Time filter

Source Type

Yamaguchi K.,Osaka University | Yamaguchi K.,Handairigaku Techno Research | Shoji M.,University of Tsukuba | Isobe H.,Okayama University | And 4 more authors.
Molecular Physics | Year: 2017

Atmospheric oxygenation and evolution of aerobic life on our earth are a result of water oxidation by oxygenic photosynthesis in photosystem II (PSII) of plants, algae and cyanobacteria. The water oxidation in the oxygen-evolving complex (OEC) in PSII is expected to proceed through five oxidation states, known as the Si (i = 0, 1, 2, 3 and 4) states in the Kok cycle, with the S1 being the most stable state in the dark. The OEC in PSII involves the active catalytic site made of four Mn ions and one Ca ion, namely the CaMn4O5 cluster. Past decades, molecular structures of the CaMn4O5 cluster in OEC in PSII have been investigated by the extended X-ray absorption fine structure (EXAFS). The magneto-structural correlations were extensively investigated by electron paramagnetic resonance (EPR) spectroscopy. Recently, Kamiya and Shen groups made great breakthrough for determination of the S1 structure of OEC of PSII by the X-ray diffraction (XRD) and X-ray free-electron laser (XFEL) experiments, providing structural foundations that are crucial for theoretical investigations of the CaMn4O5 cluster. Large-scale quantum mechanics/molecular mechanics calculations starting from the XRD structures elucidated geometrical, electronic and spin structures of the CaMn4O5 cluster, indicating an important role of the Jahn–Teller (JT) effect of Mn(III) ions. This paper presents theoretical formulas for estimation of the JT deformations of the CaMn4O5 cluster in OEC of PSII. Scope and applicability of the formulas are examined in relation to several different structures of the CaMn4O5 cluster proposed by XRD, XFEL, EXAFS and other experiments. Implications of the computational results are discussed for further refinements of geometrical parameters of the CaMn4O5 cluster. © 2017 Informa UK Limited, trading as Taylor & Francis Group


Shoji M.,University of Tsukuba | Isobe H.,Okayama University | Yamanaka S.,Osaka University | Umena Y.,Osaka City University | And 8 more authors.
Advances in Quantum Chemistry | Year: 2015

In order to confirm theoretical system models of photosystem II (PSII), quantum mechanics (QM)/molecular mechanics (MM) calculations using a large-scale QM model (QM Model V) have been performed to elucidate hydrogen bonding networks and proton wires for proton release pathways (PRPs) of water oxidation reaction in the oxygen-evolving complex (OEC) of PSII. Full geometry optimizations 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 on PSII refined to 1.9Å resolution. The optimized MnMn and CaMn distances by large-scale QM/MM are consistent with the EXAFS results, removing out the discrepancy between the refined XRD and EXAFS. Computational results from QM/MM calculations have demonstrated the labile nature of the MnaO(5)Mnd bond of the CaMn4O5 cluster in the OEC of PSII which allows left (L)-opened, quasi-central (CQ)-, and right (R)-opened structures. This confirms the feasibility of the left- and right-hand scenarios for water oxidation in the OEC of PSII that are dependent on the hydrogen bonding networks. The QM/MM computations have elucidated the networks structures: hydrogen bonding O. . .O(N) and O. . .H distances and O(N)H. . .O angles in PRP, together with the ClO(N) and Cl. . .H distances and O(N)H. . .Cl angles for chloride anions. The obtained hydrogen bonding networks are fully consistent with the results from XRD and available experiments such as EXAFS, showing the reliability of our theoretical system model that is crucial for investigations of functions of PSII such as water oxidation. The QM/MM computations have elucidated possible roles of chloride anions in OEC of PSII for proton transfers. The QM/MM computational results have provided useful information for the understanding and explanation of several experimental results obtained with mutants of the OEC of PSII. The possible implications of the present results are discussed in relation to our theoretical system models of PSII, strong or weak perturbations of the system structures by mutations, damage-free X-ray free-electron laser structure of PSII, and bioinspired working hypotheses for the development of artificial water oxidation systems which use 3d transition metal complexes. © 2015 Elsevier Inc.


Shoji M.,University of Tsukuba | Isobe H.,Okayama University | Yamanaka S.,Osaka University | Umena Y.,Osaka City University | And 5 more authors.
Catalysis Science and Technology | Year: 2013

Quantum mechanical (QM) and QM/molecular mechanics (MM) calculations of three different cluster models have been performed to shed light on hydrogen bonding networks and proton wires for proton release pathways (PRP) of water oxidation reactions in the oxygen evolving complex (OEC) of photosystem II (PSII). Positions of all the hydrogen atoms in an extended QM Model III including the second coordination sphere for the active-site CaMn 4O5 complex of OEC of PSII have been optimized assuming the geometry of heavy atoms determined by the recent high-resolution X-ray diffraction (XRD) experiment of PSII refined to 1.9 Å resolution. Full geometry optimizations of the first coordination sphere model (QM Model I) embedded in the Model III and QM (QM Model I plus seven water molecules, namely QM Model II)/MM models, together with full QM Model III, have also been conducted to elucidate confinement effects for geometrical parameters of the CaMn4O5 cluster by proteins. Computational results by these methods have elucidated the O⋯O(N), O⋯H distances and O(N)-H⋯O angles for hydrogen bonds in proton release paths (PRP) I and II that construct a proton wire from Asp61 toward His190. The hydrogen-bonding structures revealed have also been examined in relation to the possibilities of protonation of bridge oxygen dianions within the CaMn4O5 cluster. The optimized inter-atomic distances by QM Models I and III, together with QM(Model II)/MM, have elucidated the elongation of the Mn-Mn distances with hydrogen bonds and variations of the Mnd-O(5) length with confinement effects by protein. Implications of the computational results are discussed in relation to the available EXAFS experiments, and internal, semi-internal and external reductions of Mn ions and long Mn-Mn distances of the high-resolution (SP8) XRD, and rational design of artificial catalysts for water oxidation that are current topics in the field of OEC of PSII. © 2013 The Royal Society of Chemistry.


Shoji M.,University of Tsukuba | Isobe H.,Okayama University | Yamanaka S.,Osaka University | Umena Y.,Osaka City University | And 8 more authors.
Molecular Physics | Year: 2015

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. © 2014 Taylor & Francis.


Shoji M.,University of Tsukuba | Isobe H.,Okayama University | Yamanaka S.,Osaka University | Suga M.,Okayama University | And 4 more authors.
Chemical Physics Letters | Year: 2015

Several key concepts and geometrical rules for the Mn-Mn and Mn-O distances of the CaMn4O5 cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) by previous and present theoretical calculations were examined for a clear understanding of the damage-free S1 structure revealed by X-ray free electron laser (XFEL). A simple equation to estimate the Mna-Mnb distance in relation to the Mna-O(5) distance was derived taking into consideration the Jahn-Teller (JT) effects for Mn centers, indicating that the XFEL structure is regarded as a slightly right-elongated quasi-central structure in contradiction to a right-opened structure proposed by the EXAFS measurements. © 2015 Elsevier B.V. All rights reserved.


Yamaguchi K.,Osaka University | Yamaguchi K.,Handairigaku Techno Research | Yamanaka S.,Osaka University | Shoji M.,University of Tsukuba | And 5 more authors.
Molecular Physics | Year: 2014

Spin polarisation effects of labile manganese-oxygen bonds in the X-ray diffraction structure of the oxygen-evolving complex (OEC) of photosystem II (PSII) at 1.9 Å resolution have been investigated by the UB3LYP computations on the basis of three different theoretical models with and without hydrogen bonds: quantum-mechanical (QM) Model I, QM(Model II)/MM and QM Model III. The spin densities on the manganese and oxygen atoms of the CaMn 4O5 cluster revealed by these computations have elucidated internal, semi-internal and external reductions of high-valent manganese ions in the CaMn4O5 cluster in OEC of PSII. The internal reduction of Mn(IV) ions by the back charge transfer from oxygen dianions is remarkable in the small QM Model I, whereas it is significantly reduced in the case of more realistic QM Model III including hydrogen bonding stabilisations of oxygen dianions. However, semi-internal reduction of the CaMn4O 5 cluster with remote amino acid residues such as Asp61 anion occurs even in QM Model III, indicating the necessity of large QM parts for redox-active systems such as OEC of PSII. The computational results have clearly demonstrated important roles of confinement effects of the CaMn 4O5 cluster with labile Mn-O bonds with protein. These computational results have been applied to molecular design of artificial robust catalysts for water oxidation by use of sunlight. © 2013 Taylor & Francis.


Shoji M.,University of Tsukuba | Isobe H.,Okayama University | Yamanaka S.,Osaka University | Suga M.,Okayama University | And 4 more authors.
Chemical Physics Letters | Year: 2015

The structure of the oxygen evolving complex (OEC) of photosystem II (PSII) was recently analyzed by crystallography at 1.95 Å resolution using X-ray free electron laser (XFEL), but the positions of hydrogen atoms were not determined. We have examined the XFEL structure theoretically under the assumption of four protonation cases. The spin densities obtained by the high-spin UB3LYP revealed that a partial internal reduction of the high-valent Mn ions in the CaMn4O4X(H2O)3Y cluster occurs for the O(5)(=X) = O2- case, entailing its protonation (X = OH-) in the XFEL structure. © 2015 Elsevier B.V. All rights reserved.

Loading Handairigaku Techno Research collaborators
Loading Handairigaku Techno Research collaborators