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The BS hybrid DFT (HDFT) calculations starting from high-resolution (HR) XRD structure in the most stable S\n 1<\/jats:sub>\n state have been performed to elucidate structure and bonding of whole possible intermediates of the CaMn\n 4<\/jats:sub>\n O\n x<\/jats:sub>\n cluster (\n 1<\/jats:bold>\n ) in the S\n \n i<\/jats:italic>\n <\/jats:sub>\n (\n i<\/jats:italic>\n \u2009=\u20090\u2009~\u20094) 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\n 0<\/jats:sub>\n ) 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\n 1<\/jats:bold>\n embedded in protein matrix, indicating the participations of the Ca(H\n 2<\/jats:sub>\n O)\n n<\/jats:sub>\n ion and tyrosine(Yz)-O radical as a one-electron acceptor for the O\u2013O bond formation. The Ca-assisted Y\n z<\/jats:sub>\n -coupled O\u2013O bond formation mechanisms for water oxidation are consistent with recent XES and very recent time-resolved SFX XFEL and FTIR results.\n <\/jats:p>","DOI":"10.1007\/s11120-023-01053-7","type":"journal-article","created":{"date-parts":[[2023,11,9]],"date-time":"2023-11-09T12:02:31Z","timestamp":1699531351000},"page":"291-330","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["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\u2013O bond formation"],"prefix":"10.1007","volume":"162","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4411-7425","authenticated-orcid":false,"given":"Kizashi","family":"Yamaguchi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7409-3727","authenticated-orcid":false,"given":"Koichi","family":"Miyagawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7465-6326","authenticated-orcid":false,"given":"Mitsuo","family":"Shoji","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takashi","family":"Kawakami","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1990-1904","authenticated-orcid":false,"given":"Hiroshi","family":"Isobe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shusuke","family":"Yamanaka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takahito","family":"Nakajima","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,11,9]]},"reference":[{"key":"1053_CR1","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1016\/0025-5408(73)90167-0","volume":"8","author":"PW Anderson","year":"1973","unstructured":"Anderson PW (1973) Resonating valence bonds: A new kind of insulator? 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