Updated on 2026/03/10

写真a

 
ISOBE Hiroshi
 
Organization
Scheduled update Special-Appointment Associate Professor
Position
Special-Appointment Associate Professor
External link

Degree

  • 博士（理学） ( 大阪大学 )

  • 修士（理学） ( 大阪大学 )

Research Areas

  • Natural Science / Biophysics, chemical physics and soft matter physics

Education

  • 大阪大学理学部化学科    

    1993.4 - 1996.3

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    Country： Japan

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Research History

  • Research Institute for Interdisciplinary Science, Okayama University

    2016.4

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    Country：Japan

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  • Graduate School of Natural Science and Technology

    2015.10 - 2016.3

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    Country：Japan

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  • Graduate School of Natural Science and Technology

    2012.8 - 2015.9

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    Country：Japan

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Professional Memberships

 

Papers

  • Collective motions in the primary coordination sphere: a critical functional framework for catalytic activity of the oxygen-evolving complex of photosystem II. International journal

    Hiroshi Isobe, Takayoshi Suzuki, Michihiro Suga, Jian-Ren Shen, Kizashi Yamaguchi

    Chemical science   16 ( 26 )   12024 - 12042   2025.7

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    Language：English   Publishing type：Research paper (scientific journal)  

    Photosynthetic water oxidation, vital for dioxygen production and light energy conversion, is catalyzed by the oxygen-evolving complex of photosystem II, where the inorganic Mn4CaO5 cluster acts as the catalytic core. In this study, we investigate the functional significance of collective motions of amino acid side chains within the primary coordination sphere of the Mn cluster, focusing on their role in modulating the energetic demands for catalytic transformations in the S3 state. We applied regularized canonical correlation analysis to quantitatively correlate the three-dimensional arrangement of coordinating atoms with catalytic driving forces computed via density functional theory. Our analysis reveals that distinct collective side chain motions profoundly influence the energetic requirements for structural reconfigurations of the Mn cluster, achieved through expansion and contraction of the ligand cavity while fine-tuning its geometry to stabilize key intermediates. Complementary predictions from a neural network-based machine learning model indicate that the coordination sphere exerts a variable energetic impact on the catalytic transformations of the Mn cluster, depending on the S-state environment. Integrated computational analyses suggest that the extended lifetime of the S3YZ˙ state, consistently observed after three flash illuminations, may result from slow, progressive protein dynamics that continuously reshape the energy landscape, thereby shifting the equilibrium positions of rapid, reversible chemical processes over time. Overall, our findings demonstrate that collective motions in the primary coordination sphere constitute an active, dynamic framework essential for the efficient execution of multi-electron catalysis under ambient conditions, while simultaneously achieving a high selectivity with irreversible nature required for effective 3O2 evolution.

    DOI： 10.1039/d5sc02386f

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  • Correction: Collective motions in the primary coordination sphere: a critical functional framework for catalytic activity of the oxygen-evolving complex of photosystem II. International journal

    Hiroshi Isobe, Takayoshi Suzuki, Michihiro Suga, Jian-Ren Shen, Kizashi Yamaguchi

    Chemical science   16 ( 25 )   11679 - 11679   2025.6

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    [This corrects the article DOI: 10.1039/D5SC02386F.].

    DOI： 10.1039/d5sc90135a

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  • Conformational Flexibility of D1-Glu189: A Crucial Determinant in Substrate Water Selection, Positioning, and Stabilization within the Oxygen-Evolving Complex of Photosystem II

    Hiroshi Isobe, Takayoshi Suzuki, Michihiro Suga, Jian-Ren Shen, Kizashi Yamaguchi

    ACS OMEGA   9 ( 50 )   50041 - 50048   2024.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1021/acsomega.4c09981

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  • Roles of the Flexible Primary Coordination Sphere of the Mn4CaOx Cluster: What Are the Immediate Decay Products of the S3 State? International journal

    Hiroshi Isobe, Mitsuo Shoji, Takayoshi Suzuki, Jian-Ren Shen, Kizashi Yamaguchi

    The journal of physical chemistry. B   126 ( 38 )   7212 - 7228   2022.9

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    Language：English   Publishing type：Research paper (scientific journal)  

    The primary coordination sphere of the multinuclear cofactor (Mn4CaOx) in the oxygen-evolving complex (OEC) of photosystem II is absolutely conserved to maintain its structure and function. Recent time-resolved serial femtosecond crystallography identified large reorganization of the primary coordination sphere in the S2 to S3 transition, which elicits a cascade of events involving Mn oxidation and water molecule binding to a putative catalytic Mn site. We examined how the crystallographic fields, created by transient conformational states of the OEC at various time points, affect the thermodynamics of various isomers of the Mn cluster using DFT calculations, with an aim of comprehending the functional roles of the flexible primary coordination sphere in the S2 to S3 transition and in the recovery of the S2 state. The results show that the relative movements of surrounding residues change the size and shape of the cavity of the cluster and thereby affect the thermodynamics of various catalytic intermediates as well as the ability to capture a new water molecule at a coordinatively unsaturated site. The implication of these findings is that the protein dynamics may serve to gate the catalytic reaction efficiently by controlling the sequence of Mn oxidation/reduction and water binding/release. This interpretation is consistent with EPR experiments; g ∼ 5 and g ∼ 3 signals obtained after near-infrared (NIR) excitation of the S3 state at 4 K and a g ∼ 5 only signal produced after prolonged incubation of the S3 state at 77 K can be best explained as originating from water-bound S2 clusters (Stotal = 7/2) under a S3 ligand field, i.e., the immediate one-electron reduction products of the oxyl-oxo (Stotal = 6) and hydroxo-oxo (Stotal = 3) species in the S3 state.

    DOI： 10.1021/acs.jpcb.2c02596

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  • Elucidation of a multiple S3 intermediates model for water oxidation in the oxygen evolving complex of photosystem II. Calcium-assisted concerted O-O bond formation Reviewed

    K. Yamaguchi, K. Miyagawa, M. Shoji, H. Isobe, T. Kawakami

    Chem. Phys. Lett.   806   140042-1 - 140042-12   2022.9

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1016/j.cplett.2022.140042

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  • Relative energies among S3 intermediates in the photosystem II revealed by DLPNO coupled cluster and hybrid DFT calculations. Possible pathways of water insertion in the S2 to S3 transition Reviewed

    K. Miyagawa, M. Shoji, H. Isobe, T. Kawakami, T. Nakajima, K. Yamaguchi

    Chem. Phys. Lett.   793   139439-1 - 139439-12   2022.2

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1016/j.cplett.2022.139439

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  • Relative energies among proton-shifted S2 isomers in the photosystem II revealed by DLPNO coupled cluster and hybrid DFT calculations. Proton transfer coupled spin transitions of the CaMn4Ox cluster in OEC of PSII Reviewed

    K. Miyagawa, M. Shoji, H. Isobe, T. Kawakami, T. Nakajima, K. Yamaguchi

    Chem. Phys. Lett.   790   139357-1 - 139357-11   2022.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1016/j.cplett.2022.139357

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  • Exploring reaction pathways for the structural rearrangements of the Mn cluster induced by water binding in the S3 state of the oxygen evolving complex of photosystem II Reviewed

    Hiroshi Isobe, Mitsuo Shoji, Takayoshi Suzuki, Jian-Ren Shen, Kizashi Yamaguchi

    Journal of Photochemistry and Photobiology A: Chemistry   405   112905 - 112905   2021.1

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    Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.jphotochem.2020.112905

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  • An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser Reviewed

    Michihiro Suga, Fusamichi Akita, Keitaro Yamashita, Yoshiki Nakajima, Go Ueno, Hongjie Li, Takahiro Yamane, Kunio Hirata, Yasufumi Umena, Shinichiro Yonekura, Long-Jiang Yu, Hironori Murakami, Takashi Nomura, Tetsunari Kimura, Minoru Kubo, Seiki Baba, Takashi Kumasaka, Kensuke Tono, Makina Yabashi, Hiroshi Isobe, Kizashi Yamaguchi, Masaki Yamamoto, Hideo Ago, Jian-Ren Shen

    Science   366 ( 6463 )   334 - 338   2019.10

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    Publishing type：Research paper (scientific journal)   Publisher：American Association for the Advancement of Science (AAAS)  

    Inspecting S states in photosynthesis

    Oxygenic photosynthesis uses a Mn 4 CaO 5 cluster in the oxygen-evolving complex to extract electrons from water and produce dioxygen. Visualizing each of the chemical states in this process, S 0 to S 4 , and assigning chemical identities and mechanisms on the basis of structures has been a challenge addressed recently by work at x-ray free-electron lasers. Suga et al. used serial crystallography at cryogenic temperatures to trap and determine the structures of several stable states during photosystem II water oxidation (see the Perspective by Britt and Marchiori). Changes around the water cluster already happen in the S 2 state and set the stage for water insertion that occurs during transition to the S 3 state. A short 1.9-angstrom distance between the two oxygen atoms in the S 3 state is consistent with theoretical studies supporting an oxyl/oxo mechanism for oxygen-oxygen coupling.

    Science , this issue p. 334 ; see also p. 305

    DOI： 10.1126/science.aax6998

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  • Spin, Valence, and Structural Isomerism in the S3 State of the Oxygen-Evolving Complex of Photosystem II as a Manifestation of Multimetallic Cooperativity Reviewed

    Hiroshi Isobe, Mitsuo Shoji, Takayoshi Suzuki, Jian-Ren Shen, Kizashi Yamaguchi

    Journal of Chemical Theory and Computation   15 ( 4 )   2375 - 2391   2019.4

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    Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/acs.jctc.8b01055

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  • Geometric and electronic structures of the synthetic Mn4CaO4 model compound mimicking the photosynthetic oxygen-evolving complex International journal

    Mitsuo Shoji, Hiroshi Isobe, Jian-Ren Shen, Kizashi Yamaguchi

    PHYSICAL CHEMISTRY CHEMICAL PHYSICS   18 ( 16 )   11330 - 11340   2016.4

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1039/c5cp07226c

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  • Chemical Equilibrium Models for the S3 State of the Oxygen-Evolving Complex of Photosystem II Reviewed

    Hiroshi Isobe, Mitsuo Shoji, Jian-Ren Shen, Kizashi Yamaguchi

    Inorganic Chemistry   55 ( 2 )   502 - 511   2016.1

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    Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/acs.inorgchem.5b02471

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  • Strong Coupling between the Hydrogen Bonding Environment and Redox Chemistry during the S2 to S3 Transition in the Oxygen-Evolving Complex of Photosystem II Reviewed

    Hiroshi Isobe, Mitsuo Shoji, Jian-Ren Shen, Kizashi Yamaguchi

    The Journal of Physical Chemistry B   119 ( 43 )   13922 - 13933   2015.10

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    Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/acs.jpcb.5b05740

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  • Theoretical modelling of biomolecular systems I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen evolving complex of photosystem II

    Mitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Yasufumi Umena, Keisuke Kawakami, Nobuo Kamiya, Jian-Ren Shen, Takahito Nakajima, Kizashi Yamaguchi

    MOLECULAR PHYSICS   113 ( 3-4 )   359 - 384   2015.2

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1080/00268976.2014.960021

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  • Water Oxidation Chemistry of a Synthetic Dinuclear Ruthenium Complex Containing Redox-Active Quinone Ligands Reviewed

    Hiroshi Isobe, Koji Tanaka, Jian-Ren Shen, Kizashi Yamaguchi

    Inorganic Chemistry   53 ( 8 )   3973 - 3984   2014.4

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    Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/ic402340d

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  • Generalized approximate spin projection calculations of effective exchange integrals of the CaMn4O5 cluster in the S1 and S3 states of the oxygen evolving complex of photosystem II Reviewed

    H. Isobe, M. Shoji, S. Yamanaka, H. Mino, Y. Umena, K. Kawakami, N. Kamiya, J.-R. Shen, K. Yamaguchi

    Phys. Chem. Chem. Phys.   16 ( 24 )   11911 - 11923   2014

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    Authorship：Lead author   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

    <p>Broken-symmetry UB3LYP calculations have elucidated structural symmetry-breaking in the S1 and S3 states of the oxygen evolution complex (OEC) of photosystem II (PSII), providing the right (RO)- and left (LO)-opened structures.</p>

    DOI： 10.1039/c4cp00282b

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  • 2P257 Theoretical investigation on the conformation-charge relationship of the photosystem II oxygen evolving complex (PSII-OEC)(18B. Photobiology:Photosynthesis,Poster)

    Shoji Mitsuo, Isobe Hiroshi, Yamanaka Shusuke, Shen Jian-Ren, Yamaguchi Kizashi

    Seibutsu Butsuri   54 ( 1 )   S237   2014

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    Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.54.S237_5

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  • Electronic structure of the CaMn4O5 cluster in the PSII system refined to the 1.9 Å X-ray resolution. Possible mechanisms of photosynthetic water splitting

    S. Yamanaka, K. Kanda, H. Isobe, K. Nakata, Y. Umena, K. Kawakami, J. R. Shen, N. Kamiya, M. Okumura, T. Takada, H. Nakamura, K. Yamaguchi

    Advanced Topics in Science and Technology in China   250 - 254   2013

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    Language：English   Publishing type：Part of collection (book)   Publisher：Springer  

    DOI： 10.1007/978-3-642-32034-7_52

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  • Similarities of artificial photosystems by ruthenium oxo complexes and native water splitting systems Reviewed

    K. Tanaka, H. Isobe, S. Yamanaka, K. Yamaguchi

    Proceedings of the National Academy of Sciences   109 ( 39 )   15600 - 15605   2012.9

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Proceedings of the National Academy of Sciences  

    DOI： 10.1073/pnas.1120705109

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  • Role of Perferryl–Oxo Oxidant in Alkane Hydroxylation Catalyzed by Cytochrome P450: A Hybrid Density Functional Study Reviewed

    Hiroshi Isobe, Kizashi Yamaguchi, Mitsutaka Okumura, Jiro Shimada

    The Journal of Physical Chemistry B   116 ( 16 )   4713 - 4730   2012.4

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    Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/jp211184y

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  • Theoretical illumination of water-inserted structures of the CaMn4O5 cluster in the S2 and S3 states of oxygen-evolving complex of photosystem II: full geometry optimizations by B3LYP hybrid density functional Reviewed

    H. Isobe, M. Shoji, S. Yamanaka, Y. Umena, K. Kawakami, N. Kamiya, J.-R. Shen, K. Yamaguchi

    Dalton Transactions   41 ( 44 )   13727 - 13727   2012

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    Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

    DOI： 10.1039/c2dt31420g

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  • Symmetry and broken symmetry in molecular orbital description of unstable molecules IV: comparison between single- and multi-reference computational results for antiaromtic molecules Reviewed

    Toru Saito, Satomichi Nishihara, Shusuke Yamanaka, Yasutaka Kitagawa, Takashi Kawakami, Satoru Yamada, Hiroshi Isobe, Mitsutaka Okumura, Kizashi Yamaguchi

    THEORETICAL CHEMISTRY ACCOUNTS   130 ( 4-6 )   749 - 763   2011.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1007/s00214-011-0941-9

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  • Unique Structural and Electronic Features of Perferryl–Oxo Oxidant in Cytochrome P450 Reviewed

    Hiroshi Isobe, Syusuke Yamanaka, Mitsutaka Okumura, Kizashi Yamaguchi, Jiro Shimada

    The Journal of Physical Chemistry B   115 ( 36 )   10730 - 10738   2011.9

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    Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/jp206004y

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  • 3D1112 Reduction of side reaction due to mutations in P450 vitamin D3 hydroxylase : Free energy and quantum chemical calculations(3D Protein: Structure & Function 2,The 49th Annual Meeting of the Biophysical Society of Japan)

    Shimada Jiro, Fukunishi Yoshifumi, Fukunishi Hiroaki, Yagi Hirotaka, Isobe Hiroshi, Okumura Mitsutaka, Yamaguchi Kizashi, Kamijo Ken'ichi

    Seibutsu Butsuri   51   S118   2011

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    Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.51.S118_4

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  • Theoretical Investigation of Thermal Decomposition of Peroxidized Coelenterazines with and without External Perturbations. Reviewed

    H. Isobe, S. Yamanaka, M. Okumura, K. Yamaguchi

    Journal of Physical Chemistry A   113 ( 52 )   15171 - 15187   2009.10

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1021/jp905401b

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  • THEORETICAL CONSIDERATIONS ON THE ROLES OF HYDROGEN BONDING IN THERMAL DECOMPOSITION OF PEROXIDES Reviewed

    H. Isobe, S. Yamanaka, M. Okumura, K. Yamaguchi

    BIOLUMINESCENCE AND CHEMILUMINESCENCE   119 - 122   2009

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    Language：English   Publishing type：Research paper (international conference proceedings)  

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  • Theoretical studies of charge-transfer-induced luminescence in molecular and bimolecular systems Reviewed

    H. Isobe, S. Yamanaka, M. Okumura, K. Yamaguchi

    Luminescence   23 ( 2 )   74 - 74   2008.10

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  • Theoretical considerations on the roles of hydrogen bonding in thermal decomposition of peroxides Reviewed

    H. Isobe, S. Yamanaka, M. Okumura, K. Yamaguchi

    LUMINESCENCE   23 ( 2 )   74 - 74   2008.3

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Books

  • 金属錯体の量子・計算化学（錯体化学会選書１０）

    磯部 寛, 田中 晃二（ルテニウム錯体の構造と反応性（第5章2節））

    三共出版  2014.10  （ ISBN:4782707096 ）

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    Total pages：529   Language：Japanese

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MISC

Presentations

  • 新たな水分子の結合によって誘起される高酸化状態Mnクラスターの構造緩和過程に関する理論的研究

    磯部 寛, 鈴木孝義, 沈 建仁, 庄司光男, 山口 兆

    新学術領域「光合成分子機構の学理解明と時空間制御による革新的光―物質変換系の創製」第3回公開シンポジウム  2021.1.22 

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    Event date： 2021.1.22 - 2021.1.23

    Language：Japanese   Presentation type：Oral presentation (general)  

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  • Theoretical Analysis of the Electronic and Spin Structures of the Oxygen-Evolving Complex

    Hiroshi Isobe, Misuto Shoji, Takayoshi Suzuki, Jian-Ren Shen, Kizashi Yamaguchi

    International Conference on Artificial Photosynthesis-2019 (ICARP2019)  2019.11.23 

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    Event date： 2019.11.21 - 2019.11.24

    Language：English   Presentation type：Oral presentation (general)  

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  • 光合成Mnクラスターの構造変化とスピン転移の相関および基質活性化に関する理論的研究

    磯部 寛

    新学術領域「光合成分子機構の学理解明と時空間制御による革新的光―物質変換系の創製」第2回公開シンポジウム  2019.1.13 

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    Event date： 2019.1.13 - 2019.1.14

    Language：Japanese   Presentation type：Oral presentation (general)  

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  • Density Functional Study on Chemical Equilibria in the S3 State of the Oxygen-Evolving Complex of Photosystem II

    Hiroshi Isobe, Misuto Shoji, Takayoshi Suzuki, Jian-Ren Shen, Kizashi Yamaguchi

    5th International Workshop on Solar Energy for Sustainability  2018.3.20 

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    Event date： 2018.3.20 - 2018.3.22

    Language：English   Presentation type：Poster presentation  

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  • Geometric and Electronic Structures of the Mn4CaO5 in the Oxygen-Evolving Complex

    Hiroshi Isobe

    Japan-France Joint Workshop on the Structure and Function of Photosystem II  2017.12.7 

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    Event date： 2017.12.7 - 2017.12.8

    Language：English   Presentation type：Oral presentation (general)  

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  • 光合成マンガンクラスターの構造と電子状態に関する理論的研究

    磯部 寛

    第7回NTChemワークショップ  2017.3.15 

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    Event date： 2017.3.15

    Language：Japanese   Presentation type：Oral presentation (general)  

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  • Density Functional Study on Structural Trends of the Mn4CaO5 Cluster in Oxygen-Evolving Complex of Photosystem II

    Hiroshi Isobe, Mitsuo Shoji, Jian-Ren Shen, Kizashi Yamaguchi

    17th International Congress on Photosynthesis Research  2016.8.7 

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    Event date： 2016.8.8 - 2016.8.12

    Language：English   Presentation type：Poster presentation  

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  • Magneto-Structural Correlations. I. Magnetic Interaction Parameters in the S2 state of the Oxygen-Evolving Complex in Photosystem II

    H. Isobe, M. Shoji, S. Yamanaka, Y. Umena, K. Kawakami, N. Kamiya, J.-R. Shen, K. Yamaguchi

    16th International Congress on Photosynthesis Research  2013.8.13 

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    Event date： 2013.8.11 - 2013.8.16

    Language：English   Presentation type：Poster presentation  

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  • Theoretical Study of Artificial and Natural Water Oxidation

    H. Isobe, M. Shoji, S. Yamanaka, Y. Umena, K. Kawakami, N. Kamiya, K. Tanaka, J.-R. Shen, K. Yamaguchi

    The 1st Awaji International Workshop on Electron Spin Science & Technology: Biological and Materials Science Oriented Applications  2013.6.16 

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    Event date： 2013.6.17 - 2013.6.18

    Language：English   Presentation type：Poster presentation  

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  • PSIIにおけるCaMn4O5クラスターの理論計算

    磯部 寛, 庄司光男, 山中秀介, 梅名泰史, 川上恵典, 沈 建仁, 神谷信夫, 山口 兆

    第54回日本植物生理学会年会  2013.3.21 

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    Event date： 2013.3.21 - 2013.3.23

    Language：Japanese   Presentation type：Oral presentation (general)  

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  • Redox properties of ruthenium complexes containing quinone ligands: a hybrid density functional study

    Hiroshi Isobe, Koji Tanaka, Jian-Ren Shen, Kizashi Yamaguchi

    Okayama University International Symposium “Structure and Dynamics of photosynthetic Systems”  2012.10.22 

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    Event date： 2012.10.23

    Language：English   Presentation type：Poster presentation  

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Research Projects

  • 光合成マンガンクラスターの機能発現と連動したアミノ酸配位子の経時的構造変化の役割

    Grant number：22K05317  2022.04 - 2027.03

    日本学術振興会  科学研究費助成事業  基盤研究(C)

    磯部 寛

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    Grant amount：\3900000 （ Direct expense: \3000000 、 Indirect expense：\900000 ）

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  • 光合成マンガンクラスターに酸素発生機能をもたらす基本原理の抽出と検証

    Grant number：20H05103  2020.04 - 2022.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    磯部 寛

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    Grant amount：\6500000 （ Direct expense: \5000000 、 Indirect expense：\1500000 ）

    光合成Mnクラスターによる水分解・酸素発生反応の過電圧が極めて低いのは何故か？本研究では、理論的な方向からこの疑問に答え、その原理を普遍的な法則あるいは概念として構築することを目指した。その結果、正電荷（ホール）を３つ蓄積したMnクラスターの３次元空間配置がアミノ酸配位子により緻密に制御されることで自発的に発現する協同現象が本質的な役割を果たす（つまり、多電子反応の活性化エネルギーと再配置エネルギーの両方を減少させる）ことが見出された。協同効果が発現する上で重要な要素を５つ挙げると、以下のようになる。①共有結合性：基質水分子が結合したMnクラスターでは、Mnのeg軌道とO2の反結合性σ*又はπ*軌道の重なりを最大化する結合様式をとるため、電子が金属と基質間で容易に移動できる。②非局所応答性：基質由来の電子がMn(IV)のeg軌道に入ることによって生じる自発的なJahn－Teller局所歪を介して、３つのサイトが相互に絡み合う結果、クラスター全体にある特別な構造変化（open－closed cubane間の構造変化）が誘起される。③スイッチング機能：open及びclosed cubane構造はMnの価数分布（4443と3444）と一対一に対応しているが、その対応関係はMn(IV)配位不飽和サイトに結合した基質が脱プロトン化することで反転する。その結果、基質が適切な形態で結合した後でのみ非局所応答が起こり、構造変化に伴う金属の電荷状態変化を金属と基質間の３電子移動に高効率で変換できるようになる。④アミノ酸残基の経時的構造変化：時間の経過に伴って表れるアミノ酸残基の動的な構造変化は、open及びclosed cubane構造の安定性を相対的に変化させることで、触媒反応を誘導する駆動力を生み出している。⑤「歪んだ椅子」型構造：①－④を可能にしているのは、触媒の「歪んだ椅子」型構造に他ならない。

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  • 光合成マンガンクラスターに酸素発生機能をもたらす基本原理の抽出と検証

    Grant number：18H05167  2018.04 - 2020.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    磯部 寛

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    Grant amount：\6500000 （ Direct expense: \5000000 、 Indirect expense：\1500000 ）

    水を分解し生物の生存に必要な酸素を作り出す触媒であるMn4CaO5クラスターは、電子の授受に伴ってその構造を巧妙に変化させることで触媒活性を示す。本研究では、機能を発現する上で本質的に重要だと考えられる概念や原理・法則を見出すため、電子の属性である「電荷」と「スピン」に着目して、触媒がどのように化学反応を進めているのかを調べた。その結果、Mnクラスターが外部刺激に応答してその物理化学的挙動を変化させるスイッチング機能をもっていることが判明した。スイッチングは、基質水分子が高い酸化状態にあるクラスターの配位不飽和金属サイトに結合することでトポロジカル構造が異なる構造異性体と金属の電荷状態の間の対応関係が反転する現象を利用して、分子レベルで起こる。この機構において重要な役割を果たしているのが、基本構成原子であるMnイオンの電荷とスピンの可変性である。特に、Mn3+はヤーン・テラー（JT）効果によりeg軌道から生じる極めて強い方向性をもち、配位子の原子軌道と効果的な重なりを形成する。基質が捕捉されてスイッチがONになると、各MnイオンのJT歪みに起因する局所配位構造変化と電荷状態変化が協応し、ある特定の全体構造変化が誘起されることで、JT軸が１つに集まるクラスター内部の疎水空間において金属と基質間の共有結合性が高まる。この協同効果により、基質の結合により引き起こされる金属の電荷状態変化を金属と基質間の多電子移動として効率よく取り出せるようになる。つまり、スイッチ機能により、非常に困難な水の酸化反応を、適切なタイミングで、高い収率で、限りなく低い過電圧で触媒することができるようになると同時に、電荷担体の流れに整流性が発現する。このような触媒・整流器としての作動が分子レベルで可能になるのは、JT効果を鍵要素とする構成原子が「歪んだ椅子」を形成するように配置されているからに他ならない。

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  • Elucidation of the mechanism of water-splitting in photosystem II

    Grant number：24000018  2012 - 2017

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Specially Promoted Research

    SHEN Jian-Ren, NOGUCHI Takumi, YAMAGUCHI Kizashi, SHOJI Mitsuo, SUGA Michihiro, AKITA Fusamichi, MINO Hiroyuki, KATO Yuki, ISOBE Hiroshi

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    Grant amount：\519350000 （ Direct expense: \399500000 、 Indirect expense：\119850000 ）

    In order to elucidate the reaction mechanism of water-splitting performed by photosystem II (PSII) in photosynthesis, we used femtosecond X-ray free electron laser (XFEL) to analyze the radiation damage-free, high-resolution crystal structure of PSII, which revealed the Mn_4CaO_5-cluster structure in its native state. We further used XFEL to analyze the structure of one of the intermediate state, S_3-state, which identified the site of O=O bond formation. Based on these structures, theoretical calculations were performed, which identified possible reaction pathways for the water-splitting. Furthermore, spectroscopic analysis, especially Fourier-transformed infrared spectroscopic analysis, was performed, which elucidated the structural changes of amino acid residues surrounding the Mn_4CaO_5-cluster and identified hydrogen-bond pathways that may participate in the proton exit from the water-splitting reaction site.

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