Theoretical elucidation of the structure, bonding, and reactivity of the CaMn4Ox 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

• Published in: Photosynthesis research 2024-12, Vol.162 (2), p.291-330
• Main Authors: Yamaguchi, Kizashi, Miyagawa, Koichi, Shoji, Mitsuo, Kawakami, Takashi, Isobe, Hiroshi, Yamanaka, Shusuke, Nakajima, Takahito
• Format: Article
• Language: English
• Subjects: Biochemistry; Biomedical and Life Sciences; Intermediates; Life Sciences; Oxidation; Photosystem II; Plant Genetics and Genomics; Plant Physiology; Plant Sciences; Review
• ISSN: 0166-8595; 1573-5079; 1573-5079
• DOI: 10.1007/s11120-023-01053-7

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 S 1 state have been performed to elucidate structure and bonding of whole possible intermediates of the CaMn 4 O x cluster ( 1 ) in the S i ( 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(T 0 ) 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(H 2 O) n ion and tyrosine(Yz)-O radical as a one-electron acceptor for the O–O bond formation. The Ca-assisted Y z -coupled O–O bond formation mechanisms for water oxidation are consistent with recent XES and very recent time-resolved SFX XFEL and FTIR results.