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Elucidation of the complete reaction pathways of the water decomposition reactions in the oxygen-evolving complex of photosystem II

Research Project

Project/Area Number 17H04866
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypeSingle-year Grants
Research Field Physical chemistry
Research InstitutionUniversity of Tsukuba

Principal Investigator

Shoji Mitsuo  筑波大学, 計算科学研究センター, 助教 (00593550)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥25,870,000 (Direct Cost: ¥19,900,000、Indirect Cost: ¥5,970,000)
Fiscal Year 2019: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2018: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2017: ¥21,710,000 (Direct Cost: ¥16,700,000、Indirect Cost: ¥5,010,000)
KeywordsQM/MM / 反応機構 / 光化学系II / 水分解 / 酸素発生 / Mnクラスター / 反応経路探索 / 自由エネルギー / 反応経路 / コンフォメーション / O-O結合形成 / 水分解反応 / 光合成 / 酸素分子放出 / 水分子挿入 / 協奏反応機構 / 量子化学 / 酸素発生機構 / 酸素酸素結合 / 協奏機構
Outline of Final Research Achievements

In the natural world, the oxygen-evolving complex of photosystem II owns the water decomposition reaction for the photosynthetic light reaction. This reaction is critically important as the sustainable energy source, however, the detailed reaction mechanisms are still unclear. Especially, the S3 -> S4 ->S0 transition is most important as that contains insertion of substrate water molecule, O-O bond formation and O2 ejection. In the present study, details of the reaction steps were investigated theoretically. Not only we revealed these issues, but also for the origin of substrate water molecules, role of Ca2+ ion, novel O-O bond formation mechanism (CBS mechanism) were clarified. Furthermore, we have developed a novel automatic search algorithm for complicated enzymatic catalytic reactions. The new method, named GLAS, permits to improve the speed and accuracy of the theoretical investigations.

Academic Significance and Societal Importance of the Research Achievements

光合成の水分解反応は国際的に活発に研究がなされており、熾烈な研究競争がなされている。自然系の優れた水分解反応機構は自然科学の学理解明のためのみならず、次世代のクリーンなエネルギー開発にとって、鍵となる重要な反応である。本研究ではその核心とも言える水分解反応を一通り理論解析した。近年の時分割構造解析結果とも一致しており、先駆的理論研究となっている。これらの結果は、人工光合成の性能向上((高耐性(TON)、高速(TOF)、安価(低過電圧))の手がかりとしても極めて重要である。その為、今後は人工光合成との直接的対応関係について具体的に示していきたい。

Report

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

    (28 results)

All 2020 2019 2018 2017 Other

All Int'l Joint Research (1 results) Journal Article (6 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 6 results,  Open Access: 1 results) Presentation (16 results) (of which Int'l Joint Research: 12 results,  Invited: 8 results) Book (2 results) Remarks (3 results)

  • [Int'l Joint Research] University of Strasbourg(フランス)

    • Related Report
      2019 Annual Research Report
  • [Journal Article] Reaction Mechanism of Monomeric Sarcosine Oxidase with N-Cyclopropylglycine2020

    • Author(s)
      M.Shoji, Y.Abe, M.Boero, Y.Shigeta, Y.Nishiya
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: - Issue: 29 Pages: 16552-16561

    • DOI

      10.1039/d0cp01679a

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Elucidation of the entire Kok cycle for photosynthetic water oxidation by the large-scale quantum mechanics/molecular mechanics calculations: Comparison with the experimental results by the recent serial femtosecond crystallography2019

    • Author(s)
      Shoji Mitsuo、Isobe Hiroshi、Shen Jian-Ren、Suga Michihiro、Akita Fusamichi、Miyagawa Koichi、Shigeta Yasuteru、Yamaguchi Kizashi
    • Journal Title

      Chemical Physics Letters

      Volume: 730 Pages: 416-425

    • DOI

      10.1016/j.cplett.2019.06.026

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Concerted bond switching mechanism coupled with one-electron transfer for the oxygen-oxygen bond formation in the oxygen-evolving complex of photosystem II2019

    • Author(s)
      Shoji Mitsuo、Isobe Hiroshi、Yamaguchi Kizashi
    • Journal Title

      Chemical Physics Letters

      Volume: 714 Pages: 219-226

    • DOI

      10.1016/j.cplett.2018.10.041

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Concerted Mechanism of Water Insertion and O2 Release during the S4 to S0 Transition of the Oxygen-Evolving Complex in Photosystem II2018

    • Author(s)
      Shoji Mitsuo、Isobe Hiroshi、Shigeta Yasuteru、Nakajima Takahito、Yamaguchi Kizashi
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 122 Issue: 25 Pages: 6491-6502

    • DOI

      10.1021/acs.jpcb.8b03465

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A practical approach for searching stable molecular structures by introducing repulsive interactions among walkers2018

    • Author(s)
      M.Shoji, M.Kayanuma, Y.Shigeta
    • Journal Title

      The Bulletin of the Chemical Society of Japan

      Volume: 191(10) Issue: 10 Pages: 1465-1473

    • DOI

      10.1246/bcsj.20180122

    • NAID

      130007498133

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 光合成における酸素発生の反応機構2018

    • Author(s)
      庄司光男, 磯部寛, 重田育照, 中嶋隆人, 山口兆
    • Journal Title

      生物物理

      Volume: 58(3) Pages: 127-133

    • NAID

      130007378606

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Presentation] 光合成水分解反応の反応機構についての理論的探求2019

    • Author(s)
      庄司光男
    • Organizer
      ミニシンポジウム 『生命科学と物質科学の融合による新規エネルギー・物質変換技術の創造をめざして』
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Water-Splitting Reactions in the Oxygen-Evolving Complex of Photosystem II Revealed by QM/MM calculations2019

    • Author(s)
      Mitsuo Shoji
    • Organizer
      ICOPP2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Spin States and O-O bond formation mechanisms in the Oxygen-Evolving Complex of Photosystem II2019

    • Author(s)
      Mitsuo Shoji
    • Organizer
      AWEST2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 光化学系II酸素発生中心における水分解反応機構についての理論解析2019

    • Author(s)
      庄司光男
    • Organizer
      第46回生体分子科学討論会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Catalytic Reaction Mechanisms Found by using the GLAS Algorithm2019

    • Author(s)
      Mitsuo Shoji,
    • Organizer
      ICPAC 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 光合成酸素発生機構の分子メカニズム2019

    • Author(s)
      庄司光男
    • Organizer
      筑波大プレ戦略研究会「生命から学ぶ」プログラム
    • Related Report
      2019 Annual Research Report
  • [Presentation] Reaction mechanism of water splitting in photosystem II revealed by QM/MM calculations2019

    • Author(s)
      Mitsuo Shoji
    • Organizer
      11th symposium on Discovery, Fusion, Creation of New Knowledge by Multidisciplinary Computational Sciences, CCS International Symposium 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Elucidation of the Entire Kok Cycle of the Photosynthetic Water Oxidation Using QM/MM Calculations2019

    • Author(s)
      Mitsuo Shoji
    • Organizer
      3rd International Solar Fuels Conference (ISF-3) and International Conference on Artificial Photosynthesis-2019 (ICARP2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Role of Ca ion of the oxygen-evolving complex of photosytem II Revealed by QM/MM2019

    • Author(s)
      Mitsuo Shoji, Hiroshi Isobe, Yasuteru Shigeta, Takahito Nakajima, Yasuteru Shigeta, Kizashi Yamaguchi
    • Organizer
      The 99th CSJ Annual Meeting (日本化学会 第99春季年会), Konan University (2019) (oral, 口頭B講演)
    • Related Report
      2018 Annual Research Report
  • [Presentation] A new approach for searching stable molecular structures by introducing repulsive interactions among walkers2018

    • Author(s)
      M.Shoji, M.Kayanuma, H.Kitoh-Nishioka, Y.Shigeta
    • Organizer
      7thJCS, Prague, Czech Republic (Poster).
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A new algorithm searching stable molecular structures and reaction pathways by introducing repulsive interactions among walkers2018

    • Author(s)
      M.Shoji, M.Kayanuma, Y.Shigeta
    • Organizer
      ICQC 2018, Menton, France (Poster).
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 分子構造および反応機構探索アルゴリズムの新展開2018

    • Author(s)
      庄司光男
    • Organizer
      第18回日本蛋白質科学会年会
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Water insertion reactions in the oxygen-evolving complex of photosystem II revealed by QM/MM calculations2018

    • Author(s)
      M.Shoji
    • Organizer
      ICPAC Langkawi 2018, Langkawi Island, Malaysia
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] QM/MM study on a S4 -> S0 reaction of the Oxygen Evolving Complex in Photosystem II2017

    • Author(s)
      M.Shoji, H.Isobe, Y.Shigeta, T.Nakajima, K.Yamaguchi
    • Organizer
      CPMD2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Reaction mechanisms of iron-containing proteins elucidated using QM/MM calculations2017

    • Author(s)
      M.Shoji, S.Yamasaki, M.Kayanuma, Y.Shigeta
    • Organizer
      55th BSJ
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Large-scale QM/MM study on the S1 state structures of the oxygen-evolving complex in photosystem II2017

    • Author(s)
      M.Shoji, H.Isobe, Y.Shigeta, T.Nakajima, J.-R.Shen, K.Yamaguchi
    • Organizer
      JSCC67
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Book] フリーソフトで始める分子モデリング2020

    • Author(s)
      庄司光男
    • Total Pages
      70
    • Publisher
      Amazon Kindle direct publishing (電子書籍)
    • Related Report
      2019 Annual Research Report
  • [Book] Gaussian16で始める量子化学超入門2019

    • Author(s)
      庄司光男
    • Total Pages
      70
    • Publisher
      Amazon Kindle direct publishing (電子書籍)
    • Related Report
      2019 Annual Research Report
  • [Remarks] 生命物理研究グループホームページ

    • URL

      https://www2.ccs.tsukuba.ac.jp/people/mshoji/index.html

    • Related Report
      2019 Annual Research Report
  • [Remarks] 研究グループホームページ

    • URL

      https://www2.ccs.tsukuba.ac.jp/people/mshoji/index.html

    • Related Report
      2018 Annual Research Report
  • [Remarks] 研究室ホームページ

    • URL

      https://www2.ccs.tsukuba.ac.jp/people/mshoji/index.html

    • Related Report
      2017 Annual Research Report

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

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