DOI: 10.1002/qua.24117. 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 calculations

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 calculations

10.1002/qua.24117

Crossref journal-article

Wiley

International Journal of Quantum Chemistry (311)

Abstract

AbstractSeveral hybrid DFT methods were applied to full geometry optimizations of the CaMn4O4X(H2O)4 (XOH1− (1) or O2− (2)) cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) to elucidate Mn‐Mn, Mn‐Ca, and Mn‐O distances on a theoretical ground. The computed Mn‐Mn distances were compared with previous (London and Berlin) X‐ray diffraction (XRD), and Berkeley and Berlin EXAFS results, together with the recent high‐resolution XRD structure by Umena and coworkers. Present computational results by the hybrid DFT methods have elucidated several differences among these accumulated results. These DFT results led us to reassign the Mn‐Mn and Mn‐Ca distances by the EXAFS experiments, which became consistent with the results obtained by the high‐resolution XRD structure. A characteristic feature revealed via the optimized Mn‐O distances was that the degree of symmetry breaking of the Mn1‐O(57)‐Mn4 bond is not so remarkable under the UBHandHLYP approximation but it can be large by other hybrid DFT methods. The computational results for 2 indicated reduction of the Mn3‐Mn4 distance with the deprotonation of the bridging oxo group. The hybrid DFT results for 1 are not inconsistent with an experimental proposal based on the new XRD structure, namely a protonated μ3‐oxygen at the internal O(57) site of the cluster in the S1 state. On the other hand, the reduction of Mn ions (not degradation of whole cluster structure) by the X‐ray irradiation still remains an important issue for refinements of the XRD structure. The computational results are discussed in relation to those of the electron spin echo envelope modulation (ESEEM) and possible pathways for water splitting reaction. Implications of the present DFT structures are discussed in relation to the previous DFT and related computational results, together with recent XRD results for cubane‐like model clusters for OEC of PSII. © 2012 Wiley Periodicals, Inc.

Bibliography

Yamaguchi, K., Isobe, H., Yamanaka, S., Saito, T., Kanda, K., Shoji, M., Umena, Y., Kawakami, K., Shen, J. âR., Kamiya, N., & Okumura, M. (2012). Full geometry optimizations of the mixedâvalence CaMn4O4X(H2O)4 (X=OH or O) cluster in OEC of PS II: Degree of symmetry breaking of the labile MnâXâMn bond revealed by several hybrid DFT calculations. International Journal of Quantum Chemistry, 113(4), 525â541. Portico.

Authors 11

K. Yamaguchi (first)
H. Isobe (additional)
S. Yamanaka (additional)
T. Saito (additional)
K. Kanda (additional)
M. Shoji (additional)
Y. Umena (additional)
K. Kawakami (additional)
J.‐R. Shen (additional)
N. Kamiya (additional)
M. Okumura (additional)

References 63 Referenced 62

10.1021/cr950052k
10.1016/S0005-2728(00)00217-6
10.1016/S0005-2728(00)00230-9
10.1021/bi026569p
10.1039/B408146C
10.1021/ja054873a
10.1126/science.1128186
10.1098/rstb.2007.2220
10.1016/j.bbabio.2011.07.004
10.1073/pnas.0135651100
10.1126/science.1093087
10.1039/B406989G
10.1038/nature04224
10.1016/j.bbabio.2007.02.013
10.1038/nsmb.1559
10.1073/pnas.0812797106
10.1021/ja011621a
10.1007/s00723-009-0051-1
10.1039/b808792j
10.1021/ja043012j
10.1021/bi050411y
10.1021/ja071487f
10.1021/ja002104f
10.1098/rstb.2002.1144
10.1016/j.bbabio.2003.11.009
10.1038/nature09913
10.1016/j.jphotobiol.2011.03.017
10.1111/j.1751-1097.1970.tb06017.x
10.1016/j.cplett.2011.02.030
10.1016/j.cplett.2011.06.021
10.1002/qua.23218
10.1002/qua.23261
10.1098/rstb.2007.2214
10.1002/anie.200906253
10.1016/0009-2614(75)80169-2
10.1016/0009-2614(75)85320-6
10.1016/0009-2614(79)85043-5
K. Yamaguchi Y. Takahara T. Fueno V. H. Smith H. F. Schaefer K. Morokuma D. Reidel Applied Quantum Chem 155
10.1016/S0009-2614(00)00166-4
10.1021/jp0571877
{'key': 'e_1_2_8_39_2', 'first-page': '138', 'volume': '511', 'author': 'Siegbahn P. E. M.', 'year': '2011', 'journal-title': 'Photochem. Photobiol.'} / Photochem. Photobiol. by Siegbahn P. E. M. (2011)
10.1002/cphc.201100475
10.1021/bi200681q
10.1016/j.jphotobiol.2011.03.002
10.1098/rstb.2007.2208
10.1002/chem.200700003
10.1002/chem.200701865
10.1016/j.jinorgbio.2006.01.017
10.1021/ja076130q
{'key': 'e_1_2_8_48_2', 'volume-title': 'Gaussian 09, Revision B.01', 'author': 'Frisch M. J.', 'year': '2010'} / Gaussian 09, Revision B.01 by Frisch M. J. (2010)
{'key': 'e_1_2_8_49_2', 'first-page': '583', 'volume': '55', 'author': 'Cruickshank D. W.', 'year': '1999', 'journal-title': 'Acta Crystallogr.'} / Acta Crystallogr. by Cruickshank D. W. (1999)
10.1038/35055589
10.1021/ja110145v
10.1002/qua.20286
10.1002/qua.21201
10.1002/qua.22914
1990 Elsevier Amsterdam K. Yamaguchi R. Carbo M. Klobukowski Self‐Consistent Field Theory and Applications 727
10.1016/j.poly.2011.04.042
10.1126/science.1206036
10.1021/bi035489y
10.1021/bi052146m
10.1021/ja2041805
10.1016/0014-5793(92)80092-U

Dates

Type	When
Created	13 years, 4 months ago (April 13, 2012, 3:40 a.m.)
Deposited	1 year, 11 months ago (Sept. 12, 2023, 10:14 a.m.)
Indexed	1 month, 3 weeks ago (July 9, 2025, 7:01 p.m.)
Issued	13 years, 4 months ago (April 13, 2012)
Published	13 years, 4 months ago (April 13, 2012)
Published Online	13 years, 4 months ago (April 13, 2012)
Published Print	12 years, 6 months ago (Feb. 15, 2013)

Funders 0

None

BibTeX

@article{Yamaguchi_2012, title={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 calculations}, volume={113}, ISSN={1097-461X}, url={http://dx.doi.org/10.1002/qua.24117}, DOI={10.1002/qua.24117}, number={4}, journal={International Journal of Quantum Chemistry}, publisher={Wiley}, author={Yamaguchi, K. and Isobe, H. and Yamanaka, S. and Saito, T. and Kanda, K. and Shoji, M. and Umena, Y. and Kawakami, K. and Shen, J.‐R. and Kamiya, N. and Okumura, M.}, year={2012}, month=apr, pages={525–541} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        7,
        9
      ]
    ],
    "date-time": "2025-07-09T23:01:42Z",
    "timestamp": 1752102102806
  },
  "reference-count": 63,
  "publisher": "Wiley",
  "issue": "4",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2012,
            4,
            13
          ]
        ],
        "date-time": "2012-04-13T00:00:00Z",
        "timestamp": 1334275200000
      },
      "content-version": "vor",
      "delay-in-days": 0,
      "URL": "http://onlinelibrary.wiley.com/termsAndConditions#vor"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2013,
        2,
        15
      ]
    ]
  },
  "abstract": "<jats:title>Abstract</jats:title><jats:p>Several hybrid DFT methods were applied to full geometry optimizations of the CaMn<jats:sub>4</jats:sub>O<jats:sub>4</jats:sub>X(H<jats:sub>2</jats:sub>O)<jats:sub>4</jats:sub> (X\uf8feOH<jats:sup>1\u2212</jats:sup> (1) or O<jats:sup>2\u2212</jats:sup> (2)) cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) to elucidate Mn\u2010Mn, Mn\u2010Ca, and Mn\u2010O distances on a theoretical ground. The computed Mn\u2010Mn distances were compared with previous (London and Berlin) X\u2010ray diffraction (XRD), and Berkeley and Berlin EXAFS results, together with the recent high\u2010resolution XRD structure by Umena and coworkers. Present computational results by the hybrid DFT methods have elucidated several differences among these accumulated results. These DFT results led us to reassign the Mn\u2010Mn and Mn\u2010Ca distances by the EXAFS experiments, which became consistent with the results obtained by the high\u2010resolution XRD structure. A characteristic feature revealed via the optimized Mn\u2010O distances was that the degree of symmetry breaking of the Mn<jats:sub>1</jats:sub>\u2010O(57)\u2010Mn<jats:sub>4</jats:sub> bond is not so remarkable under the UBHandHLYP approximation but it can be large by other hybrid DFT methods. The computational results for 2 indicated reduction of the Mn<jats:sub>3</jats:sub>\u2010Mn<jats:sub>4</jats:sub> distance with the deprotonation of the bridging oxo group. The hybrid DFT results for 1 are not inconsistent with an experimental proposal based on the new XRD structure, namely a protonated \u03bc<jats:sub>3</jats:sub>\u2010oxygen at the internal O(57) site of the cluster in the S<jats:sub>1</jats:sub> state. On the other hand, the reduction of Mn ions (not degradation of whole cluster structure) by the X\u2010ray irradiation still remains an important issue for refinements of the XRD structure. The computational results are discussed in relation to those of the electron spin echo envelope modulation (ESEEM) and possible pathways for water splitting reaction. Implications of the present DFT structures are discussed in relation to the previous DFT and related computational results, together with recent XRD results for cubane\u2010like model clusters for OEC of PSII. \u00a9 2012 Wiley Periodicals, Inc.</jats:p>",
  "DOI": "10.1002/qua.24117",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2012,
        4,
        13
      ]
    ],
    "date-time": "2012-04-13T07:40:44Z",
    "timestamp": 1334302844000
  },
  "page": "525-541",
  "source": "Crossref",
  "is-referenced-by-count": 62,
  "title": "Full geometry optimizations of the mixed\u2010valence CaMn<sub>4</sub>O<sub>4</sub>X(H<sub>2</sub>O)<sub>4</sub> (X=OH or O) cluster in OEC of PS II: Degree of symmetry breaking of the labile Mn\u2010X\u2010Mn bond revealed by several hybrid DFT calculations",
  "prefix": "10.1002",
  "volume": "113",
  "author": [
    {
      "given": "K.",
      "family": "Yamaguchi",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "H.",
      "family": "Isobe",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "S.",
      "family": "Yamanaka",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "T.",
      "family": "Saito",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "K.",
      "family": "Kanda",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "M.",
      "family": "Shoji",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Y.",
      "family": "Umena",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "K.",
      "family": "Kawakami",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "J.\u2010R.",
      "family": "Shen",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "N.",
      "family": "Kamiya",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "M.",
      "family": "Okumura",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "311",
  "published-online": {
    "date-parts": [
      [
        2012,
        4,
        13
      ]
    ]
  },
  "reference": [
    {
      "key": "e_1_2_8_1_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/cr950052k"
    },
    {
      "key": "e_1_2_8_2_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0005-2728(00)00217-6"
    },
    {
      "key": "e_1_2_8_3_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0005-2728(00)00230-9"
    },
    {
      "key": "e_1_2_8_4_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi026569p"
    },
    {
      "key": "e_1_2_8_5_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1039/B408146C"
    },
    {
      "key": "e_1_2_8_6_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/ja054873a"
    },
    {
      "key": "e_1_2_8_7_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.1128186"
    },
    {
      "key": "e_1_2_8_8_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1098/rstb.2007.2220"
    },
    {
      "key": "e_1_2_8_9_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.bbabio.2011.07.004"
    },
    {
      "key": "e_1_2_8_10_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.0135651100"
    },
    {
      "key": "e_1_2_8_11_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.1093087"
    },
    {
      "key": "e_1_2_8_12_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1039/B406989G"
    },
    {
      "key": "e_1_2_8_13_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature04224"
    },
    {
      "key": "e_1_2_8_14_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.bbabio.2007.02.013"
    },
    {
      "key": "e_1_2_8_15_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nsmb.1559"
    },
    {
      "key": "e_1_2_8_16_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.0812797106"
    },
    {
      "key": "e_1_2_8_17_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/ja011621a"
    },
    {
      "key": "e_1_2_8_18_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1007/s00723-009-0051-1"
    },
    {
      "key": "e_1_2_8_19_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1039/b808792j"
    },
    {
      "key": "e_1_2_8_20_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/ja043012j"
    },
    {
      "key": "e_1_2_8_21_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi050411y"
    },
    {
      "key": "e_1_2_8_22_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/ja071487f"
    },
    {
      "key": "e_1_2_8_23_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/ja002104f"
    },
    {
      "key": "e_1_2_8_24_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1098/rstb.2002.1144"
    },
    {
      "key": "e_1_2_8_25_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.bbabio.2003.11.009"
    },
    {
      "key": "e_1_2_8_26_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature09913"
    },
    {
      "key": "e_1_2_8_27_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.jphotobiol.2011.03.017"
    },
    {
      "key": "e_1_2_8_28_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1111/j.1751-1097.1970.tb06017.x"
    },
    {
      "key": "e_1_2_8_29_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.cplett.2011.02.030"
    },
    {
      "key": "e_1_2_8_30_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.cplett.2011.06.021"
    },
    {
      "key": "e_1_2_8_31_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/qua.23218"
    },
    {
      "key": "e_1_2_8_32_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/qua.23261"
    },
    {
      "key": "e_1_2_8_33_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1098/rstb.2007.2214"
    },
    {
      "key": "e_1_2_8_34_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/anie.200906253"
    },
    {
      "key": "e_1_2_8_35_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0009-2614(75)80169-2"
    },
    {
      "key": "e_1_2_8_35_3",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0009-2614(75)85320-6"
    },
    {
      "key": "e_1_2_8_35_4",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0009-2614(79)85043-5"
    },
    {
      "key": "e_1_2_8_36_2",
      "unstructured": "K. Yamaguchi Y. Takahara T. Fueno V. H. Smith H. F. Schaefer K. Morokuma D. Reidel Applied Quantum Chem 155"
    },
    {
      "key": "e_1_2_8_37_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0009-2614(00)00166-4"
    },
    {
      "key": "e_1_2_8_38_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/jp0571877"
    },
    {
      "key": "e_1_2_8_39_2",
      "first-page": "138",
      "volume": "511",
      "author": "Siegbahn P. E. M.",
      "year": "2011",
      "journal-title": "Photochem. Photobiol."
    },
    {
      "key": "e_1_2_8_40_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/cphc.201100475"
    },
    {
      "key": "e_1_2_8_41_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi200681q"
    },
    {
      "key": "e_1_2_8_42_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.jphotobiol.2011.03.002"
    },
    {
      "key": "e_1_2_8_43_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1098/rstb.2007.2208"
    },
    {
      "key": "e_1_2_8_44_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/chem.200700003"
    },
    {
      "key": "e_1_2_8_45_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/chem.200701865"
    },
    {
      "key": "e_1_2_8_46_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.jinorgbio.2006.01.017"
    },
    {
      "key": "e_1_2_8_47_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/ja076130q"
    },
    {
      "key": "e_1_2_8_48_2",
      "volume-title": "Gaussian 09, Revision B.01",
      "author": "Frisch M. J.",
      "year": "2010"
    },
    {
      "key": "e_1_2_8_49_2",
      "first-page": "583",
      "volume": "55",
      "author": "Cruickshank D. W.",
      "year": "1999",
      "journal-title": "Acta Crystallogr."
    },
    {
      "key": "e_1_2_8_50_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/35055589"
    },
    {
      "key": "e_1_2_8_51_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/ja110145v"
    },
    {
      "key": "e_1_2_8_52_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/qua.20286"
    },
    {
      "key": "e_1_2_8_53_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/qua.21201"
    },
    {
      "key": "e_1_2_8_54_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/qua.22914"
    },
    {
      "key": "e_1_2_8_55_2",
      "unstructured": "1990 Elsevier Amsterdam K. Yamaguchi R. Carbo M. Klobukowski Self\u2010Consistent Field Theory and Applications 727"
    },
    {
      "key": "e_1_2_8_56_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.poly.2011.04.042"
    },
    {
      "key": "e_1_2_8_57_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.1206036"
    },
    {
      "key": "e_1_2_8_58_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi035489y"
    },
    {
      "key": "e_1_2_8_59_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/bi052146m"
    },
    {
      "key": "e_1_2_8_60_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1021/ja2041805"
    },
    {
      "key": "e_1_2_8_61_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0014-5793(92)80092-U"
    }
  ],
  "container-title": "International Journal of Quantum Chemistry",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fqua.24117",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/qua.24117",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2023,
        9,
        12
      ]
    ],
    "date-time": "2023-09-12T14:14:56Z",
    "timestamp": 1694528096000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://onlinelibrary.wiley.com/doi/10.1002/qua.24117"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2012,
        4,
        13
      ]
    ]
  },
  "references-count": 63,
  "journal-issue": {
    "issue": "4",
    "published-print": {
      "date-parts": [
        [
          2013,
          2,
          15
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1002/qua.24117"
  ],
  "URL": "http://dx.doi.org/10.1002/qua.24117",
  "relation": {},
  "ISSN": [
    "0020-7608",
    "1097-461X"
  ],
  "subject": [],
  "container-title-short": "Int J of Quantum Chemistry",
  "published": {
    "date-parts": [
      [
        2012,
        4,
        13
      ]
    ]
  }
}