Handairigaku Techno Research NPO

Toyonaka, Japan

Handairigaku Techno Research NPO

Toyonaka, Japan

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Yamaguchi K.,Handairigaku Techno Research NPO | Yamaguchi K.,Toyota Physical and Chemical Research Institute | Isobe H.,Handairigaku Techno Research NPO | Yamanaka S.,Osaka University | And 8 more authors.
International Journal of Quantum Chemistry | Year: 2013

Several hybrid DFT methods were applied to full geometry optimizations of the CaMn4O4X(H2O)4 (Xï£/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 Mn 1-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-Mn 4 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.


Isobe H.,Handairigaku Techno Research NPO | Isobe H.,Okayama University | Shoji M.,University of Tsukuba | Yamanaka S.,Osaka University | And 6 more authors.
Dalton Transactions | Year: 2012

Full geometry optimizations of several inorganic model clusters, CaMn 4O4XYZ(H2O)2 (X, Y, Z = H 2O, OH- or O2-), by the use of the B3LYP hybrid density functional theory (DFT) have been performed to illuminate plausible molecular structures of the catalytic site for water oxidation in the S 0, S1, S2 and S3 states of the Kok cycle for the oxygen-evolving complex (OEC) of photosystem II (PSII). Optimized geometries obtained by the energy gradient method have revealed the degree of symmetry breaking of the unstable three-center Mna-X-Mnd bond in CaMn4O4XYZ(H2O)2. The right-elongated (R) Mna-X⋯Mnd and left-elongated (L) Mna⋯X-Mnd structures appear to occupy local minima on a double-well potential for several key intermediates in these states. The effects of insertion of one extra water molecule to the vacant coordination site, Mnd (Mna), for R (L) structures have also been examined in detail. The greater stability of the L-type structure over the R-type has been concluded for key intermediates in the S2 and S 3 states. Implications of the present DFT structures are discussed in relation to previous DFT and related results, together with recent X-ray diffraction results for model compounds of cubane-like OEC cluster of PSII. © The Royal Society of Chemistry 2012.


Shoji M.,University of Tsukuba | Isobe H.,Okayama University | Shen J.-R.,Okayama University | Yamaguchi K.,Osaka University | Yamaguchi K.,Handairigaku Techno Research NPO
Physical Chemistry Chemical Physics | Year: 2016

Water oxidation by photosystem II (PSII) converts light energy into chemical energy with the concomitant production of molecular oxygen, both of which are indispensable for sustaining life on Earth. This reaction is catalyzed by an oxygen-evolving complex (OEC) embedded in the huge PSII complex, and its mechanism remains elusive in spite of the extensive studies of the geometric and electronic structures. In order to elucidate the water-splitting mechanism, synthetic approaches have been extensively employed to mimic the native OEC. Very recently, a synthetic complex [Mn4CaO4(ButCOO)8(py)(ButCOOH)2] (1) closely mimicking the structure of the native OEC was obtained. In this study, we extensively examined the geometric, electronic and spin structures of 1 using the density functional theory method. Our results showed that the geometric structure of 1 can be accurately reproduced by theoretical calculations, and revealed many similarities in the ground valence and spin states between 1 and the native OEC. We also revealed two different valence states in the one-electron oxidized state of 1 (corresponding to the S2 state), which lie in the lower and higher ground spin states (S = 1/2 and S = 5/2), respectively. One remarkable difference between 1 and the native OEC is the presence of a non-negligible antiferromagnetic interaction between the Mn1 and Mn4 sites, which slightly influenced their ground spin structures (spin alignments). The major reason causing the difference can be attributed to the short Mn1-O5 and Mn1-Mn4 distances in 1. The introduction of the missing O4 atom and the reorientation of the Ca coordinating ligands improved the Mn1-O5 and Mn1-Mn4 distances comparable to the native OEC. These modifications will therefore be important for the synthesis of further advanced model complexes more closely mimicking the native OEC beyond 1. © 2016 the Owner Societies.


Shoji M.,University of Tsukuba | Isobe H.,Okayama University | Nakajima T.,RIKEN | Yamaguchi K.,Osaka University | Yamaguchi K.,Handairigaku Techno Research NPO
Chemical Physics Letters | Year: 2016

Large-scale QM/MM calculations including hydrogen-bonding networks in the oxygen evolving complex (OEC) of photosystem II (PSII) were performed to elucidate the geometric structures of the CaMn4O5 cluster in the key catalytic states (Si (i = 0–3)). The optimized Mn–Mn, Ca–Mn and Mn–O distances by the large-scale QM/MM starting from the high-resolution XRD structure were consistent with those of the EXAFS experiments in the dark stable S1 state by the Berkeley and Berlin groups. The optimized geometrical parameters for other Si (i = 0, 2, 3) states were also consistent with those of EXAFS, indicating the importance of the large-scale QM/MM calculations for the PSII-OEC. © 2016 Elsevier B.V.


Shoji M.,University of Tsukuba | Isobe H.,Okayama University | Nakajima T.,RIKEN | Yamaguchi K.,Osaka University | Yamaguchi K.,Handairigaku Techno Research NPO
Chemical Physics Letters | Year: 2015

Full geometry optimizations of ([CaMn4O4(CH3COO)8(py)(CH3COOH)2], (py: pyridine) (1)) were performed at the UB3LYP theoretical level. 1 is a theoretical model for the synthetic model ([CaMn4O4(ButCOO)8(py)(ButCOOH)2], (But: t-butyl) (2)) which closely mimicks the native oxygen evolving complex (OEC) in photosystem II. It was shown that the X-ray structure of 2 was well reproduced by 1 in the (Mn1(III), Mn2(IV), Mn3(IV), Mn4(III)) valence state with the unprotonated O5 (O5 = O2-), and two different valence states were obtained in the one-electron oxidized state. Importance of the Jahn-Teller effect of the Mn(III) site for the structural deformations was presented. © 2015 Elsevier B.V. All rights reserved.


Shoji M.,University of Tsukuba | Isobe H.,Okayama University | Yamaguchi K.,Osaka University | Yamaguchi K.,Handairigaku Techno Research NPO
Chemical Physics Letters | Year: 2015

Abstract Catalytic reactions of the proton and electron transfers occurring at the oxygen-evolving complex (OEC) of photosystem II during the S2-S3 transition were investigated by the quantum mechanics/molecular mechanics (QM/MM) methodology. Two favorable reaction pathways were elucidated. Both reactions start by moving the Ca-bound water (W3) to the vacant Mn(III) coordination at the left-opened (L) or right-opened (R) form. The former reaction pathway, in which W3 coordinates to the Mn4 at the S2-L form, has lower activation barriers than the latter. Thus, easier proton transfers from W3 to the Tyr161 phenol anion can be performed. © 2015 Elsevier B.V.


Full geometry optimizations of several inorganic model clusters, CaMn(4)O(4)XYZ(H(2)O)(2) (X, Y, Z = H(2)O, OH(-) or O(2-)), by the use of the B3LYP hybrid density functional theory (DFT) have been performed to illuminate plausible molecular structures of the catalytic site for water oxidation in the S(0), S(1), S(2) and S(3) states of the Kok cycle for the oxygen-evolving complex (OEC) of photosystem II (PSII). Optimized geometries obtained by the energy gradient method have revealed the degree of symmetry breaking of the unstable three-center Mn(a)-X-Mn(d) bond in CaMn(4)O(4)XYZ(H(2)O)(2). The right-elongated (R) Mn(a)-XMn(d) and left-elongated (L) Mn(a)X-Mn(d) structures appear to occupy local minima on a double-well potential for several key intermediates in these states. The effects of insertion of one extra water molecule to the vacant coordination site, Mn(d) (Mn(a)), for R (L) structures have also been examined in detail. The greater stability of the L-type structure over the R-type has been concluded for key intermediates in the S(2) and S(3) states. Implications of the present DFT structures are discussed in relation to previous DFT and related results, together with recent X-ray diffraction results for model compounds of cubane-like OEC cluster of PSII.

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