Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn                         4                         O                         X                          (X = 5, 6) cluster in the Kok cycle S                         i                          (i = 0–3) of oxygen evolving complex of photosystem II

Kizashi Yamaguchi; Shusuke Yamanaka; Hiroshi Isobe; Mitsuo Shoji; Kouichi Miyagawa; Takahito Nakajima; Takashi Kawakami; Mitsutaka Okumura

doi:10.1111/ppl.12960

Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn ₄ O _X (X = 5, 6) cluster in the Kok cycle S _i (i = 0–3) of oxygen evolving complex of photosystem II

Kizashi Yamaguchi, Shusuke Yamanaka, Hiroshi Isobe, Mitsuo Shoji, Kouichi Miyagawa, Takahito Nakajima, Takashi Kawakami, Mitsutaka Okumura

Research Institute for Interdisciplinary Science

Research output: Contribution to journal › Article

4 Citations (Scopus)

Abstract

The optimized geometries of the CaMn ₄ O _X (X = 5, 6) cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) by large-scale quantum mechanics (QM) and molecular mechanics (MM) calculations are compared with recent serial femtosecond crystallography (SFX) results for the S _i (i = 0–3) states. The valence states of four Mn ions by the QM/MM calculations are also examined in relation to the experimental results by the X-ray emission spectroscopy (XES) for the S _i intermediates. Geometrical and valence structures of right-opened Mn-hydroxide, Mn-oxo and Mn-peroxide intermediates in the S ₃ state are investigated in detail in relation to recent SFX and XES experiments for the S ₃ state. Interplay between theory and experiment indicates that the Mn-oxo intermediate is a new possible candidate for the S ₃ state. Implications of the computational results are discussed in relation to possible mechanisms of the oxygenoxygen bond formation for water oxidation in OEC of PSII.

Original language	English
Pages (from-to)	44-59
Number of pages	16
Journal	Physiologia Plantarum
Volume	166
Issue number	1
DOIs	https://doi.org/10.1111/ppl.12960
Publication status	Published - May 2019

ASJC Scopus subject areas

Physiology
Genetics
Plant Science
Cell Biology

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Yamaguchi, K., Yamanaka, S., Isobe, H., Shoji, M., Miyagawa, K., Nakajima, T., Kawakami, T., & Okumura, M. (2019). Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn ₄ O _X (X = 5, 6) cluster in the Kok cycle S _i (i = 0–3) of oxygen evolving complex of photosystem II Physiologia Plantarum, 166(1), 44-59. https://doi.org/10.1111/ppl.12960

Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn ₄ O _X (X = 5, 6) cluster in the Kok cycle S _i (i = 0–3) of oxygen evolving complex of photosystem II . / Yamaguchi, Kizashi; Yamanaka, Shusuke; Isobe, Hiroshi; Shoji, Mitsuo; Miyagawa, Kouichi; Nakajima, Takahito; Kawakami, Takashi; Okumura, Mitsutaka.

In: Physiologia Plantarum, Vol. 166, No. 1, 05.2019, p. 44-59.

Research output: Contribution to journal › Article

Yamaguchi, K, Yamanaka, S, Isobe, H, Shoji, M, Miyagawa, K, Nakajima, T, Kawakami, T & Okumura, M 2019, ' Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn ₄ O _X (X = 5, 6) cluster in the Kok cycle S _i (i = 0–3) of oxygen evolving complex of photosystem II ', Physiologia Plantarum, vol. 166, no. 1, pp. 44-59. https://doi.org/10.1111/ppl.12960

Yamaguchi K, Yamanaka S, Isobe H, Shoji M, Miyagawa K, Nakajima T et al. Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn ₄ O _X (X = 5, 6) cluster in the Kok cycle S _i (i = 0–3) of oxygen evolving complex of photosystem II Physiologia Plantarum. 2019 May;166(1):44-59. https://doi.org/10.1111/ppl.12960

Yamaguchi, Kizashi ; Yamanaka, Shusuke ; Isobe, Hiroshi ; Shoji, Mitsuo ; Miyagawa, Kouichi ; Nakajima, Takahito ; Kawakami, Takashi ; Okumura, Mitsutaka. / Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn ₄ O _X (X = 5, 6) cluster in the Kok cycle S _i (i = 0–3) of oxygen evolving complex of photosystem II In: Physiologia Plantarum. 2019 ; Vol. 166, No. 1. pp. 44-59.

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title = " Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn 4 O X (X = 5, 6) cluster in the Kok cycle S i (i = 0–3) of oxygen evolving complex of photosystem II ",

abstract = " The optimized geometries of the CaMn 4 O X (X = 5, 6) cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) by large-scale quantum mechanics (QM) and molecular mechanics (MM) calculations are compared with recent serial femtosecond crystallography (SFX) results for the S i (i = 0–3) states. The valence states of four Mn ions by the QM/MM calculations are also examined in relation to the experimental results by the X-ray emission spectroscopy (XES) for the S i intermediates. Geometrical and valence structures of right-opened Mn-hydroxide, Mn-oxo and Mn-peroxide intermediates in the S 3 state are investigated in detail in relation to recent SFX and XES experiments for the S 3 state. Interplay between theory and experiment indicates that the Mn-oxo intermediate is a new possible candidate for the S 3 state. Implications of the computational results are discussed in relation to possible mechanisms of the oxygenoxygen bond formation for water oxidation in OEC of PSII. ",

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AU - Isobe, Hiroshi

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AU - Miyagawa, Kouichi

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