### Abstract

Quantum mechanical (QM)/molecular mechanics (MM) calculations by the use of a large-scale QM model (QM Model V) have been performed to elucidate hydrogen-bonding networks and proton wires for proton release pathways (PRP) of water oxidation reaction in the oxygen evolving complex (OEC) of photosystem II (PSII). Full geometry optimisations of PRP by the QM/MM model have been carried out starting from the geometry of heavy atoms determined by the recent high-resolution X-ray diffraction (XRD) experiment of PSII refined to 1.9 Å resolution. Computational results by the QM/MM calculations have elucidated the hydrogen-bonding O⋯O(N) and O⋯H distances and O(N)-H⋯O angles in PRP, together with the Cl-O(N) and Cl⋯H distances and O(N)-H⋯Cl angles for chloride anions. The optimised hydrogen-bonding networks are well consistent with the XRD results and available experiments such as extended X-ray absorption fine structure, showing the reliability of channel structures of OEC of PSII revealed by the XRD experiment. The QM/MM computations have elucidated possible roles of chloride anions in the OEC of PSII. The QM/MM computational results have provided useful information for understanding and explanation of accumulated mutation experiments of key amino acid residues in the OEC of PSII. Implications of the present results are discussed in relation to three steps for theoretical modelling of water oxidation in the OEC of PSII and bio-inspired working hypotheses for developments of artificial water oxidation systems by use of 3d transition-metal complexes.

Original language | English |
---|---|

Pages (from-to) | 359-384 |

Number of pages | 26 |

Journal | Molecular Physics |

Volume | 113 |

DOIs | |

Publication status | Published - Feb 16 2015 |

### Fingerprint

### Keywords

- CaMn4O5
- hydrogen bonds networks
- mutations
- photosystem II
- QM/MM

### ASJC Scopus subject areas

- Physical and Theoretical Chemistry
- Condensed Matter Physics
- Biophysics
- Molecular Biology

### Cite this

*Molecular Physics*,

*113*, 359-384. https://doi.org/10.1080/00268976.2014.960021

**Theoretical modelling of biomolecular systems I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen evolving complex of photosystem II.** / Shoji, Mitsuo; Isobe, Hiroshi; Yamanaka, Shusuke; Umena, Yasufumi; Kawakami, Keisuke; Kamiya, Nobuo; Shen, Jian-Ren; Nakajima, Takahito; Yamaguchi, Kizashi.

Research output: Contribution to journal › Article

*Molecular Physics*, vol. 113, pp. 359-384. https://doi.org/10.1080/00268976.2014.960021

}

TY - JOUR

T1 - Theoretical modelling of biomolecular systems I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen evolving complex of photosystem II

AU - Shoji, Mitsuo

AU - Isobe, Hiroshi

AU - Yamanaka, Shusuke

AU - Umena, Yasufumi

AU - Kawakami, Keisuke

AU - Kamiya, Nobuo

AU - Shen, Jian-Ren

AU - Nakajima, Takahito

AU - Yamaguchi, Kizashi

PY - 2015/2/16

Y1 - 2015/2/16

N2 - Quantum mechanical (QM)/molecular mechanics (MM) calculations by the use of a large-scale QM model (QM Model V) have been performed to elucidate hydrogen-bonding networks and proton wires for proton release pathways (PRP) of water oxidation reaction in the oxygen evolving complex (OEC) of photosystem II (PSII). Full geometry optimisations of PRP by the QM/MM model have been carried out starting from the geometry of heavy atoms determined by the recent high-resolution X-ray diffraction (XRD) experiment of PSII refined to 1.9 Å resolution. Computational results by the QM/MM calculations have elucidated the hydrogen-bonding O⋯O(N) and O⋯H distances and O(N)-H⋯O angles in PRP, together with the Cl-O(N) and Cl⋯H distances and O(N)-H⋯Cl angles for chloride anions. The optimised hydrogen-bonding networks are well consistent with the XRD results and available experiments such as extended X-ray absorption fine structure, showing the reliability of channel structures of OEC of PSII revealed by the XRD experiment. The QM/MM computations have elucidated possible roles of chloride anions in the OEC of PSII. The QM/MM computational results have provided useful information for understanding and explanation of accumulated mutation experiments of key amino acid residues in the OEC of PSII. Implications of the present results are discussed in relation to three steps for theoretical modelling of water oxidation in the OEC of PSII and bio-inspired working hypotheses for developments of artificial water oxidation systems by use of 3d transition-metal complexes.

AB - Quantum mechanical (QM)/molecular mechanics (MM) calculations by the use of a large-scale QM model (QM Model V) have been performed to elucidate hydrogen-bonding networks and proton wires for proton release pathways (PRP) of water oxidation reaction in the oxygen evolving complex (OEC) of photosystem II (PSII). Full geometry optimisations of PRP by the QM/MM model have been carried out starting from the geometry of heavy atoms determined by the recent high-resolution X-ray diffraction (XRD) experiment of PSII refined to 1.9 Å resolution. Computational results by the QM/MM calculations have elucidated the hydrogen-bonding O⋯O(N) and O⋯H distances and O(N)-H⋯O angles in PRP, together with the Cl-O(N) and Cl⋯H distances and O(N)-H⋯Cl angles for chloride anions. The optimised hydrogen-bonding networks are well consistent with the XRD results and available experiments such as extended X-ray absorption fine structure, showing the reliability of channel structures of OEC of PSII revealed by the XRD experiment. The QM/MM computations have elucidated possible roles of chloride anions in the OEC of PSII. The QM/MM computational results have provided useful information for understanding and explanation of accumulated mutation experiments of key amino acid residues in the OEC of PSII. Implications of the present results are discussed in relation to three steps for theoretical modelling of water oxidation in the OEC of PSII and bio-inspired working hypotheses for developments of artificial water oxidation systems by use of 3d transition-metal complexes.

KW - CaMn4O5

KW - hydrogen bonds networks

KW - mutations

KW - photosystem II

KW - QM/MM

UR - http://www.scopus.com/inward/record.url?scp=84921918331&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84921918331&partnerID=8YFLogxK

U2 - 10.1080/00268976.2014.960021

DO - 10.1080/00268976.2014.960021

M3 - Article

AN - SCOPUS:84921918331

VL - 113

SP - 359

EP - 384

JO - Molecular Physics

JF - Molecular Physics

SN - 0026-8976

ER -