2013 Fiscal Year Final Research Report
Development of QM/MM hybrid method for strongly correlated systems and its applications to reaction centers of bioenzyemes
| Project/Area Number |
23550016
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Physical chemistry
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| Research Institution | Osaka University |
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Principal Investigator |
YAMANAKA Shusuke 大阪大学, 理学(系)研究科(研究院), 助教 (10324865)
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| Project Period (FY) |
2011 – 2013
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| Keywords | 密度汎関数理論 / 光化学系II / 磁性 / マンガンクラスター / QM/MM理論 |
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| Research Abstract |
In 2011, the structure of the the water oxydation reaction center of photosystem II is presented. We performed calculations with using their X-ray structure and published the results of electronic ans spin structures of their structure, in which we examined all possible oxidation states with all possible spin structures. To our knowledge, this is the first paper on computational results of the Mn clusters of photosystem II. Subsequently, we examined natural orbitals and geometry changes to propose the possible reaction mechanisms to oxidize the water molecules. On the other side, because there is slight contradiction between calculational results and experimental results, we examined functional dependency of the description of magnetism of Mn complexes with constructing original test sets of Mn complexes. We also examined noncollinear magnetism of Mn clusters and proposed a QM/MM boundary guideline based on linear response function of spin density.
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Research Products
(42 results)
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[Journal Article] Full geometry optimizations of the mixed-valence CaMn_4O_4X(H_2O)_4 (X=OH or O) cluster in OEC of PS II : Degree of symmetry breaking of the labile Mn-X-Mn bond revealed by several hybrid DFT calculations2013
Author(s)
Yamaguchi, H. Isobe, S. Yamanaka, T. Saito, K. Kanda, M. Shoji, Y. Umena, K. Kawakami, J.-R. Shen, N. Kamiya, M. Okumura
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Journal Title
Int. J. Quantum Chem
Volume: 113
Pages: 525-541
Peer Reviewed
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[Journal Article] The nature of chemical bonds of the CaMn_4O_5 cluster in oxygen evolving complex of photosystem II : Jahn-Teller distortion and its suppression by Ca doping in cubane structures2013
Author(s)
K. Yamaguchi, S. Yamanaka, H. Isobe, T. Saito, K. Kanda, Y. Umena, K. Kawakami, J.-R. Shen, N. Kamiya, M. Okumura, H. Nakamura, M. Shoji, Y. Yoshioka
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Journal Title
Int. J. Quantum Chem
Volume: 113
Pages: 453-473
Peer Reviewed
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[Journal Article] Structure and Reactivity of the Mixed-Valence CaMn_4O_5(H_2O)_4 Clusters at Oxygen Evolution Complex of Photosystem II. Hybrid DFT (UB3LYP and UBHandHLYP) Calculations2012
Author(s)
S. Yamanaka, T. Saito, K. Kanda, H. Isobe, Y. Umena, K. Kawakami, J-R. Shen, N. Kamiyta, M. Okumura, H. Nakamura, K. Yamaguchi
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Journal Title
Int. J. Quantum Chem
Volume: 112
Pages: 321-343
Peer Reviewed
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[Journal Article] Possible mechanisms for the O-O bond formation in oxygen evolution reaction at the CaMn_4O_5(H_2O)_4 cluster of PSII refined to 1.9 Å X-ray resolution2011
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
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Journal Title
Chem. Phys. Lett
Volume: 511
Pages: 138-145
Peer Reviewed
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[Journal Article] Possible mechanism of water splitting reaction based on proton and electron release pathways revealed for CaMn_4O_5 cluster of PS IIrefined to 1.9 Å X-ray resolution2011
Author(s)
T. Saito, S. Yamanaka, K. Kanda, H. Isobe, Y. Takano, Y. Shigeta, Y. Umena, K. Kawakami, J-R.Shen, N. Kamiya, Y. Kitagawa, T. Kawakami, M. Okumura, M. Shoji, Y. Yoshioka, K. Yamaguchi
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Journal Title
Int. J. Quantum Chem.
Volume: 112
Pages: 253-276
Peer Reviewed
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[Book] 計算化学における多階層連結コンピューティング2011
Author(s)
山中秀介, 神田慧太, 西原慧径, 鵜飼健史, 武田亮, 中田一人, 斉藤徹, 木下啓二, 磯部寛, 山田悟, 北河康隆, 川上貴資, 奥村光隆, 中村春木, 山口兆
Total Pages
153-204
Publisher
財団法人国際高等研究所
