掲載種別：研究論文（学術雑誌）   出版者・発行元：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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担当区分：筆頭著者,　責任著者   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/acs.jctc.8b01055

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：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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担当区分：筆頭著者,　責任著者   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/acs.inorgchem.5b02471

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担当区分：筆頭著者,　責任著者   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/acs.jpcb.5b05740

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：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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担当区分：筆頭著者,　責任著者   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/ic402340d

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担当区分：筆頭著者   掲載種別：研究論文（学術雑誌）   出版者・発行元：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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記述言語：英語   出版者・発行元：一般社団法人 日本生物物理学会  

DOI： 10.2142/biophys.54.S237_5

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記述言語：英語   掲載種別：論文集(書籍)内論文   出版者・発行元：Springer  

Broken-symmetry (BS) UB3LYP calculations have been performed for the CaMn4O5 cluster (1) in the oxygen-evolving complex (OEC) of the PSII system refined to 1.9 Å resolution by Umena, Kawakami, Kamiya, Shen to elucidate its electronic structure that is crucial for consideration of possible mechanisms of photosynthetic water splitting. Our UB3LYP computations have elucidated the position of protonated oxygen of the CaMn(III)2Mn(IV)2O4(OH) cluster (1a) at the S1 stage of Kok cycle. Starting from the newly elucidated S1 structure of 1a, we have calculated the electronic structure of proton and electron released CaMn(IV)4O5 cluster (1b) that mimics the S4 stage of the cycle. The LUMOs of 1b are depicted for pictorial understanding of electrophilic oxygen sites that are responsible for nucleophilic attack of hydroxide anion (or water) for the O-O bond formation. Implications of present computational results are discussed in relation to possible mechanisms of photosynthetic water splitting.

DOI： 10.1007/978-3-642-32034-7_52

Scopus

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：National Academy of Sciences  

The nature of chemical bonds of ruthenium(Ru)-quinine(Q) complexes, mononuclear [Ru(trpy)(3, 5-t-Bu(2)Q)(OH(2))](ClO(4))(2) (trpy = 2, 2('):6('), 2('')-terpyridine, 3, 5-di-tert-butyl-1, 2-benzoquinone) (1), and binuclear [Ru(2)(btpyan)(3, 6-di-Bu(2)Q)(2)(OH(2))](2+) (btpyan = 1, 8-bis(2, 2('):6('), 2('')-terpyrid-4(')-yl)anthracene, 3, 6-t-Bu(2)Q = 3, 6-di-tert-butyl-1, 2-benzoquinone) (2), has been investigated by broken-symmetry (BS) hybrid density functional (DFT) methods. BS DFT computations for the Ru complexes have elucidated that the closed-shell structure (2b) Ru(II)-Q complex is less stable than the open-shell structure (2bb) consisting of Ru(III) and semiquinone (SQ) radical fragments. These computations have also elucidated eight different electronic and spin structures of tetraradical intermediates that may be generated in the course of water splitting reaction. The Heisenberg spin Hamiltonian model for these species has been derived to elucidate six different effective exchange interactions (J) for four spin systems. Six J values have been determined using total energies of the eight (or seven) BS solutions for different spin configurations. The natural orbital analyses of these BS DFT solutions have also been performed in order to obtain natural orbitals and their occupation numbers, which are useful for the lucid understanding of the nature of chemical bonds of the Ru complexes. Implications of the computational results are discussed in relation to the proposed reaction mechanisms of water splitting reaction in artificial photosynthesis systems and the similarity between artificial and native water splitting systems.

DOI： 10.1073/pnas.1120705109

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CiNii Books

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担当区分：筆頭著者,　責任著者   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/jp211184y

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担当区分：筆頭著者,　責任著者   掲載種別：研究論文（学術雑誌）   出版者・発行元：Royal Society of Chemistry (RSC)  

DOI： 10.1039/c2dt31420g

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：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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担当区分：筆頭著者,　責任著者   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Chemical Society (ACS)  

DOI： 10.1021/jp206004y

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記述言語：英語   出版者・発行元：一般社団法人 日本生物物理学会  

DOI： 10.2142/biophys.51.S118_4

CiNii Article

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1021/jp905401b

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記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）   出版者・発行元：WORLD SCIENTIFIC PUBL CO PTE LTD  

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

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記述言語：英語   出版者・発行元：JOHN WILEY & SONS LTD  

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