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Yamaguchi K, Miyagawa K, Shoji M, Kawakami T, Isobe H, Yamanaka S, Nakajima T. Theoretical elucidation of the structure, bonding, and reactivity of the CaMn 4O x clusters in the whole Kok cycle for water oxidation embedded in the oxygen evolving center of photosystem II. New molecular and quantum insights into the mechanism of the O-O bond formation. PHOTOSYNTHESIS RESEARCH 2024; 162:291-330. [PMID: 37945776 PMCID: PMC11614991 DOI: 10.1007/s11120-023-01053-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/25/2023] [Indexed: 11/12/2023]
Abstract
This paper reviews our historical developments of broken-symmetry (BS) and beyond BS methods that are applicable for theoretical investigations of metalloenzymes such as OEC in PSII. The BS hybrid DFT (HDFT) calculations starting from high-resolution (HR) XRD structure in the most stable S1 state have been performed to elucidate structure and bonding of whole possible intermediates of the CaMn4Ox cluster (1) in the Si (i = 0 ~ 4) states of the Kok cycle. The large-scale HDFT/MM computations starting from HR XRD have been performed to elucidate biomolecular system structures which are crucial for examination of possible water inlet and proton release pathways for water oxidation in OEC of PSII. DLPNO CCSD(T0) computations have been performed for elucidation of scope and reliability of relative energies among the intermediates by HDFT. These computations combined with EXAFS, XRD, XFEL, and EPR experimental results have elucidated the structure, bonding, and reactivity of the key intermediates, which are indispensable for understanding and explanation of the mechanism of water oxidation in OEC of PSII. Interplay between theory and experiments have elucidated important roles of four degrees of freedom, spin, charge, orbital, and nuclear motion for understanding and explanation of the chemical reactivity of 1 embedded in protein matrix, indicating the participations of the Ca(H2O)n ion and tyrosine(Yz)-O radical as a one-electron acceptor for the O-O bond formation. The Ca-assisted Yz-coupled O-O bond formation mechanisms for water oxidation are consistent with recent XES and very recent time-resolved SFX XFEL and FTIR results.
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Affiliation(s)
- Kizashi Yamaguchi
- Center for Quantum Information and Quantum Biology, Osaka University, Toyonaka, Osaka, 560-0043, Japan.
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan.
- SANKEN, Osaka University, Ibaraki, Osaka, 567-0047, Japan.
| | - Koichi Miyagawa
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Mitsuo Shoji
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takashi Kawakami
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Shusuke Yamanaka
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Takahito Nakajima
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
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Drosou M, Mitsopoulou CA, Pantazis DA. Reconciling Local Coupled Cluster with Multireference Approaches for Transition Metal Spin-State Energetics. J Chem Theory Comput 2022; 18:3538-3548. [PMID: 35582788 PMCID: PMC9202354 DOI: 10.1021/acs.jctc.2c00265] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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Spin-state energetics
of transition metal complexes remain one
of the most challenging targets for electronic structure methods.
Among single-reference wave function approaches, local correlation
approximations to coupled cluster theory, most notably the domain-based
local pair natural orbital (DLPNO) approach, hold the promise of bringing
the accuracy of coupled cluster theory with single, double, and perturbative
triple excitations, CCSD(T), to molecular systems of realistic size
with acceptable computational cost. However, recent studies on spin-state
energetics of iron-containing systems raised doubts about the ability
of the DLPNO approach to adequately and systematically approximate
energetics obtained by the reference-quality complete active space
second-order perturbation theory with coupled-cluster semicore correlation,
CASPT2/CC. Here, we revisit this problem using a diverse set of iron
complexes and examine several aspects of the application of the DLPNO
approach. We show that DLPNO-CCSD(T) can accurately reproduce both
CASPT2/CC and canonical CCSD(T) results if two basic principles are
followed. These include the consistent use of the improved iterative
(T1) versus the semicanonical perturbative triple corrections
and, most importantly, a simple two-point extrapolation to the PNO
space limit. The latter practically eliminates errors arising from
the default truncation of electron-pair correlation spaces and should
be viewed as standard practice in applications of the method to transition
metal spin-state energetics. Our results show that reference-quality
results can be readily achieved with DLPNO-CCSD(T) if these principles
are followed. This is important also in view of the applicability
of the method to larger single-reference systems and multinuclear
clusters, whose treatment of dynamic correlation would be challenging
for multireference-based approaches.
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Affiliation(s)
- Maria Drosou
- Inorganic Chemistry Laboratory, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou 15771, Greece
| | - Christiana A Mitsopoulou
- Inorganic Chemistry Laboratory, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou 15771, Greece
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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Swain A, Sen A, Rajaraman G. Are lanthanide-transition metal direct bonds a route to achieving new generation {3d-4f} SMMs? Dalton Trans 2021; 50:16099-16109. [PMID: 34647556 DOI: 10.1039/d1dt02256c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lanthanide based single-molecule magnets are gaining wide attention due to their potential applications in emerging technologies. One of the main challenges in this area is quenching quantum tunnelling of magnetisation (QTM), which often undercuts the magnetisation reversal barrier. Among the several strategies employed, enhancing exchange coupling has been studied in detail, with large exchanges resulting in stronger quenching of QTM effects. Lanthanides, however, suffer from weak exchanges offered by the deeply buried 4f orbitals and the numerous attempts to enhance the exchange coupling in the {3d-4f} pairs have not exceeded values larger than 30 cm-1. In this work, using a combination of DFT and the ab initio CASSCF/RASSI-SO method, we have explored lanthanide-transition metal direct bonds as a tool to quench QTM effects. In this direction, we have modelled [PyCp2LnMCp(CO)2] (Ln = Gd(III), Dy(III), and Er(III) and M = V(0), Mn(0), Co(0) and Fe(I) and here PyCp2 = [2,6-(CH2C5H3)2C5H3N]2- using [PyCp2DyFeCp(CO)2] as an example as reported by Nippe et al. (C. P. Burns, X. Yang, J. D. Wofford, N. S. Bhuvanesh, M. B. Hall and M. Nippe, Angew. Chem., Int. Ed. 2018, 57, 8144). Bonding analysis reveals a dative Ln-TM bond with a donation of π(V/Mndxy-π*CO) to 5dz2 (Gd) in the case of Gd-V and Gd-Mn and 4s(Co) to 5dxy/5dyz (Gd) for Gd-Co with the transition metal ion being found in the low-spin S = ½ configurations in all the cases. B3LYP/TZV (Gd;CSDZ) calculations on [PyCp2GdMCp(CO)2] yield JGd-V = -46.1 cm-1, JGd-Mn = -57.1 cm-1, JGd-Co = +55.3 cm-1, JGd-Fe+ = +13.9 cm-1, JGd-Vhs = -162.1 cm-1 and JGd-Mnhs = -343.9 cm-1 and unveiling record-high J values for {3d-4f} complexes. The mechanism of magnetic coupling is developed, which discloses the dominating presence of strong 3d-4f orbital overlaps in most of the cases studied, leading to antiferromagnetic exchange. When these overlaps are weaker and 3d to Gd(5dz2), charge transfer dominates, yielding a ferromagnetic coupling for the Gd-Co/Gd-Fe+ complexes. Calculations performed on the anisotropic Dy(III) and Er(III) complexes reveal that the ground state gzz axis lies along the Cp-Ln-Cp axis and the Ln-TM bonds, respectively. Thus the Ln-TM bond hinders the single-ion anisotropy of Dy(III) by offering equatorial ligation and lowering the mJ = ±½ state energy, and at the same time, helping in enhancing the axiality of Er(III). When strong {3d-4f} exchange couplings are introduced, record-high barrier heights as high as 229 cm-1 were accomplished. Furthermore, the exchange coupling annihilates the QTM effects and suggests the lanthanide-transition metal direct bond as a viable alternative to enhance exchange coupling to bring {3d-4f} complexes back in the race for high-blocking SMMs.
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Affiliation(s)
- Abinash Swain
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai - 400076, India.
| | - Asmita Sen
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai - 400076, India.
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai - 400076, India.
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Tada K, Hayashi A, Maruyama T, Koga H, Yamanaka S, Okumura M, Tanaka S. Effect of surface interactions on spin contamination errors of homogeneous spin dimers, chains, and films: model calculations of Au/MgO and Au/BaO systems. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1791989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Kohei Tada
- Research Institute of Electrochemical Energy, Department of Energy and Environment, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Japan
| | - Akihide Hayashi
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Tomohiro Maruyama
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Hiroaki Koga
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Japan
- Research Organization for Information Science and Technology (RIST), Tokyo, Japan
- Element Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto, Japan
| | - Shusuke Yamanaka
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Mitsutaka Okumura
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Japan
- Element Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto, Japan
| | - Shingo Tanaka
- Research Institute of Electrochemical Energy, Department of Energy and Environment, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Japan
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Miyagawa K, Kawakami T, Isobe H, Shoji M, Yamanaka S, Nakatani K, Okumura M, Nakajima T, Yamaguchi K. Domain-based local pair natural orbital CCSD(T) calculations of six different S1 structures of oxygen evolving complex of photosystem II. Proposal of multi-intermediate models for the S1 state. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Miyagawa K, Kawakami T, Suzuki Y, Isobe H, Shoji M, Yamanaka S, Okumura M, Nakajima T, Yamaguchi K. Domain-based local pair natural orbital CCSD(T) calculations of strongly correlated electron systems: Examination of dynamic equilibrium models based on multiple intermediates in S1 state of photosystem II. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1666171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- K. Miyagawa
- Institute for Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
| | - T. Kawakami
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Y. Suzuki
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - H. Isobe
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - M. Shoji
- Center of Computational Sciences, Tsukuba University, Tsukuba, Ibaraki 305-8577, Japan
| | - S. Yamanaka
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - M. Okumura
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - T. Nakajima
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - K. Yamaguchi
- Institute for Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
- RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
- Insitute for Nanoscience Design, Osaka University, Toyonaka 560-0043, Japan
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Isobe H, Shoji M, Suzuki T, Shen JR, Yamaguchi K. Spin, Valence, and Structural Isomerism in the S 3 State of the Oxygen-Evolving Complex of Photosystem II as a Manifestation of Multimetallic Cooperativity. J Chem Theory Comput 2019; 15:2375-2391. [PMID: 30855953 DOI: 10.1021/acs.jctc.8b01055] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Photosynthetic water oxidation is catalyzed by a Mn4CaO5-cluster in photosystem II through an S-state cycle. Understanding the roles of heterogeneity in each S-state, as identified recently by the EPR spectroscopy, is very important to gain a complete description of the catalytic mechanism. We performed herein hybrid DFT calculations within the broken-symmetry formalism and associated analyses of Heisenberg spin models to study the electronic and spin structures of various isomeric structural motifs (hydroxo-oxo, oxyl-oxo, peroxo, and superoxo species) in the S3 state. Our extensive study reveals several factors that affect the spin ground state: (1) (formal) Mn oxidation state; (2) metal-ligand covalency; (3) coordination geometry; and (4) structural change of the Mn cluster induced by alternations in Mn···Mn distances. Some combination of these effects could selectively stabilize/destabilize some spin states. We found that the high spin state ( Stotal = 6) of the oxyl-oxo species can be causative for catalytic function, which manifests through mixing of the metal-ligand character in magnetic orbitals at relatively short O5···O6 distances (<2.0 Å) and long MnA···O5 distances (>2.0 Å). These results will serve as a basis to conceptually identify and rationalize the physicochemical synergisms that can be evoked by the unique "distorted chair" topology of the cluster through cooperative Jahn-Teller effects on multimetallic centers.
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Affiliation(s)
- Hiroshi Isobe
- Research Institute for Interdisciplinary Science , Okayama University , Okayama 700-8530 , Japan
| | - Mitsuo Shoji
- Center for Computational Science , University of Tsukuba , Tsukuba , Ibaraki 305-8577 , Japan
| | - Takayoshi Suzuki
- Research Institute for Interdisciplinary Science , Okayama University , Okayama 700-8530 , Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science , Okayama University , Okayama 700-8530 , Japan
| | - Kizashi Yamaguchi
- Institute for NanoScience Design , Osaka University , Toyonaka , Osaka 560-0043 , Japan
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Van Der Goetz BW, Otis L, Neuscamman E. Clean and Convenient Tessellations for Number Counting Jastrow Factors. J Chem Theory Comput 2019; 15:1102-1121. [DOI: 10.1021/acs.jctc.8b01139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Leon Otis
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Eric Neuscamman
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Yamaguchi K, Shoji M, Isobe H, Miyagawa K, Nakatani K. Theory of chemical bonds in metalloenzymes XXII: a concerted bond-switching mechanism for the oxygen–oxygen bond formation coupled with one electron transfer for water oxidation in the oxygen-evolving complex of photosystem II. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1552799] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- K. Yamaguchi
- Institute for Nanoscience Design, Osaka University, Toyonaka, Osaka, Japan
- The Institute for Scientific and Industrial Research, Osaka University, Osaka, Japan
- Handairigaku Techno-Research, Toyonaka, Osaka, Japan
| | - M. Shoji
- Center of Computational Sciences, Tsukuba University, Tsukuba, Ibaraki, Japan
| | - H. Isobe
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - K. Miyagawa
- The Institute for Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - K. Nakatani
- The Institute for Scientific and Industrial Research, Osaka University, Osaka, Japan
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