Full geometry optimizations of several inorganic model clusters, CaMn₄O₄XYZ(H₂O)₂ (X, Y, Z = H₂O, OH⁻ or O²⁻), by the use of the B3LYP hybrid density functional theory (DFT) have been performed to illuminate plausible molecular structures of the catalytic site for water oxidation in the S₀, S₁, S₂ and S₃ states of the Kok cycle for the oxygen-evolving complex (OEC) of photosystem II (PSII). Optimized geometries obtained by the energy gradient method have revealed the degree of symmetry breaking of the unstable three-center Mn_a–X–Mn_d bond in CaMn₄O₄XYZ(H₂O)₂. The right-elongated (R) Mn_a–X⋯Mn_d and left-elongated (L) Mn_a⋯X–Mn_d structures appear to occupy local minima on a double-well potential for several key intermediates in these states. The effects of insertion of one extra water molecule to the vacant coordination site, Mn_d (Mn_a), for R (L) structures have also been examined in detail. The greater stability of the L-type structure over the R-type has been concluded for key intermediates in the S₂ and S₃ states. Implications of the present DFT structures are discussed in relation to previous DFT and related results, together with recent X-ray diffraction results for model compounds of cubane-like OEC cluster of PSII.

Quantum mechanical (QM) and QM/molecular mechanics (MM) calculations of three different cluster models have been performed to shed light on hydrogen bonding networks and proton wires for proton release pathways (PRP) of water oxidation reactions in the oxygen evolving complex (OEC) of photosystem II (PSII). Positions of all the hydrogen atoms in an extended QM Model III including the second coordination sphere for the active-site CaMn₄O₅ complex of OEC of PSII have been optimized assuming the geometry of heavy atoms determined by the recent high-resolution X-ray diffraction (XRD) experiment of PSII refined to 1.9 Å resolution. Full geometry optimizations of the first coordination sphere model (QM Model I) embedded in the Model III and QM (QM Model I plus seven water molecules, namely QM Model II)/MM models, together with full QM Model III, have also been conducted to elucidate confinement effects for geometrical parameters of the CaMn₄O₅ cluster by proteins. Computational results by these methods have elucidated the O⋯O(N), O⋯H distances and O(N)–H⋯O angles for hydrogen bonds in proton release paths (PRP) I and II that construct a proton wire from Asp61 toward His190. The hydrogen-bonding structures revealed have also been examined in relation to the possibilities of protonation of bridge oxygen dianions within the CaMn₄O₅ cluster. The optimized inter-atomic distances by QM Models I and III, together with QM(Model II)/MM, have elucidated the elongation of the Mn–Mn distances with hydrogen bonds and variations of the Mn_d–O₍₅₎ length with confinement effects by protein. Implications of the computational results are discussed in relation to the available EXAFS experiments, and internal, semi-internal and external reductions of Mn ions and long Mn–Mn distances of the high-resolution (SP8) XRD, and rational design of artificial catalysts for water oxidation that are current topics in the field of OEC of PSII.