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Development of QM/MM hybrid method for strongly correlated systems and its applications to reaction centers of bioenzyemes

Research Project

Project/Area Number 23550016
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Physical chemistry
Research InstitutionOsaka University

Principal Investigator

YAMANAKA Shusuke  大阪大学, 理学(系)研究科(研究院), 助教 (10324865)

Project Period (FY) 2011 – 2013
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2013: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2012: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2011: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
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 / 光合成光化学系II / 磁性状態 / QM/MM境界問題 / 結合次数の線形応答関数解析 / 酸化状態 / Mn多核錯体 / 第一原理計算 / 水分解反応
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.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Research-status Report
  • 2011 Research-status Report
  • Research Products

    (80 results)

All 2014 2013 2012 2011 Other

All Journal Article (46 results) (of which Peer Reviewed: 45 results) Presentation (21 results) Book (13 results)

  • [Journal Article] A spin density version of linear response function: Toward guidelines of QM/MM boundaries for reliable computations2014

    • Author(s)
      Shusuke Yamanaka, Kazuto Nakata, Mitsutaka Okumura, Kizashi Yamaguchi, Haruki Nakamura
    • Journal Title

      Journal of Physical Society Conference Series

      Volume: 1

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Theory of chemical bonds in metalloenzymes XIX: labile manganese oxygen bonds of the CaMn4O5 cluster in oxygen evolving complex of photosystem II2014

    • Author(s)
      K. Yamaguchi, S. Yamanaka, M. Shoji , H. Isobe , Y. Kitagawa , T. Kawakami , S. Yamada, M. Okumura
    • Journal Title

      Molecular Physics

      Volume: 112 Issue: 3-4 Pages: 485-507

    • DOI

      10.1080/00268976.2013.842009

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Spin Density Version of Linear Response Function: Toward Guidelines of QM/MM Boundaries for Reliable Computations2014

    • Author(s)
      S. Yamanaka, K. Nakata, M. Okumura, K. Yamaguchi, H. Nakamura
    • Journal Title

      Journal of the Physical Society of Japan Conference Proceedings

      Volume: 1

    • DOI

      10.7566/jpscp.1.016015

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical study of magnetism of manganese clusters2014

    • Author(s)
      S. Yamanaka, Y. Mitsuta, T. Kawakami, Y. Kitagawa, H. Nakamura, M. Okumura, K. Yamaguchi
    • Journal Title

      Journal of the Physical Society of Japan Conference Proceedings

      Volume: 未定

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Combination of approximate spin-projection and spin-restricted calculations based on ONIOM method for geometry optimization of large biradical systems2013

    • Author(s)
      Y. Kitagawa , N. Yasuda, H. Hatake, T. Saito, Y. Kataoka, T. Matsui, T. Kawakami, S. Yamanaka, M. Okumura, K. Yamaguchi
    • Journal Title

      Int. J. Quantum Chem

      Volume: 113 Pages: 290-295

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Theory of chemical bonds in metalloenzymes XVIII. Importance of mixed-valence configurations for Mn_5O_5, CaMn_4O_5 and Ca_2 Mn_3O_5 clusters revealed by UB3LYP computations. A bio-inspired strategy for artificial photosynthesis2013

    • Author(s)
      K. Yamaguchi , Y. Kitagawa, H. Isobe , M. Shoji, S. Yamanaka, M. Okumura
    • Journal Title

      Polyhedron

      Volume: 57 Pages: 138-149

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Linear response function approach for the boundary problem of QM/MM methods2013

    • Author(s)
      K. Ueda, S. Yamanaka, K.Nakata, M. Ehara, M. Okumura, K. Yamaguchi, H. Nakamura
    • Journal Title

      Int. J. Quantum Chem

      Volume: 113 Pages: 336-341

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Ab initio DFT study of magneto-structural correlation of dinuclear mixed-valence Mn complexes2013

    • Author(s)
      Shusuke Yamanaka, Kyohei Komi, Koki Ueda, Yasutaka Kitagawa, Takashi Kawakami, Mitsutaka Okumura, Haruki Nakamura, Kizashi Yamaguchi
    • Journal Title

      Journal of Physics: Conference Series

      Volume: vol. 428

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [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
    • Journal Title

      Int. J. Quantum Chem

      Volume: 113 Pages: 525-541

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] How to determine boundaries for QM/MM calculations : A guideline based on linear response function for glutathione2013

    • Author(s)
      Shusuke Yamanaka, Koki Ueda, Kazuto Nakata, Mitsutaka Okumura, Kizashi Yamaguchi, Haruki Nakamura
    • Journal Title

      Journal of Physics : Conference Series

      Volume: vol. 454

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [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
    • Journal Title

      Int. J. Quantum Chem

      Volume: 113 Pages: 453-473

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Theory of chemical bonds in metalloenzymes XVI. Oxygen activation by high-valent transition metal ions in native and artificial systems2013

    • Author(s)
      K. Yamaguchi, M. Shoji, H. Isobe, Y. Kitagawa, S. Yamada, T. Kawakami, S. Yamanaka, M. Okumura
    • Journal Title

      Polyhedron

      Volume: 66 Pages: 228-244

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] The Nature of chemical bonds of the CaMn4O5cluster 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 and Y. Yoshioka
    • Journal Title

      Internat. J. Quantum Chem

      Volume: 113 Issue: 4 Pages: 453-473

    • DOI

      10.1002/qua.24280

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Full Geometry Optimizations of the Mixed-Valence CaMn4O4X(H2O) 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)
      K. Yamaguchi, H. Isobe, S. Yamanaka, T. Saito, K. Kanda, M. Shoji, Y. Umena, K. Kawakami, J.-R.. Shen, N. Kamiya, M. Okumura
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 113 Issue: 4 Pages: 525-541

    • DOI

      10.1002/qua.24117

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theory of chemical bonds in metalloenzymes XVI. Oxygen activation by high-valent transition metal ions in native and artificial systems2013

    • Author(s)
      K. Yamaguchi, M. Shoji, H. Isobe, Y. Kitagawa, S. Yamada, T. Kawakami S. Yamanaka M. Okumura
    • Journal Title

      Polyhedron

      Volume: 66 Pages: 228-244

    • DOI

      10.1016/j.poly.2013.05.001

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theory of chemical bonds in metalloenzymes XVIII. Importance of mixed-valence configurations for Mn5O5, CaMn4O5 and Ca2Mn3O5 clusters revealed by UB3LYP computations. A bio-inspired strategy for artificial photosynthesis2013

    • Author(s)
      K. Yamaguchi , Y. Kitagawa, H. Isobe ,M. Shoji, S. Yamanaka, M. Okumura
    • Journal Title

      Polyhedron

      Volume: 57 Pages: 138-149

    • DOI

      10.1016/j.poly.2013.04.019

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ab initio DFT study of magneto-structural correlation of dinuclear mixed-valence Mn complexes2013

    • Author(s)
      S. Yamanaka, K. Komi, K. Ueda, . Kitagawa, T. Kawakami, M. Okumura, H. Nakamura, K. Yamaguchi
    • Journal Title

      Journal of Physics : Conference Series

      Volume: 428 Pages: 12035-12035

    • DOI

      10.1088/1742-6596/428/1/012035

    • Related Report
      2013 Annual Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] How to determine boundaries for QM/MM calculations: A guideline based on linear response function for glutathione2013

    • Author(s)
      S. Yamanaka, K. Ueda, K. Nakata, M. Okumura, K. Yamaguchi, H. Nakamura
    • Journal Title

      Journal of Physics Conference Series

      Volume: 454 Pages: 012055-012055

    • DOI

      10.1088/1742-6596/454/1/012055

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Combination of approximate spin-projection and spin-restricted calculations based on ONIOM method for geometry optimization of large biradical systems2013

    • Author(s)
      Y. Kitagawa, N. Yasuda, H. Hatake, T. Saito, Y. Kataoka, T. Matsui, T. Kawakami, S. Yamanaka, M. Okumura, K. Yamaguchi
    • Journal Title

      Int. J. Quant. Chem

      Volume: 113 Issue: 3 Pages: 290-295

    • DOI

      10.1002/qua.24018

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Linear response function approach for the boundary problem of QM/MM methods2013

    • Author(s)
      K. Ueda, S. Yamanaka, K. Nakata, M. Ehara, M. Okumura, K. Yamaguchi, H. Nakamura
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 113 Issue: 3 Pages: 336-341

    • DOI

      10.1002/qua.24106

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Does B3LYP correctly describe magnetism of manganese complexes with various oxidation numbers and structural motifs?2012

    • Author(s)
      S. Yamanaka, K. Kanda, T. Saito, Y. Kitagawa, T. Kawakami, M. Ehara, M. Okumura, H. Nakamura, K. Yamaguchi
    • Journal Title

      Chem. Phys. Lett

      Volume: 519-520 Pages: 134-140

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Electronic and spin structures of the CaMn_4O_5(H_2O)_4 cluster in OEC of PS II refined to 1.9 Å X-ray resolution2012

    • Author(s)
      S. Yamanaka, K. Kanda, T. Saito, Y. Umena, K. Kawakami, J-R. Shen, N. Kamiya, H. Nakamura, K. Yamaguchi
    • Journal Title

      Adv. Quantum Chem

      Volume: 64 Pages: 121-187

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [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
    • Journal Title

      Int. J. Quantum Chem

      Volume: 112 Pages: 321-343

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical illumination of water-inserted structures of the CaMn_4O_5(H_2O)_4 cluster in the S2 and S3 states of oxygen-evolving complex of photosystem II: full geometry optimizations by B3LYP hybrid density functional2012

    • Author(s)
      H. Isobe, M. Shoji, S. Yamanaka, Y. Umena, K. Kawakami, N. Kamiya, J.-R. Shen, K. Yamaguchi
    • Journal Title

      Dalton Trans

      Volume: 41 Pages: 3727-13740

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Locality and nonlocality of electronic structures of molecular systems : Toward QM/MM and QM/QM approaches2012

    • Author(s)
      S. Yamanaka, Y. Yonezawa, K. Nakata, S. Nishihara, M. Okumura, T. Takada, K. Yamaguchi, H. Nakamura
    • Journal Title

      AIP Conf. Proc

      Volume: 1504 Pages: 916-919

    • Related Report
      2013 Final Research Report
  • [Journal Article] Similarities of artificial photosystems by ruthenium oxo complexes and native water splitting systems2012

    • Author(s)
      Koji Tanaka, Hiroshi Isobe, Shusuke Yamanaka, Kizashi Yamaguchi
    • Journal Title

      PNAS

      Volume: 109 Pages: 15600-15605

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Spin hamiltonian models for artificial and native water splitting systems revealed by hybrid DFT calculations. Oxygen activation by high-valent Mn and Ru ions2012

    • Author(s)
      K. Yamaguchi, S. Yamanaka, H. Isobe, K. Tanaka, N. Ueyama
    • Journal Title

      Int. J. Quantum Chem

      Volume: 112 Pages: 3849-3866

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Electronic and Spin Structures of the CaMn4O5(H2O)4 Cluster in OEC of PSII Refined to 1.9 A X-ray Resolution2012

    • Author(s)
      S. Yamanaka, K. Kanda, T. Saito, Y. Umena, K. Kawakami, J. -R. Shen, N. Kamiya, M. Okumura, H. Nakamura, K. Yamaguchi
    • Journal Title

      Advances in Quantum Chemsitry

      Volume: 64 Pages: 121-187

    • DOI

      10.1016/b978-0-12-396498-4.00016-8

    • ISBN
      9780123964984
    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Locality and nonlocality of electronic structures of molecular systems : Toward QM/MM and QM/QM approaches2012

    • Author(s)
      S. Yamanaka, Y. Yonezawa, K. Nakata, S. Nishihara, M. Okumura, T. Takada, K. Yamaguchi, H. Nakamura
    • Journal Title

      AIP Conference Proceedings

      Volume: 1504 Pages: 916-919

    • DOI

      10.1063/1.4771844

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Does B3LYP correctly describe magnetism of manganese complexes with various oxidation numbers and various structural motifs?2012

    • Author(s)
      S. Yamanaka, K. kanda, T. Saito, Y. Kitagawa, T. Kawakami, M. Ehara, M. Okumura, H. Nakamura, K. Yamaguchi
    • Journal Title

      CHEMICAL PHYSICS LETTERS

      Volume: 519-20 Pages: 134-140

    • DOI

      10.1016/j.cplett.2011.11.025

    • Related Report
      2012 Research-status Report 2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Structure and reactivity of the mixed-alence CaMn_4O_5(H_2O)_4 and CaMn_4O_4(OH)(H_2O)_4 clusters at oxygen evolution complex of photosystem II.Hybrid DFT (UB3LYP and UBHANDHLYP) calculations2012

    • Author(s)
      T.Saito, S.Yamanaka, K.Kanda, H.Isobe, Y.Takano, Y.Shigeta, Y.Umena, K.Kawakami, J.-R.Shen, N.Kamiya, M.Okumura, M.Shoji, Y.Yoshioka, K.Yamaguchi
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Issue: 1 Pages: 321-343

    • DOI

      10.1002/qua.23261

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] 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 functional2012

    • Author(s)
      H. Isobe, M. Shoji, S. Yamanaka, Y. Umena, K. Kawakami, N. Kamiya, J.-R. Shen, K. Yamaguchi
    • Journal Title

      Dalton Transactions

      Volume: 41 Issue: 44 Pages: 13727-13740

    • DOI

      10.1039/c2dt31420g

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Similarities of artificial photosystems by ruthenium oxo complexes and native water splitting systems2012

    • Author(s)
      Koji Tanaka, Hiroshi Isobe, Shusuke Yamanaka, Kizashi Yamaguchi
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 109 Issue: 39 Pages: 15600-15605

    • DOI

      10.1073/pnas.1120705109

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Theory of Chemical Bonds in Metalloenzymes XVII. Symmetry Breaking in Manganese Cluster Structures and Chameleonic Mechanisms for the O-O Bond Formation of Water Splitting Reaction2012

    • Author(s)
      Toru Saito
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Issue: 1 Pages: 121-135

    • DOI

      10.1002/qua.23255

    • Related Report
      2012 Research-status Report 2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Possible Mechanisms of Water Splitting Reaction Based on Proton and Electron Release Pathways Revealed for CaMn_4O_5 Cluster of PSII Refined to 1.9 Å X-Ray Resolution2012

    • Author(s)
      Toru Saito
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Issue: 1 Pages: 253-276

    • DOI

      10.1002/qua.23218

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Spin Hamiltonian Models for Artificial and Native Water Splitting Systems Revealed by Hybrid DFT Calcuations. Oxygen Activation by High-Valent Mn and Ru Ions2012

    • Author(s)
      K. Yamaguchi, S. Yamanaka, H. Isobe, K. Tanaka, N. Ueyama
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 112 Issue: 24 Pages: 3849-3866

    • DOI

      10.1002/qua.24270

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Labile electronic and spin states of the CaMn_4O_5 cluster in the PSII system refined to the 1.9 Å X-ray resolution. UB3LYP computational results2011

    • 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

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [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
    • Journal Title

      Chem. Phys. Lett

      Volume: 511 Pages: 138-145

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Ab initio study of magnetic interactions of manganese-oxide clusters2011

    • Author(s)
      K. Kanda, S. Yamanaka, T. Saito, T. Kawakami, Y. Kitagawa, M. Okumura, H. Nakamura, K. Yamaguchi
    • Journal Title

      Polyhedron

      Volume: 30 Pages: 3256-3261

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Theory of chemical bonds in metalloenzymes. XVII. Symmetry breaking in manganese cluster structures and chameleonic mechanisms for the O-O bond formation of water splitting reaction2011

    • Author(s)
      T. Saito, M. Shoji, K. Kanda, H. Isobe, S. Yamanaka, Y. Kitagawa, S. Yamada, T. Kawakami, M. Okumura, K. Yamaguchi
    • Journal Title

      Int. J. Quantum Chem

      Volume: 112 Pages: 121-135

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [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
    • Journal Title

      Int. J. Quantum Chem.

      Volume: 112 Pages: 253-276

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Ab initio Study of Magnetic Interactions of Manganese-Oxide Clusters2011

    • Author(s)
      K.Kanda, T.Saito, K.Yamaguchi, et al
    • Journal Title

      Polyhedron

      Volume: 30 Issue: 18 Pages: 3256-3261

    • DOI

      10.1016/j.poly.2011.04.042

    • Related Report
      2011 Research-status Report
    • 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 results2011

    • 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 Issue: 1-3 Pages: 98-103

    • DOI

      10.1016/j.cplett.2011.02.030

    • Related Report
      2011 Research-status Report
    • 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 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
    • Journal Title

      Chem. Phys. Lett

      Volume: 511 Issue: 1-3 Pages: 138-145

    • DOI

      10.1016/j.cplett.2011.06.021

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Theory of chemical bonds in metalloenzymes XVIII. Importance of mixed-valence configurations for Mn5O5, CaMn4O5 and Ca2Mn3O5 clusters revealed by UB3LYP computations. A bio-inspired strategy for artificial photosynthesis

    • Author(s)
      K. Yamaguchi, M. Shoji, H. Isobe, Y. Kitagawa, S. Yamada, T. Kawakami, S. Yamanaka, M. Okumura
    • Journal Title

      Polyhedron

      Volume: 57 Pages: 138-149

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical study of magnetism of manganese clusters

    • Author(s)
      Shusuke Yamanaka, Yuki Mitsuta, Takashi Kawakami, Yasutaka Kitagawa, Haruki Nakamura, Mitsutaka Okumura, Kizashi Yamaguchi
    • Journal Title

      Journal of Physical Society Conference Series

      Volume: (in press)

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Presentation] Linear response analysis of finite systems: the reasons why "nearsightedness" holds even for finite systems2014

    • Author(s)
      Shusuke Yamanaka
    • Organizer
      The 54th Sanibel Symposium
    • Place of Presentation
      St. Simons Island, Georgia, US
    • Year and Date
      2014-02-19
    • Related Report
      2013 Final Research Report
  • [Presentation] Density functional study of noncollinear magnetism of Mn clsuters2013

    • Author(s)
      Shusuke Yamanaka
    • Organizer
      International Symposium on Theoretical Chemistry
    • Place of Presentation
      Todaiji Culture Center, Nara
    • Year and Date
      2013-12-03
    • Related Report
      2013 Final Research Report
  • [Presentation] スピン及び結合次数に対する線形応答関数に基づく QM/MM 境界問題への理論的アプローチ2013

    • Author(s)
      山中秀介
    • Organizer
      分子科学討論会
    • Place of Presentation
      京都テルサ
    • Year and Date
      2013-09-26
    • Related Report
      2013 Final Research Report
  • [Presentation] Density functional study of magnetism of manganese clusters2013

    • Author(s)
      Shusuke Yamanaka
    • Organizer
      The International Conference on strongly correlated electron systems
    • Place of Presentation
      Ito International Research Center Conference, The Hongo campus of the University of Tokyo
    • Year and Date
      2013-08-06
    • Related Report
      2013 Final Research Report
  • [Presentation] Bond-order and spin density versions of linear response function:Toward guidelines of QM/MM boundaries for reliable computations2013

    • Author(s)
      Shusuke Yamanaka
    • Organizer
      The 12th Asian Pacific Physic Conference. The third Asia-Europe Physics Summit
    • Place of Presentation
      Makuharimesse Chiba
    • Year and Date
      2013-07-16
    • Related Report
      2013 Final Research Report
  • [Presentation] 線形応答関数に基づく QM/MM 境界問題への理論的アプローチ2013

    • Author(s)
      山中秀介
    • Organizer
      日本化学会第93春年会
    • Place of Presentation
      立命館大学, 草津キャンパス
    • Year and Date
      2013-03-23
    • Related Report
      2013 Final Research Report
  • [Presentation] How to determine boundaries of QM/MM calculations. A guideline based on linear response function2012

    • Author(s)
      Shusuke Yamanaka
    • Organizer
      JSST 2012 International conference on Simulation Technology
    • Place of Presentation
      兵庫県ポートアイランド
    • Year and Date
      2012-09-27
    • Related Report
      2013 Final Research Report
  • [Presentation] Ab initio study of structural effects of dinuclear mixed valence Mn complexes2012

    • Author(s)
      Shusuke Yamanaka
    • Organizer
      XXIst International Symposium on the Jahn-Teller Effect
    • Place of Presentation
      Tsukuba University
    • Year and Date
      2012-08-27
    • Related Report
      2013 Final Research Report
  • [Presentation] Mn複核錯体の磁性の密度汎関数理論~遷移金属酵素中心解析に向けて~2011

    • Author(s)
      山中秀介
    • Organizer
      大阪大学蛋白研セミナー「蛋白質科学の未来を語る:実験理論研究者の対話」
    • Place of Presentation
      大阪大学蛋白質研究所
    • Year and Date
      2011-11-21
    • Related Report
      2013 Final Research Report
  • [Presentation] Towards reliable density functional approaches for manganese complexes2011

    • Author(s)
      Shusuke Yamanaka
    • Organizer
      XVIth International Workshop on Quantum Systems in Chemistry and Physics
    • Place of Presentation
      Ishikawa Prefecture Museum of Art, Kanazawa
    • Year and Date
      2011-09-16
    • Related Report
      2013 Final Research Report
  • [Presentation] Assessment of density functional theory2011

    • Author(s)
      Shusuke Yamanaka
    • Organizer
      The VIIIth congress of the international society of theoretical chemical physics
    • Place of Presentation
      Waseda University
    • Year and Date
      2011-09-03
    • Related Report
      2013 Final Research Report
  • [Presentation] Density functional study of manganese complexes2011

    • Author(s)
      Shusuke Yamanaka
    • Organizer
      Fukui International Symposium for theoretical chemistry, Fukui Institute for fundamental chemistry
    • Place of Presentation
      Kyoto University
    • Year and Date
      2011-08-31
    • Related Report
      2013 Final Research Report
  • [Presentation] Ab initio DFT(UB3LYP)による光合成光化学系 II の電子状態の解析2011

    • Author(s)
      山中秀介
    • Organizer
      日本化学会コンピュータ化学部会「理論化学で探る触媒」
    • Place of Presentation
      大阪科学技術センター
    • Year and Date
      2011-06-21
    • Related Report
      2013 Final Research Report
  • [Presentation] Ab initio DFT(UB3LYP)による光合成光化学系IIの電子状態の解析2011

    • Author(s)
      山中秀介
    • Organizer
      日本化学会コンピュータ化学部会「理論化学で探る触媒化学」
    • Place of Presentation
      大阪科学技術センター
    • Related Report
      2011 Research-status Report
  • [Presentation] Mn複核錯体の磁性の密度汎関数理論~遷移金属酵素中心解析に向けて~2011

    • Author(s)
      山中秀介
    • Organizer
      大阪大学蛋白研セミナー「タンパク質科学の未来を語る:実験・理論研究者の対話」
    • Place of Presentation
      大阪大学蛋白質研究所
    • Related Report
      2011 Research-status Report
  • [Presentation] Towards reliable density functional ..2011

    • Author(s)
      山中秀介
    • Organizer
      QSTCP XVI
    • Place of Presentation
      石川県立美術館
    • Related Report
      2011 Research-status Report
  • [Presentation] Density functional study of manganese complexes2011

    • Author(s)
      山中秀介
    • Organizer
      Fukui International Symposium ..
    • Place of Presentation
      福井謙一記念研究センター
    • Related Report
      2011 Research-status Report
  • [Presentation] Assessment of density functional theory2011

    • Author(s)
      山中秀介
    • Organizer
      ISTCP VII
    • Place of Presentation
      早稲田大学
    • Related Report
      2011 Research-status Report
  • [Presentation] Ab initio DFT study of structural effects of dinuclear mixed-valence Mn complexes

    • Author(s)
      山中秀介
    • Organizer
      XXIst International Symposium on the Jahn-Teller Effect
    • Place of Presentation
      茨城県筑波市筑波大学
    • Related Report
      2012 Research-status Report
  • [Presentation] 線形応答関数に基づくQM/MM境界問題への理論的アプローチ

    • Author(s)
      山中秀介
    • Organizer
      日本化学会第93春年会
    • Place of Presentation
      滋賀県草津市立命館大学びわこ・くさつキャンパス
    • Related Report
      2012 Research-status Report
  • [Presentation] How to determine boundaries for QM/MM calculations: A guideline based on linear response function

    • Author(s)
      山中秀介
    • Organizer
      JSST2012 International Conference on Simulation Technology
    • Place of Presentation
      兵庫県神戸市ポートアイランド
    • Related Report
      2012 Research-status Report
  • [Book] 錯体化学選書 『金属錯体の量子計算化学』(榊 茂好・山口 兆・増田秀樹編), 1章3節「独立粒子モデル・対称性の破れと多電子問題」2014

    • Author(s)
      山中秀介, 奥村光隆
    • Publisher
      三共出版(印刷中)
    • Related Report
      2013 Final Research Report
  • [Book] 錯体化学選書 『金属錯体の量子計算化学』(榊 茂好・山口 兆・増田秀樹編), 4章2節「錯体の磁性の量子化学」2014

    • Author(s)
      山中秀介, 川上貴資
    • Publisher
      三共出版(印刷中)
    • Related Report
      2013 Final Research Report
  • [Book] 金属錯体の量子計算化学, (1章3節)「独立粒子モデル・対称性の破れと多電子問題」2014

    • Author(s)
      山中秀介、奥村光隆
    • Publisher
      三共出版
    • Related Report
      2013 Annual Research Report
  • [Book] 金属錯体の量子計算化学, (4章2節)「錯体の磁性の量子化学」2014

    • Author(s)
      山中秀介、川上貴資
    • Publisher
      三共出版
    • Related Report
      2013 Annual Research Report
  • [Book] Calculation of Magnetic Properties and Spectroscopic Parameters of Manganese Clusters with Density Functional Theory2012

    • Author(s)
      K. Kanda, S. Yamanaka, T. Saito, Y. Kitagawa, T. Kawakami, M. Okumura, K. Yamaguchi
    • Publisher
      Springer
    • Related Report
      2013 Final Research Report
  • [Book] Density functional study of manganese complexes: Protonation effects on geometries and magnetism2012

    • Author(s)
      S. Yamanaka, K. Kanda, T. Saito, Y. Kitagawa, T. Kawakami, M. Ehara, M. Okumura, H. Nakamura, K. Yamaguchi
    • Publisher
      Springer
    • Related Report
      2013 Final Research Report
  • [Book] DFT Calculations of the Heterojunction Effect for Precious Metal Cluster Catalysis2012

    • Author(s)
      M. Okumura, K. Sakata, T. Tada, S. Yamada, K. Okazaki, Y. Kitagawa, T. Kawakami, S. Yamanaka
    • Publisher
      Springer
    • Related Report
      2013 Final Research Report
  • [Book] Progress in Theoretical Chemistry and Physics2012

    • Author(s)
      K. Kanda, S. Yamanaka, T. Saito, Y. Kitagawa, T. Kawakami, M. Okumura, K. Yamaguchi
    • Publisher
      Springer
    • Related Report
      2012 Research-status Report
  • [Book] Progress in Theoretical Chemistry and Physics2012

    • Author(s)
      S. Yamanaka, K. Kanda, T. Saito, Y. Kitagawa, T. Kawakami, M. Ehara, M. Okumura, H. Nakamura, K. Yamaguchi
    • Publisher
      Springer
    • Related Report
      2012 Research-status Report
  • [Book] Progress in Theoretical Chemistry and Physics2012

    • Author(s)
      M. Okumura, K. Sakata, K. Tada, S. Yamada, K. Okazaki, Y. Kitagawa, T. Kawakami, S. Yamanaka
    • Publisher
      Springer
    • Related Report
      2012 Research-status Report
  • [Book] Progress in Theoretical Chemistry and Physics2012

    • Author(s)
      N. Yasuda, Y. Kitagawa, H. Hatake, T. Saito, Y. Kataoka, T. Matsui, T. Kawakami, S. Yamanaka, M. Okumura
    • Publisher
      Springer
    • Related Report
      2012 Research-status Report
  • [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
    • Publisher
      財団法人国際高等研究所
    • Related Report
      2013 Final Research Report
  • [Book] 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)
      山中秀介 他
    • Total Pages
      52
    • Publisher
      財団法人国際高等研究所
    • Related Report
      2011 Research-status Report

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Published: 2011-08-05   Modified: 2019-07-29  

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