaki Matsubara
    • Organizer
      Drug Discovery & Therapy World Congress 2017
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited

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Published: 2017-04-28   Modified: 2021-02-19  

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