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Theoretical elucidation of dynamical solvent effects in controling chemical reactions

Research Project

Project/Area Number 16KT0050
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeMulti-year Fund
Section特設分野
Research Field Transition State Control
Research InstitutionShizuoka University

Principal Investigator

Kawai Shinnosuke  静岡大学, 理学部, 准教授 (90624065)

Co-Investigator(Kenkyū-buntansha) 山下 雄史  東京大学, 先端科学技術研究センター, 特任准教授 (50615622)
Project Period (FY) 2016-07-19 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥9,750,000 (Direct Cost: ¥7,500,000、Indirect Cost: ¥2,250,000)
Fiscal Year 2019: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Fiscal Year 2018: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2017: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Fiscal Year 2016: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Keywords反応動力学 / 機械学習 / エネルギー移動 / 反応性境界 / 相空間構造 / 異性化反応 / 化学物理 / 溶媒効果 / クラスター / 化学反応動力学 / 反応境界
Outline of Final Research Achievements

Phase space structures in the vicinity of transition state were investigated with the focus on the effects of surrounding molecules. As the target system, the effect of the presence of Ar on the isomerization reaction HCN->CNH was investigated. The potential energy surface function is developed based on ab initio calculations, and phase space structures in the transition state region were extracted through classical trajectory simulations. Subsequently, the reactivity, that is, whether the reaction occurs or not from a given initial condition, was learned as a function of the initial condition. The prediction accuracy was found to be greater than 95 %, indicating that the machine learning captured the features of the phase space that affect the reactivity. Subsequent analyses on the machine learning results revealed the importance of each coordinate in the initial condition.

Academic Significance and Societal Importance of the Research Achievements

化学反応は原子が動くことによって起こるものであり,特に反応途中にある遷移状態とよばれる分割面の付近での原子の動きが,反応の成否を決定するうえで重要である。本研究では,遷移状態付近の原子の動きに対する「溶媒」などの周辺分子の影響を,機械学習を通じて詳細に解析した。それによって,各原子の初期位置および初速度の中で,反応の成否を決定づけるうえで重要度の高い因子と低い因子を判別することを可能にした。この結果は,化学反応に対する基礎科学的知見を推進するとともに,将来的には多様な化学反応の制御につながっていく可能性がある。

Report

(8 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Research-status Report
  • 2020 Research-status Report
  • 2019 Research-status Report
  • 2018 Research-status Report
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (10 results)

All 2021 2020 2019 2018 2017

All Journal Article (2 results) (of which Peer Reviewed: 1 results,  Open Access: 1 results) Presentation (8 results) (of which Int'l Joint Research: 6 results,  Invited: 3 results)

  • [Journal Article] Modified AMBER force-field (FUJI) parameters for sulfated and phosphorylated tyrosine residues: Development and application to CCR5-derived peptide systems2019

    • Author(s)
      Yamashita Takefumi, Okajima Ryo, Miyanabe Kazuhiro, Tsumoto Kouhei
    • Journal Title

      AIP Conf. Proc.

      Volume: 2186 Pages: 030013-030013

    • DOI

      10.1063/1.5137924

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] 構造生物学2.0としての分子動力学シミュレーション:創薬応用への道 Molecular Dynamics Simulations as Structural Biology 2.0: Application to Drug Design2019

    • Author(s)
      山下雄史
    • Journal Title

      月刊「細胞」(The Cell)

      Volume: 51(12) Pages: 606-607

    • Related Report
      2019 Research-status Report
  • [Presentation] Dynamical boundaries for the isomerization reaction HCN ←→ CNH in the presence of a buffer molecule2021

    • Author(s)
      Shinnosuke KAWAI, and Takefumi YAMASHITA
    • Organizer
      ICCMSE 2021 (17th International Conference of Computational Methods in Sciences and Engineering),Galaxy Hotel, Heraklion, Crete, Greece
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Extraction of Essential Coordinates for Analysis of Molecular Dynamics2020

    • Author(s)
      Shinnosuke KAWAI
    • Organizer
      ICCMSE 2020 (International Conference of Computational Methods in Sciences and Engineering 2020)
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Environmental Coordinates in the Structural Dynamics of a Dipeptide2019

    • Author(s)
      Shinnosuke Kawai
    • Organizer
      35th Symposium on Chemical Kinetics and Dynamics(第35回化学反応討論会)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] ジペプチド分子の構造ダイナミクスにおける運動モード間相互作用の解析2019

    • Author(s)
      河合 信之輔
    • Organizer
      第13回分子科学討論会
    • Related Report
      2019 Research-status Report
  • [Presentation] Extraction of multi-dimensional molecular dynamics from limited observations2018

    • Author(s)
      Shinnosuke KAWAI
    • Organizer
      34th Symposium on Chemical Kinetics and Dynamics
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Essential Dynamical Coordinates to Describe Quantum Mechanical Systems2018

    • Author(s)
      Shinnosuke KAWAI
    • Organizer
      ICCMSE 2018(14TH INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Extraction of effective dynamical modes in quantum systems2018

    • Author(s)
      Shinnosuke KAWAI
    • Organizer
      日本化学会第98春季年会
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] 量子多自由度系ダイナミクスのデータ解析による隠れた運動モードの抽出2017

    • Author(s)
      河合信之輔
    • Organizer
      コンピュータ化学会2017秋季年会
    • Related Report
      2017 Research-status Report

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Published: 2016-07-20   Modified: 2024-01-30  

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