Theoretical studies of electronic structure, chemical reaction and function of multi-nuclear transition-metal complexes in biological systems

2011 Fiscal Year Final Research Report

• Project/Area Number: 21550014
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Physical chemistry
• Research Institution: 公益財団法人豊田理化学研究所 (2011); Toyota Physical & Chemical Research Institute (2009-2010)
• Principal Investigator: YAMAGUCHI Kizashi 公益財団法人豊田理化学研究所, フェロー (80029537)
• Co-Investigator(Renkei-kenkyūsha): KAMIYA Nobuo 大阪市立大学, 理学研究科, 教授 (60152865) ; SHEN Kenjin 岡山大学, 自然科学研究科, 教授 (60261161) ; NAKAMURA Haruki 大阪大学, 蛋白質研究所, 教授 (80134485) ; OKUMURA Mitsutaka 大阪大学, 理学研究科, 教授 (40356712) ; YAMANAKA Syusuke 大阪大学, 理学研究科, 助教 (10324865) ; KAWAKAMI Takashi 大阪大学, 理学研究科, 助教 (30321748) ; KITAGAWA Yasutaka 大阪大学, 理学研究科, 助教 (60362612) ; KITAGAWA Yasutaka 大阪大学, 理学研究科, 助教 (60362612)
• Project Period (FY): 2009 – 2011
• Keywords: 生体内多核遷移金属錯体 / 電子構造 / 化学反応性 / 機能発現 / 理論的研究 / p. 450 / MMO, OEC, PSII

Research Abstract

We have developed theoretical methods for elucidation of electronic and spin structures of multi-nuclear transition-metal complexes in biological systems such as CaM4O5 cluster in the oxygen-evolving complex(OEC) of photosystem II(PSII). The electronic and spin structures elucidated by theoretical calculations have been applied for investigation and prediction of chemical reactivity such as water oxidation mechanism at OEC of PSII and biological functions such as electron transfer.

Research Products

• [Journal Article] Broken-symmetry Natural Orbital(BANO)-Mk-MRCC Study on the Exchange Coupling in the Bunuclear Copper(II) Compounds (2011)
  • Author(s): T. Saito, N. Yasuda, S. Nishihara, S. Yamanaka, Y. Kitagawa, T. Kawakami, M. Okumura, K. Yamaguchi
  • Journal Title: Chem. Phys. Lett Volume: 505 Pages: 11-15
  • DOI: DOI:10.1016/j.cplett.2011.02.-18
  • Peer Reviewed
• [Journal Article] Unique Structural and Electronic Features of Perferryl-Oxo Oxidant in Cytochrome p-450 (2011)
  • Author(s): H. Isobe, S. Yamanaka, M. Okumura, K. Yamaguchi, J. Shimada
  • Journal Title: J. Phys. Chem Volume: A115 Pages: 10730-10738
  • DOI: DOI:10.1021/jp206004y
  • Peer Reviewed
• [Journal Article] Labile electronic and spin states of the CaMn4O5 cluster in the PSII system refined to the 1.9A X-ray resolution UB3LYP computational results (2011)
  • Author(s): K. Kanda, S. Yamanaka, T. Saito, Y. Umena, K. Kawakami, J. R. Shen, N. Kamiya, M. Okumura, H. Nakamura, K. Yamaguchi
  • Journal Title: Chem. Phys. Lett Volume: 506 Pages: 98-103
  • DOI: DOI:10.1016/j.cplett.2011.02.030
  • Peer Reviewed
• [Journal Article] Possible Mechanisms for the O-O Bond Formation in Oxygen Evolution Reaction at the CaMn4O5(H2O) 4 Cluster of PSII refined to 1.9A X-ray Resolution (2011)
  • Author(s): S. Yamanaka, H. Isobe, K. Kanda, T. Saito, Y. Umena, K. Kawakami, J. R. Shen, N. Kamiya, M. Okumura, H. Nakamura, K. Yamaguchi
  • Journal Title: Chem. Phys. Lett Volume: 511 Pages: 138-145
  • DOI: DOI:10.1016/j.cplett.2011.06.021
  • Peer Reviewed
• [Journal Article] Symmetry and Broken Symmetry in Molecular Orbital Description of Unstable Molecules IV : Comparison between single and multi-reference computational results for antiaromatic molecules (2011)
  • Author(s): T. Saito, S. Nishihara, S. Yamanaka, Y. Kitagawa, T. Kawakami, S. Yamada, H. Isobe, M. Okumura, K. Yamaguchi
  • Journal Title: Theoret. Chem. Acc Volume: 130 Pages: 749-763
  • DOI: DOI:10.1007/s00214-011-0941-9
• [Journal Article] Singlet-triplet Energy Gap for Trimethylenemethane, Oxyallyl Diradical, and Related Species : Single and Multi-reference Computational Results (2011)
  • Author(s): T. Saito, S. Nishihara, S. Yamanaka, Y. Kitagawa, T. Kawakami, S. Yamada, H. Isobe, M. Okumura, K. Yamaguchi
  • Journal Title: Theoret. Chem. Acc Volume: 130 Pages: 739-748
  • DOI: DOI:10.1007/s00214-011-0914-z
• [Journal Article] MRCC, APUCC and APUBD Calculations of Didehydropolyene Diradicals, The Nature of Through-Bond Effective Exchange Integrals for Diradicals (2010)
  • Author(s): S, Nishihara, T. Saito, S. Yamanaka, Y. Kitagawa, T. Kawakami, M. Okumura, K. Yamaguchi
  • Journal Title: Mol. Phys Volume: 19 Pages: 2559-2578
  • DOI: DOI:10.1155/2010/908132
  • Peer Reviewed
• [Journal Article] Reinvestigation of the Reaction of Ethylene and Singlet Oxygen by the Approximate Spin Projection Method. Comparison with Multi-reference Coupled-Cluster Calculations (2010)
  • Author(s): T. Saito, S. Nishihara, Y. Kataoka, Y. Nakanishi, Y. Kitagawa, T. Kawakami, S. Yamanaka, M. Okumura, K. Yamaguchi
  • Journal Title: J. Phys. Chem Volume: A114 Pages: 7969-7874
  • DOI: DOI:10.1021/jp102772v
  • Peer Reviewed
• [Journal Article] Which Hybrid GGA DFT is Suitable for Cu2O2 Systems if the Spin Contamination Error Is Removed (2010)
  • Author(s): T. Saito, Y. Kataoka, Y. Nakanishi, T. Matsui, Y. Kitagawa, T. Kawakami, M. Okumura, K. Yamaguchi
  • Journal Title: Chem. Phys Volume: 368 Pages: 1-6
  • DOI: DOI:10.1016/j.chemphys.2009.12.014
  • Peer Reviewed
• [Journal Article] Theory of Chemical Bonds in Metalloenzymes. XV. Local Singlet and Triplet Diradical Mechanisms for Radical Coupling Reactions in the Oxygen Evolution Complex (2010)
  • Author(s): K. Yamaguchi, M. Shoji, T. Saito, H. Isobe, S. Nishihara, K. Koizumi, S. Yamada, T. Kawakami, Y. Kitagawa, S. Yamanaka, M. Okumura
  • Journal Title: Int. J. Quant. Chem Volume: 110 Pages: 3101-3128
  • DOI: DOI:10.1002/quq.22914
  • Peer Reviewed
• [Journal Article] Resonating Coupled-Cluster CI Approach to Ion-Radical Systems : Comparison with the unrestricted Coupled-Cluster Approach (2009)
  • Author(s): S. Yamanaka, S. Nishihara, K. Nakata, Y. Yonezawa, M. Okumura, T. Takada, H. Nakamura, K. Yamaguchi
  • Journal Title: Int. J. Quant. Chem Volume: 109 Pages: 3811-3818
  • DOI: DOI:10.1002/qua.22441
  • Peer Reviewed
• [Journal Article] Resonating Broken-Symmetry Configuration Interaction Approach for Double Exchange Magnetic Systems (2009)
  • Author(s): S. Nishihara, S. Yamanaka, K. Kusakabe, K. Nakata, Y. Yonezawa, H. Nakamura, K. Yamaguchi
  • Journal Title: J. Phys. Condens. Matter Volume: 21 Pages: 064227
  • DOI: DOI:10.1088/0953-8984/21/6/064227
  • Peer Reviewed
• [Journal Article] Symmetry and Broken Symmetry in Molecular Orbital Descriptions of Unstable Molecules 3.The Nature of Chemical Bonds of Spin Frustrated Systems (2009)
  • Author(s): T. Kawakami, R. Takeda, S. Nishihara, S. Yamanaka, T. Saito, M. Shoji, S. Yamada, Y. Kitagawa, M. Okumura, K. Yamaguchi
  • Journal Title: J. Phys. Chem Volume: A113 Pages: 15281-15297
  • DOI: DOI:10.1021/jp905991r
  • Peer Reviewed
• [Journal Article] Transition State Optimization Based on Approximate Spin-projected(AP) method (2009)
  • Author(s): T. Saito, S. Nishihara, Y. Kataoka, Y. Nakanishi, T. Matsui, Y. Kitagawa, T. Kawakami, M. Okumura, K. Yamaguchi
  • Journal Title: Chem. Phys. Lett Volume: 483 Pages: 168-171
  • DOI: DOI:10.1016/j.cplett.2009.10055
  • Peer Reviewed
• [Presentation] Development of Broken-Symmetry Methods. Application to the CaMn4O5 Cluster st OEC of PSII Refined to 1.9A X-Ray Resolution (2011)
  • Author(s): K. Yamaguchi
  • Organizer: The Seventh Congress of the International Society for Theoretical Chemical Physics
  • Place of Presentation: Waseda
  • Year and Date: 20110900
• [Presentation] Electronic and Spin Sates of the CaMn4O5 Cluster at OEC of PSII Refined to 1.9A X-Ray Resolution (2011)
  • Author(s): K. Yamaguchi
  • Organizer: International Symposium on Activation of Dioxygen and Homogeneous Catalytic Oxidation
  • Place of Presentation: Okinawa
  • Year and Date: 20110700
• [Presentation] First Principle Calculations of Effective Exchange Integrals-Comparison between SR(BS) and MRCC Computational Results (2010)
  • Author(s): K. Yamaguchi
  • Organizer: ICCMSE VIII
  • Place of Presentation: Greece
  • Year and Date: 20101000
• [Book] Broken-Symmetry法の発展 (2011)
  • Author(s): 山口兆
  • Total Pages: 177-182
  • Publisher: 化学同人編集部
• [Book] 計算化学における多階層連結コンピューティング(エネルギー科学における多階層連結コンピューティング) (2011)
  • Author(s): 山口兆、山中秀介
  • Total Pages: 155-205
  • Publisher: 国際高等研究所
• [Book] Broke-Symmetry法の発展.マンガン酸化物クラスターの水分解酸素発生機構(理論化学編) (2010)
  • Author(s): 山口兆
  • Total Pages: 71-77
  • Publisher: 化学同人
• [Remarks]
  • URL: http://www.toyotariken.jp/researcher/j_yamaguchi.html