Reaction dynamics of nano- and bio-molecules with multiple reaction sites and its atom-resolved energy picture
| Project/Area Number |
16H04091
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Physical chemistry
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| Research Institution | Tohoku University |
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Principal Investigator |
Kono Hirohiko 東北大学, 理学研究科, 客員研究者 (70178226)
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| Co-Investigator(Kenkyū-buntansha) |
小関 史朗 大阪府立大学, 理学(系)研究科(研究院), 教授 (80252328)
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| Project Period (FY) |
2016-04-01 – 2019-03-31
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| Project Status |
Completed (Fiscal Year 2019)
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| Budget Amount *help |
¥15,860,000 (Direct Cost: ¥12,200,000、Indirect Cost: ¥3,660,000)
Fiscal Year 2018: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2017: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2016: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
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| Keywords | 多電子ダイナミクス / １電子有効ポテンシャル / 強レーザーパルス / 非断熱遷移 / ヒドロキシルラジカル / DNA鎖切断 / 光駆動分子モーター / クーロン爆発 / 1電子有効ポテンシャル / X線自由電子レーザー / 電子ダイナミクス / ポリヒドロキシフラーレン / クーロン爆発イメージング / 分子モーター / 原子分割エネルギー / 自然軌道 / 分子イメージング / 高次高調波発生 |
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| Outline of Final Research Achievements |
We developed the atom-resolved method for energy and the nonadiabatic surface hopping method suitable for large systems to deeply investigate the reaction dynamics of nano- and bio-molecules. The methods are applied to simulate the dynamics of DNA damage. We found the mechanism of a double strand break: Dense, high energy OH radicals generated by radiation or light penetrate the water barrier around a DNA and cause a cluster of single strand breaks via H-abstraction from pentose moieties (leading to P-O skeletal breaks). We also clarified the dynamics of the light-transformation of OH-functionalized fullerenes into nanocarbons and ultrafast trans-cis isomerization of a light-driven molecular motor. For electron dynamics, using the multiconfiguration time-dependent method, we revealed that a hump structure due to electron correlation is formed on the top of the field-induced distorted barrier, which provides a new picture of tunnel ionization beyond the single-electron approximation.
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| Academic Significance and Societal Importance of the Research Achievements |
ラジカルによるDNAの2本鎖切断の理論的解明により、現在、実験グループと鎖切断のみならず塩基酸化などDNA損傷の全貌解明のための共同研究が進展している。強レーザー場化学、DNA損傷の定性・定量解析、損傷検出化学プローブの設計・合成、反応動力学理論の4チームが連携し、遺伝子の損傷・修復・複製の分子論構築を目指している。また、XFELパルスによる分子のクーロン爆発のシミュレーションを行い、実験で得られた解離イオンのエネルギーや角度相関から、反応中の分子構造を抽出するイメージング理論も構築した。以上、本理論研究は、観測された動力学過程の機構解明のみならず、さらなる実験立案を導く成果をもたらした。
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Report
(4 results)
Research Products
(69 results)
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[Journal Article] Diffractive Imaging of C60 Structural Deformations Induced by Intense Femtosecond Midinfrared Laser Fields2019
Author(s)
H. Fuest, Y. H. Lai, C. I. Blaga, K. Suzuki, J. Xu, P. Rupp, H. Li, P. Wnuk, P. Agostini, K. Yamazaki, M. Kanno, H. Kono, M. F. Kling, and L. F. DiMauro
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Journal Title
Physical Review Letters
Volume: 122
Issue: 5
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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[Journal Article] Ultrafast Dynamics of a Nucleobase Analogue Illuminated by a Short Intense X-ray Free Electron Laser Pulse2016
Author(s)
K. Nagaya, K. Motomura, E. Kukk, H. Fukuzawa, S. Wada, T. Tachibana, Y. Ito, S. Mondal, T. Sakai, K. Matsunami, R. Koga, S. Ohmura, Y. Takahashi, M. Kanno, A. Rudenko, C. Nicolas, X.-J. Liu, Y. Zhang, J. Chen, M. Anand, Y. H. Jiang, D.-E. Kim, K. Tono, M. Yabashi, H. Kono, C. Miron, M. Yao, and K. Ueda
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Journal Title
Phys. Rev. X
Volume: 6
Issue: 2
Pages: 0210351-9
DOI
NAID
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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[Journal Article] Femtosecond Charge and Molecular Dynamics of I-containing organic molecules Induced by Intense X-Ray Free-Electron Laser Pulses2016
Author(s)
K.Nagaya, K.Motomura, E.Kukk, Y.Takahashi, K.Yamazaki, S.Ohmura, H.Fukuzawa, S.Wada, S.Mondal, T.Tachibana, Y.Ito, R.Koga, T.Sakai, K.Matsunami, K.Nakamura, M.Kanno, A.Rudenko, C.Nicolas, X-J.Liu, C.Miron, Y.Zhang, Y.Jiang, J.Chen, M.Anand, D.E.Kim, K.Tono, M.Yabashi, M.Yao, H.Kono, K.Ueda
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Journal Title
Faraday Discussions
Volume: 194
Pages: 537-562
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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[Presentation] XFEL 誘起超高速ダイナミクスの実験・理論展開2017
Author(s)
河野 裕彦, 中村 公亮, 落合 宏平, 岡田 朝彦, 及川 啓太, 菱沼 直樹, 花崎 浩太, 菅野 学, 高梨 司, 永谷 清信, 上田 潔
Organizer
第20回理論化学討論会
Related Report
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[Presentation] Development of a reaction dynamics model for the Coulomb explosion of I-containing molecules induced by intense XFELs2017
Author(s)
K. Ochiai, K. Nakamura, Y. Takahashi, M. Kanno, K. Yamazaki, T. Takanashi, H. Fukuzawa, K. Tono, K. Nagaya, K. Ueda, H. Kono
Organizer
33rd Symposium on Chemical Kinetics and Dynamics
Related Report
Int'l Joint Research
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[Presentation] Femtosecond Charge and Molecular Dynamics of I-containing organic molecules Induced by Intense X-Ray Free-Electron Laser Pulses2016
Author(s)
K.Ueda, K.Nagaya, K.Motomura, E.Kukk, Y.Takahashi, K.Yamazaki, S.Ohmura, H.Fukuzawa, S.Wada, S.Mondal, T.Tachibana, Y.Ito, R.Koga, T.Sakai, K.Matsunami, K.Nakamura, M.Kanno, A.Rudenko, C.Nicolas, X.-J.Liu, C.Miron, Y.Zhang, Y.Jiang, J.Chen, M.Anand, D.E.Kim, K.Tono, M.Yabashi, M.Yao, H.Kono
Organizer
Ultrafast Imaging of Photochemical Dynamics: Faraday Discussion
Place of Presentation
Edinburgh, United Kingdom
Related Report
Int'l Joint Research / Invited
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