Publishing type：Research paper (scientific journal)   Publisher：American Association for the Advancement of Science (AAAS)  

Inspecting S states in photosynthesis

Oxygenic photosynthesis uses a Mn ₄ CaO ₅ cluster in the oxygen-evolving complex to extract electrons from water and produce dioxygen. Visualizing each of the chemical states in this process, S ₀ to S ₄ , and assigning chemical identities and mechanisms on the basis of structures has been a challenge addressed recently by work at x-ray free-electron lasers. Suga et al. used serial crystallography at cryogenic temperatures to trap and determine the structures of several stable states during photosystem II water oxidation (see the Perspective by Britt and Marchiori). Changes around the water cluster already happen in the S ₂ state and set the stage for water insertion that occurs during transition to the S ₃ state. A short 1.9-angstrom distance between the two oxygen atoms in the S ₃ state is consistent with theoretical studies supporting an oxyl/oxo mechanism for oxygen-oxygen coupling.

Science , this issue p. 334 ; see also p. 305

DOI： 10.1126/science.aax6998

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jctc.8b01055

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ROYAL SOC CHEMISTRY  

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 S-2 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.

DOI： 10.1039/c5cp07226c

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PubMed

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.inorgchem.5b02471

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpcb.5b05740

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

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 angstrom resolution. Computational results by the QM/MM calculations have elucidated the hydrogen-bonding O center dot center dot center dot O(N) and O center dot center dot center dot H distances and O(N)-H center dot center dot center dot O angles in PRP, together with the Cl-O(N) and Cl center dot center dot center dot H distances and O(N)-H center dot center dot center dot 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.

DOI： 10.1080/00268976.2014.960021

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/ic402340d

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Authorship：Lead author   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

<p>Broken-symmetry UB3LYP calculations have elucidated structural symmetry-breaking in the S₁ and S₃ states of the oxygen evolution complex (OEC) of photosystem II (PSII), providing the right (RO)- and left (LO)-opened structures.</p>

DOI： 10.1039/c4cp00282b

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.54.S237_5

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Proceedings of the National Academy of Sciences  

DOI： 10.1073/pnas.1120705109

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CiNii Books

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/jp211184y

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

DOI： 10.1039/c2dt31420g

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER  

First principle calculations of the effective exchange integrals (J) in the Heisenberg model for diradical species are presented for both symmetry-adapted multi-reference (MR) and single-reference broken-symmetry (BS) methods. The Mukherjee-type state-specific MR coupled cluster singles and doubles (MkCCSD) method with several different reference orbitals including BS natural orbitals is used to calculate the singlet-triplet energy gaps (S-T energy gap or 2J) and diradical characters for the antiaromatic molecules [a cyclopropenyl anion (CPA), b cyclobutadiene (CBD), and c cyclopentadienyl cation (CPC)], the cyclobutadiene derivatives with polar substitutents [d aminocyclobutadiene (ACBD), e formylcyclobutadiene (FCBD), and f 1-amino-2-formyl-cyclobutadiene (AFCBD)] and finally the cyclobutadine derivatives with radical substitutents [g 1,2-bis(methylene)cyclobutadiene (1,2-BMCBD) and h 1,3-bis(methylene)cyclobutadiene (1,3-BMCBD)]. For the BS methods, the spin-unrestricted Hartree-Fock based CCSD (UHF-CCSD), the CCD with the spin-unrestricted Brueckner determinant (UBD), and BS density functional theory (UDFT) computations are performed. Comparison between MkCCSD and the UHF-CCSD results indicates that spin-contamination of UHF-CCSD solutions still remains. In comparison with UHF-CCSD, the UBD results show that spin-contamination involved in BS solutions is greatly suppressed. To eliminate the spin contamination, an approximate spin-projection (AP) scheme is applied to the BS solutions. The AP procedure with the use of the expectation value of the total-spin operator corresponding to UHF-CCSD and UBD results yields good agreement with the MkCCSD results. As for the AP correction of the UDFT methods, three different computational schemes for predicting the expectation value of the total-spin operator are examined. Systematic comparisons between these methods are presented for the S-T energy gaps (2J). Implications of the present computational results have been discussed in relation to the design of magnetic oligomers and polymers.

DOI： 10.1007/s00214-011-0941-9

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

DOI： 10.1021/jp206004y

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Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

DOI： 10.2142/biophys.51.S118_4

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Thermal decomposition of peroxidized coelenterazines with and without external perturbations has been studied theoretically using the hybrid density functional theory (B3LYP) and the Coulomb-attenuating method (CAM). Possible roles of a hydrogen-bonding interface constituted by amino acid residues in the coelenterazine-biding site of aequorin are addressed by using simple model clusters with a polarizable continuum model to grasp some important aspects that may affect the electronic mechanism operating within the photoprotein. Calculations have revealed that the electronic property and stability of the peroxide are greatly affected by its protonation state and/or environmental effects, such as a polarizing medium and specific (localized) short-range electrostatic interactions, which may be critical for the bioluminescence activity. Theory highlights two mechanisms by which the neutral species can be activated, which otherwise decomposes by a homolytic O-O dissociation with a high barrier. In the first mechanism, the Tyr82-His 16-Trp86 triad motif facilitates the deprotonation process of the phenolic OH group at the C-6 position of the coelenterazine and thereby makes it a sufficiently good electron donor to activate the O-O bond. In the second mechanism, intramolecular charge transfer is accomplished within the neutral peroxide by a proton delivery mediated via another triad motif, Tyr 184-His 169-Trp 173, without the activation of the Substrate itself. The combination of the first and second mechanisms leads to complete electron transfer for the formation of a radical pair as a local intermediate stabilized by the nearby triad motifs.

DOI： 10.1021/jp905401b

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：WORLD SCIENTIFIC PUBL CO PTE LTD  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JOHN WILEY & SONS LTD  

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Language：English   Publisher：JOHN WILEY & SONS LTD  

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Event date： 2017.3.15

Language：Japanese   Presentation type：Oral presentation (general)  

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Event date： 2016.8.8 - 2016.8.12

Language：English   Presentation type：Poster presentation  

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Event date： 2013.8.11 - 2013.8.16

Language：English   Presentation type：Poster presentation  

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Event date： 2013.6.17 - 2013.6.18

Language：English   Presentation type：Poster presentation  

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Event date： 2013.3.21 - 2013.3.23

Language：Japanese   Presentation type：Oral presentation (general)  

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Event date： 2012.10.23

Language：English   Presentation type：Poster presentation  

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