TY - JOUR
T1 - Possibility of the right-opened Mn-oxo intermediate (R-oxo(4444)) among all nine intermediates in the S3 state of the oxygen-evolving complex of photosystem II revealed by large-scale QM/MM calculations
AU - Shoji, Mitsuo
AU - Isobe, Hiroshi
AU - Miyagawa, Koichi
AU - Yamaguchi, Kizashi
N1 - Funding Information:
One of the author (K.Y) thanks Prof. J.-R. Shen for through discussions on the SFX result for the S
Funding Information:
One of the author (K.Y) thanks Prof. J.-R. Shen for through discussions on the SFX result for the S 3 state and the (3443) valence state of the Mn peroxide [40] before the publication of his nature paper [38] and for helpful discussions on the present QM/MM results. He also thanks Dr. V. Yachandra for through discussions on the SFX result [37] and for the S 3 state. He thanks Prof. N. Kamiya for helpful discussions on the Fourier difference maps of the SFX [38] , and possible experimental uncertainty and X-ray damages of the XRD and SFX results on OEC of PSII. This work has been supported by MEXT KAKENHI Grant Nos. JP18H05154, JP18H05167, JP17H06434 (MS, HI, KY) and JSPS KAKENHI Grant No. JP17H04866. Numerical calculations were carried out under the supports from (1) the “Multidisciplinary Cooperative Research Program” at the Center for Computational Sciences ( CCS ) in University of Tsukuba , (2) Research Center for Computational Science, Okazaki, Japan, and (3) HPCI systems (Project ID: hp180163 and hp180154).
Publisher Copyright:
© 2018 Elsevier B.V.
PY - 2019/2/1
Y1 - 2019/2/1
N2 - Large-scale quantum mechanics/molecular mechanics (QM/MM) calculations were performed to elucidate the possible intermediates in the S3 state of the oxygen-evolving complex of photosystem II. We have investigated nine S3 candidates in the R-/L-opened Mn-hydroxide, Mn-oxo, Mn-peroxide and Mn-superoxide intermediate states, and their optimized CaMn4O6 structures and the Mn valence states were compared to the experimental results revealed by recent serial femtosecond crystallography (SFX) and X-ray emission spectroscopy (XES). By using the Jahn-Teller (JT) deformation formulae, the Mn4-O(5) and O(5)-O(6) distances were estimated from the Mn4-Mn3 distances. Among all the calculated S3 intermediates, not only the right-opened hydroxo intermediate (R-hydroxo), but also the right-opened Mn-oxo intermediate (R-oxo(4444)) were found to be plausible based on the calculated CaMn4O6 structure and the Mn valence state (4444).
AB - Large-scale quantum mechanics/molecular mechanics (QM/MM) calculations were performed to elucidate the possible intermediates in the S3 state of the oxygen-evolving complex of photosystem II. We have investigated nine S3 candidates in the R-/L-opened Mn-hydroxide, Mn-oxo, Mn-peroxide and Mn-superoxide intermediate states, and their optimized CaMn4O6 structures and the Mn valence states were compared to the experimental results revealed by recent serial femtosecond crystallography (SFX) and X-ray emission spectroscopy (XES). By using the Jahn-Teller (JT) deformation formulae, the Mn4-O(5) and O(5)-O(6) distances were estimated from the Mn4-Mn3 distances. Among all the calculated S3 intermediates, not only the right-opened hydroxo intermediate (R-hydroxo), but also the right-opened Mn-oxo intermediate (R-oxo(4444)) were found to be plausible based on the calculated CaMn4O6 structure and the Mn valence state (4444).
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U2 - 10.1016/j.chemphys.2018.11.003
DO - 10.1016/j.chemphys.2018.11.003
M3 - Article
AN - SCOPUS:85058009076
VL - 518
SP - 81
EP - 90
JO - Chemical Physics
JF - Chemical Physics
SN - 0301-0104
ER -