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Study on chemical reaction dynamics in the color determination mechanism in bioluminescence

Research Project

Project/Area Number 15K05379
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Physical chemistry
Research InstitutionGunma University (2017)
The University of Tokyo (2015-2016)

Principal Investigator

Hiyama Miyabi  群馬大学, 大学院理工学府, 准教授 (90399311)

Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2017: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2016: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2015: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Keywordsホタル生物発光 / オキシルシフェリン / 水和 / 量子化学計算 / 分子動力学計算 / 発光体 / 振電相互作用 / 吸収スペクトル / 蛍光スペクトル / フランクコンドン因子
Outline of Final Research Achievements

We elucidated the vibronic effect on the absorption and fluorescence spectra of the oxyluciferin and its conjugate bases. While the energies of the excited states were calculated with the time-dependent density functional theory, the solvent effect was incorporated using the polarized continuum model. Then, the effects of hydrogen bonding interactions were clarified through a theoretical study on the stability of the oxyluciferin anions with explicit water molecules using the first-principles molecular dynamics (FPMD) simulations. These simulations showed that enol type is more stable than keto type because of the unique features of the static and dynamical hydration structures. The absorption spectra of aqueous oxyluciferin anions were derived using the structures obtained from the FPMD simulations at room temperature for each isomeric form, in order to account for the effects of vibrations of oxyluciferin anions and dynamical fluctuations of their hydration structures.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (25 results)

All 2017 2016 2015

All Journal Article (4 results) (of which Peer Reviewed: 4 results,  Acknowledgement Compliant: 3 results) Presentation (21 results) (of which Int'l Joint Research: 9 results,  Invited: 5 results)

  • [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 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Theoretical insights into the effect of pH values on oxidation processes in the emission of firefly luciferin in aqueous solution2017

    • Author(s)
      Hiyama Miyabi、Akiyama Hidefumi、Koga Nobuaki
    • Journal Title

      Luminescence:The Journal of Biological and Chemical Luminescence

      Volume: 32 Issue: 6 Pages: 1100-1108

    • DOI

      10.1002/bio.3308

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [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] Vibronic structures in absorption and fluorescence spectra of firefly oxyluciferin in aqueous solutions2015

    • Author(s)
      Miyabi Hiyama, Yoshifumi Noguchi, Hidefumi Akiyama, Kenta Yamada, Nobuaki Koga
    • Journal Title

      Photochemistry and Photobiology

      Volume: 91 Issue: 4 Pages: 819-827

    • DOI

      10.1111/php.12463

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] pH dependence of oxidation reaction pathway of firefly luciferin2017

    • Author(s)
      Miyabi Hiyama, Hidefumi Akiyama, Nobuaki Koga
    • Organizer
      The 55th Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] クマリン・ケージドルシフェリンの電子励起状態の理論的研究2017

    • Author(s)
      薄倉淳子、樋山みやび、倉田麻貴、挾間優治、Xingping Qiu、Francoise Winnik, 古賀伸明、秋山英文
    • Organizer
      第11回分子科学討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] ホタルオキシルシフェリン吸収スペクトルにおける水分子鎖の構造ゆらぎの影響2017

    • Author(s)
      樋山みやび、野口良史、志賀基之、杉野修、秋山英文、古賀伸明
    • Organizer
      第11回分子科学討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] GRRM 法による水溶液中ケージドルシフェリンの構造探索2017

    • Author(s)
      薄倉淳子、樋山みやび、倉田麻貴、挾間優治、Xingping Qiu、Francoise Winnik, 古賀伸明、秋山英文
    • Organizer
      シンポジウム「化学反応経路探索のニューフロンティア」
    • Related Report
      2017 Annual Research Report
  • [Presentation] nstantaneous absorption spectra of firefly oxyluciferin using the first principle molecular dynamics simulations2017

    • Author(s)
      Miyabi Hiyama, Yoshifumi Noguchi, Motoyuki Shiga, Osamu Sugino, Hidefumi Akiyama, Nobuaki Koga
    • Organizer
      1th Triennial Congress of the World Association of Theoretical and Computational Chemists, 27 August-1 September 2017, Munich, Germany
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Effects of water solvation on absorption spectra of firefly oxyluciferin2017

    • Author(s)
      Nobuaki Koga, Miyabi Hiyama, Yoshifumi Noguchi, Motoyuki Shiga, Osamu Sugino, Hidefumi Akiyama
    • Organizer
      The 28th International Conference on Photochemistry (ICP 2017)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 水溶液中のオキシルシフェリン異性体の安定性2016

    • Author(s)
      野口良史、樋山みやび、志賀基之、杉野修、秋山英文
    • Organizer
      第30回分子シミュレーション討論会
    • Place of Presentation
      大阪大学(大阪府・豊中市)
    • Year and Date
      2016-11-30
    • Related Report
      2016 Research-status Report
  • [Presentation] Hydration effects on absorption and fluorescence spectra of firefly oxyluciferin2016

    • Author(s)
      Miyabi Hiyama, Yoshifumi Noguchi, Hidefumi Akiyama Kenta Yamada, Nobuaki Koga
    • Organizer
      The 54rd Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      つくば国際会議場(茨城県・つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] ホタルルシフェリン酸化反応経路の理論的研究2016

    • Author(s)
      樋山みやび、秋山英文、古賀伸明
    • 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(兵庫県・神戸市)
    • Year and Date
      2016-09-13
    • Related Report
      2016 Research-status Report
  • [Presentation] Effects of vibronic transitions and water solvation on absorption and fluorescence spectra of firefly oxyluciferin2016

    • Author(s)
      Miyabi Hiyama, Yoshifumi Noguchi, Kenta Yamada, Hidefumi Akiyama, Nobuaki Koga,
    • Organizer
      19th International Symposium on Bioluminescence and Chemiluminescence 2016
    • Place of Presentation
      つくば国際会議場(茨城県・つくば市)
    • Year and Date
      2016-05-29
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Stability of keto-, enol-, enolate-type oxyluciferin anions in aqueous solutions2016

    • Author(s)
      Yoshifumi Noguchi, Miyabi Hiyama, Motoyuki Shiga, Osamu Sugino, Hidefumi Akiyama
    • Organizer
      19th International Symposium on Bioluminescence and Chemiluminescence 2016
    • Place of Presentation
      つくば国際会議場(茨城県・つくば市)
    • Year and Date
      2016-05-29
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Theoretical study for photoluminescence of firefly-bioluminescence-related molecules2015

    • Author(s)
      (1)Miyabi Hiyama, Yoshifumi Noguchi, Toshimitsu Michizuki, Kenta Yamada, Hidefumi Akiyama, Nobuaki Koga
    • Organizer
      環太平洋国際化学会議 THE INTERNATIONAL CHEMICAL CONGRESS OF PACIFIC BASIN SOCIETIES (Pacifichem 2015
    • Place of Presentation
      ホノルル(米国)
    • Year and Date
      2015-12-16
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] All-electron first-principles X-ray adsorption spectra calculations for acetone and acetic acid.2015

    • Author(s)
      2.Yoshifumi Noguchi, Miyabi Hiyama, Hidefumi Akiyama, Yoshihisa Harada, Nobuaki Koga
    • Organizer
      環太平洋国際化学会議 THE INTERNATIONAL CHEMICAL CONGRESS OF PACIFIC BASIN SOCIETIES (Pacifichem 2015)
    • Place of Presentation
      ホノルル(米国)
    • Year and Date
      2015-12-15
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] ホタル生物発光の量子化学計算と反応機構2015

    • Author(s)
      樋山みやび
    • Organizer
      量子化学探索研究所講演会2015
    • Place of Presentation
      東京大学 (東京都・文京区)
    • Year and Date
      2015-11-29
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] 生物発光における量子化学計算2015

    • Author(s)
      樋山みやび
    • Organizer
      第3回津田沼RBKフォーラム
    • Place of Presentation
      千葉工業大学 (千葉県・習志野市)
    • Year and Date
      2015-11-28
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] 生物発光における分子科学2015

    • Author(s)
      樋山みやび
    • Organizer
      原子衝突学会第40回年会
    • Place of Presentation
      首都大学東京 (東京都・八王子市)
    • Year and Date
      2015-09-30
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] 水溶液中オキシルシフェリンの吸収・蛍光スペクトルにおける振電構造の解析2015

    • Author(s)
      樋山みやび, 野口良史, 秋山英文, 山田健太, 古賀伸明
    • Organizer
      第9回分子科学討論会
    • Place of Presentation
      東京工業大学 (東京都・目黒区)
    • Year and Date
      2015-09-19
    • Related Report
      2015 Research-status Report
  • [Presentation] 生物発光の光制御に向けたケージド・ルシフェリンの分光評価2015

    • Author(s)
      倉田麻貴, 樋山みやび, 挟間優治, 東暉舜, 吉田正裕, 望月敏光, 秋山英文
    • Organizer
      第9回分子科学討論会
    • Place of Presentation
      東京工業大学 (東京都・目黒区)
    • Year and Date
      2015-09-18
    • Related Report
      2015 Research-status Report
  • [Presentation] イクオリン生物発光の量子収率測定2015

    • Author(s)
      挾間優治, 東暉舜, 倉田麻貴, 樋山みやび, 吉田正裕, 久保田英博, 井上敏, 秋山英文
    • Organizer
      日本物理学会2015年秋季大会
    • Place of Presentation
      関西大学 (大阪府・吹田市)
    • Year and Date
      2015-09-17
    • Related Report
      2015 Research-status Report
  • [Presentation] Analysis of Photoluminescence Pathways of Firefly Oxyluciferin in Aqueous Solution2015

    • Author(s)
      Miyabi Hiyama, Toshimitsu Mochizuki, Hidefumi Akiyama, Nobuaki Koga
    • Organizer
      The 53rd Annual Meeting of the Biophysical Society of Japan
    • Place of Presentation
      金沢大学 (石川県・金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] オキシルシフェリン光ルミネッセンスにおける発光反応経路と振動構造2015

    • Author(s)
      樋山みやび、野口良史、望月敏光、秋山英文、古賀伸明
    • Organizer
      物性研究所短期研究会 機能物性融合科学研究会シリーズ(3)「反応と輸送」
    • Place of Presentation
      東京大学物性研究所 (千葉県・柏市)
    • Year and Date
      2015-06-24
    • Related Report
      2015 Research-status Report

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Published: 2015-04-16   Modified: 2019-03-29  

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