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Computational Green Chemistry of Reactions in Water

Research Project

Project/Area Number 16K05675
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Physical chemistry
Research InstitutionJapan Atomic Energy Agency

Principal Investigator

Shiga Motoyuki  国立研究開発法人日本原子力研究開発機構, システム計算科学センター, 研究主幹 (40370407)

Project Period (FY) 2016-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2019: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
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: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Keywordsグリーンケミストリー / 計算化学 / 水 / 化学反応 / 第一原理計算 / 水溶液 / 反応機構 / 有機反応 / 第一原理分子動力学 / 分子動力学
Outline of Final Research Achievements

From the viewpoint of green chemistry, the use of abundant and non-toxic water has attracted attention, and reaction control technology using aqueous solutions has advanced. For better reaction design, detailed knowledge of how the reaction proceeds in an aqueous solution and the role played by water is required, but existing experimental methods have limitations. In this research, we have clarified the detailed reaction mechanism and the role played by water, targeting organic reactions in high-temperature water using computational chemistry techniques. Through this research, we have established a novel free energy calculation technique for reactions in solution using multi-scale molecular dynamics and first-principles molecular dynamics methods.

Academic Significance and Societal Importance of the Research Achievements

この計算化学的研究によって、高温水中における有機反応の詳細な反応機構と、水の果たす役割への理解が飛躍的に進んだ。特に、温度や酸性度など、様々な実験条件において反応速度が変化する原因を突き止めることができた。今後、計算結果から高温水中における新たな有機合成ルートを探査、予測し、実験で実証可能なものを導き出す可能性に繋がった。また、溶液反応自由エネルギー計算技術は、高温水のみならず、幅広い応用が期待できる。

Report

(5 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (55 results)

All 2020 2019 2018 2017 2016 Other

All Int'l Joint Research (8 results) Journal Article (15 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 15 results,  Open Access: 3 results,  Acknowledgement Compliant: 2 results) Presentation (25 results) (of which Int'l Joint Research: 8 results,  Invited: 16 results) Remarks (6 results) Funded Workshop (1 results)

  • [Int'l Joint Research] バルセロナ大学(スペイン)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] ニューヨーク大学(米国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] ニューヨーク大学(米国)

    • Related Report
      2018 Research-status Report
  • [Int'l Joint Research] バルセロナ大学(スペイン)

    • Related Report
      2018 Research-status Report
  • [Int'l Joint Research] University of Barcelona(スペイン)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] New York University(米国)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] Indian Institute of Technology Kanpur(インド)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] University of Barcelona(Spain)

    • Related Report
      2016 Research-status Report
  • [Journal Article] Nuclear quantum effect for hydrogen adsorption on Pt(111)2020

    • Author(s)
      Lei Yan, Yoshiyuki Yamamoto, Motoyuki Shiga, Osamu Sugino
    • Journal Title

      Physical Review B

      Volume: 101 Issue: 16

    • DOI

      10.1103/physrevb.101.165414

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Photoabsorption Spectra of Aqueous Oxyluciferin Anions Elucidated by Explicit Quantum Solvent2019

    • Author(s)
      Noguchi Yoshifumi、Hiyama Miyabi、Shiga Motoyuki、Akiyama Hidefumi、Sugino Osamu
    • Journal Title

      Journal of Chemical Theory and Computation

      Volume: 15 Issue: 10 Pages: 5474-5482

    • DOI

      10.1021/acs.jctc.9b00392

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Unraveling anomalous isotope effect on hydrogen diffusivities in fcc metals from first principles including nuclear quantum effects2019

    • Author(s)
      Kimizuka Hajime、Ogata Shigenobu、Shiga Motoyuki
    • Journal Title

      Physical Review B

      Volume: 100 Issue: 2 Pages: 024104-024104

    • DOI

      10.1103/physrevb.100.024104

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Understanding Competition of Polyalcohol Dehydration Reactions in Hot Water2019

    • Author(s)
      Chang Yong Lik、Sasaki Takehiko、Ribas-Ari?o Jordi、Machida Masahiko、Shiga Motoyuki
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 123 Issue: 7 Pages: 1662-1671

    • DOI

      10.1021/acs.jpcb.8b11615

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Ab initio quantum mechanics/molecular mechanics method with periodic boundaries employing Ewald summation technique to electron-charge interaction: Treatment of the surface-dipole term2019

    • Author(s)
      Yukio Kawashima, Kazuya Ishimura, Motoyuki Shiga
    • Journal Title

      The Journal of Chemical Physics

      Volume: 150 Issue: 12 Pages: 124103-124103

    • DOI

      10.1063/1.5048451

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Finding Free-Energy Landmarks of Chemical Reactions2018

    • Author(s)
      Motoyuki Shiga, Mark E Tuckerman
    • Journal Title

      The journal of physical chemistry letters

      Volume: 9 Issue: 21 Pages: 6207-6214

    • DOI

      10.1021/acs.jpclett.8b01958

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Quantum Simulation Verifies the Stability of an 18‐Coordinated Actinium–Helium Complex2018

    • Author(s)
      Eiki Ozama, Sadia Adachi, Toshiyuki Takayanagi, Motoyuki Shiga
    • Journal Title

      Chemistry: A European Journal

      Volume: 24 Issue: 48 Pages: 12716-12721

    • DOI

      10.1002/chem.201802554

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Nuclear quantum effects of light and heavy water studied by all-electron first principles path integral simulations2018

    • Author(s)
      Machida Masahiko、Kato Koichiro、Shiga Motoyuki
    • Journal Title

      The Journal of Chemical Physics

      Volume: 148 Issue: 10 Pages: 102324-102324

    • DOI

      10.1063/1.5000091

    • NAID

      120006708276

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Mechanism of fast lattice diffusion of hydrogen in palladium: Interplay of quantum fluctuations and lattice strain2018

    • Author(s)
      Kimizuka Hajime、Ogata Shigenobu、Shiga Motoyuki
    • Journal Title

      Physical Review B

      Volume: 97 Issue: 1

    • DOI

      10.1103/physrevb.97.014102

    • NAID

      120006731609

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Photoexcited Ag ejection from a low-temperature He cluster: a simulation study by nonadiabatic Ehrenfest ring-polymer molecular dynamics2017

    • Author(s)
      Seki Yusuke、Takayanagi Toshiyuki、Shiga Motoyuki
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 19 Issue: 21 Pages: 13798-13806

    • DOI

      10.1039/c7cp00888k

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] The effect of dynamical fluctuations of hydration structures on the absorption spectra of oxyluciferin anions in an aqueous solution2017

    • Author(s)
      Miyabi Hiyama, Motoyuki Shiga, Nobuaki Koga, Osamu Sugino, Hidefumi Akiyama and Yoshifumi Noguchi
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 19 Issue: 15 Pages: 10028-10035

    • DOI

      10.1039/c7cp01067b

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] マルチスケール法:複雑分子系の計算科学2017

    • Author(s)
      志賀基之
    • Journal Title

      日本物理学会誌

      Volume: 72 Pages: 772-773

    • NAID

      130007431139

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] The Reaction Mechanism of Polyalcohol Dehydration in Hot Pressurized Water2016

    • Author(s)
      S. Ruiz-Barragan, J. Ribas-Arino, M. Shiga
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 18 Issue: 47 Pages: 32438-32447

    • DOI

      10.1039/c6cp05695d

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Reverse Stability of Oxyluciferin Isomers in Aqueous Solutions2016

    • Author(s)
      Yoshifumi Noguchi, Miyabi Hiyama, Motoyuki Shiga, Osamu Sugino, and Hidefumi Akiyama
    • Journal Title

      The Journal of Physics Chemistry B

      Volume: 120 Issue: 34 Pages: 8776-8783

    • DOI

      10.1021/acs.jpcb.6b04963

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Effects of temperature and isotopic substitution on electron attachment dynamics of guanine-cytosine base pair: Ring-polymer and classical molecular dynamics simulations2016

    • Author(s)
      Yusuke Minoshima, Yusuke Seki, Toshiyuki Takayanagi, Motoyuki Shiga
    • Journal Title

      Chemical Physics

      Volume: 472 Pages: 1-8

    • DOI

      10.1016/j.chemphys.2016.02.019

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Presentation] Nuclear Quantum Effects of Hydrogen in Materials2020

    • Author(s)
      Motoyuki Shiga
    • Organizer
      1st International Symposium Hydrogenomics combined with 14th International Symposium Hydrogen & Energy,
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] PIMD hands on tutorial2020

    • Author(s)
      Motoyuki Shiga
    • Organizer
      東京大学物性研究所セミナー
    • Related Report
      2019 Annual Research Report
  • [Presentation] Recent Advances in Quantum Simulations of Aqueous Solutions II2019

    • Author(s)
      Motoyuki Shiga
    • Organizer
      東京大学生産技術研究所セミナー
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Ab initio Molecular Simulations of Hydrogen Bonded Systems2019

    • Author(s)
      Motoyuki Shiga
    • Organizer
      Seminar at Department of Chemistry New York University
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 水素系の新しい第一原理計算法の開発と応用2019

    • Author(s)
      志賀基之
    • Organizer
      第2回ハイドロジェノミクス研究会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 分子シミュレーションにおけるレア・イベント解析手法2019

    • Author(s)
      志賀基之
    • Organizer
      大阪大学大学院基礎工学研究科機能創成セミナー
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Recent Advances in Quantum Simulations of Aqueous Solutions2019

    • Author(s)
      Motoyuki Shiga
    • Organizer
      原子力機構先端基礎セミナー
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Introduction to path integral simulations2019

    • Author(s)
      Motoyuki Shiga
    • Organizer
      大阪大学大学院工学研究科精密科学・応用物理学専攻セミナー
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Basics of biased sampling, umbrella sampling, WHAM, Bluemoon ensemble, quantum effects2019

    • Author(s)
      Motoyuki Shiga
    • Organizer
      Free Energy Calculations For Chemical And Biological Systems
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] 自由エネルギー面上の化学反応経路探索2018

    • Author(s)
      志賀基之
    • Organizer
      第12回分子科学討論会
    • Related Report
      2018 Research-status Report
  • [Presentation] Locating Free Energy Landmarks of Chemical Reactions2018

    • Author(s)
      Motoyuki Shiga
    • Organizer
      3rd International Symposium on Research and Education of Computational Science
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] 水素の量子効果を考慮した第一原理計算2018

    • Author(s)
      志賀基之
    • Organizer
      第15回 水素量子アトミクス研究会 / 第1回ハイドロジェノミクス研究会
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] 自由エネルギー面上における停留点の探索法2018

    • Author(s)
      志賀基之
    • Organizer
      第32回分子シミュレーション討論会
    • Related Report
      2018 Research-status Report
  • [Presentation] Finding Free Energy Landmarks of Reactions in Solution2018

    • Author(s)
      Motoyuki Shiga
    • Organizer
      IQTC seminar, University of Barcelona
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Ab initio simulations of hexanediol dehydration reaction in water2018

    • Author(s)
      Motoyuki Shiga
    • Organizer
      Indo-Japan Conference: New Insights into Multifunctional Catalysis for Biomass Transformations
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 溶液反応の計算法:ポリアルコール脱水反応を例として2018

    • Author(s)
      志賀基之
    • Organizer
      岩手大学理工学部応用化学・生命理工学科セミナー
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 並列分子シミュレーションコード PIMD の開発と応用2018

    • Author(s)
      志賀基之
    • Organizer
      NTChemワークショップ2018
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] 並列分子シミュレーションコード PIMD について2017

    • Author(s)
      志賀基之
    • Organizer
      第20回理論化学討論会
    • Related Report
      2017 Research-status Report
  • [Presentation] QM/MM molecular dynamics of open boundary systems2017

    • Author(s)
      志賀基之
    • Organizer
      北大理論化学セミナー
    • Related Report
      2017 Research-status Report
  • [Presentation] Free Energy Landmark Search For Chemical Reactions2017

    • Author(s)
      Motoyuki Shiga
    • Organizer
      Recent Advances in Modelling Rare Events 2017
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] A QM/MM method for open boundary systems II2016

    • Author(s)
      Motoyuki Shiga
    • Organizer
      Joint seminar at NYU Shanghai and China East Normal University
    • Place of Presentation
      NYU Shanghai, 中国上海市
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] A QM/MM method for open boundary systems I2016

    • Author(s)
      Motoyuki Shiga
    • Organizer
      International Conference on Molecular Simulation 2016
    • Place of Presentation
      Crown Plaza Hotel Shanghai, 中国上海市
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Exploration of rare events based on ab initio simulations2016

    • Author(s)
      Motoyuki Shiga
    • Organizer
      International Workshop on Frontiers in Molecular Biophysics
    • Place of Presentation
      NYU Shanghai, 中国上海市
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] A theoretical study of hexanediol dehydration reaction2016

    • Author(s)
      Motoyuki Shiga
    • Organizer
      32nd Symposium on Chemical Kinetics and Dynamics
    • Place of Presentation
      大宮ソニックシティ、埼玉県さいたま市
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] 高温水における多価アルコール脱水反応に関する理論的研究2016

    • Author(s)
      志賀基之
    • Organizer
      第19回理論化学討論会
    • Place of Presentation
      早稲田大学大久保キャンパス、東京都新宿区
    • Related Report
      2016 Research-status Report
  • [Remarks] 志賀基之の公式ページ

    • URL

      https://ccse2.jaea.go.jp/Simu/?%E5%BF%97%E8%B3%80+%E5%9F%BA%E4%B9%8B

    • Related Report
      2019 Annual Research Report
  • [Remarks] 分子シミュレーションコード PIMD

    • URL

      https://ccse.jaea.go.jp/ja/download/pimd/index.jp.html

    • Related Report
      2018 Research-status Report
  • [Remarks] 並列分子シミュレーションコード PIMD のホームページ(英語版)

    • URL

      https://ccse.jaea.go.jp/ja/download/pimd/index.en.html

    • Related Report
      2017 Research-status Report
  • [Remarks] 並列分子シミュレーションコード PIMD のホームページ(日本語版)

    • URL

      https://ccse.jaea.go.jp/ja/download/pimd/index.jp.html

    • Related Report
      2017 Research-status Report
  • [Remarks] 並列分子シミュレーションコード PIMD のホームページ(英語版)

    • URL

      http://ccse.jaea.go.jp/ja/download/pimd/index.en.html

    • Related Report
      2016 Research-status Report
  • [Remarks] 並列分子シミュレーションコード PIMD のホームページ(日本語版)

    • URL

      http://ccse.jaea.go.jp/ja/download/pimd/index.jp.html

    • Related Report
      2016 Research-status Report
  • [Funded Workshop] Recent Advances in Modelling Rare Events 20172017

    • Related Report
      2017 Research-status Report

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Published: 2016-04-21   Modified: 2022-02-21  

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