Large-scale QM/MM calculations of the CaMn₄O₅ cluster in the S₃ state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures

Abstract

Large-scale QM/MM calculations were performed to elucidate an optimized geometrical structure of a CaMnO cluster with and without water insertion in the S state of the oxygen evolving complex (OEC) of photosystem II (PSII). The left (L)-opened structure was found to be stable under the assumption of no hydroxide anion insertion in the S state, whereas the right (R)-opened structure became more stable if one water molecule is inserted to the MnCa cluster. The optimized Mn-Mn distance determined by QM/MM was about 5.0 Å for the S structure without an inserted hydroxide anion, but this is elongated by 0.2-0.3 Å after insertion. These computational results are discussed in relation to the possible mechanisms of O-O bond formation in water oxidation by the OEC of PSII.

Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn4OX (X = 5, 6) cluster in the Kok cycle Si (i = 0–3) of oxygen evolving complex of photosystem II

“…Previous and new SFX structures for the S 3 state of OEC of PSII provided structural information for elucidation of scope and applicability of the QM/MM results (Shoji et al , , ). The Mn‐peroxide with a short O (5) ‐O (6) distance (1.5 Å) was compatible with the SFX structure by Okayama group (Suga et al ).…”

“…Fig. A,B show variations of the optimized geometrical structures by QM/MM at the S 2 to S 3 transition (Shoji et al , 2018), where the yellow and red colors are used for the R‐opened S 2 (4443) and S 3 (4444) structures, respectively. From Fig.…”

“…B. After water (H 2 O (6) ) insertion in the S 3 state (Isobe et al , Shoji et al ), the HV Mnoxo bond may be formed at the Mn 4 or Mn 1 site of the CaMn 4 O 6 cluster. Therefore, the nucleophilic attacks of H 2 O(W3) coordinated to Ca to the electrophilic O (6) site of the Mn 4 O (6) bond and the O (6) site of the Mn 1 O (6) bond are feasible as illustrated in Fig.…”

Manganese–Hydroxido Complexes Supported by a Urea/Phosphinic Amide Tripodal Ligand

“…17,55–59 Results from structural biology on the oxygen evolving complex (OEC) suggest that H-bonding networks to coordinate water molecules assist in forming Mn–OH complexes that can be in either the Mn III or Mn IV oxidation states. 60–64 One approach toward studying the structural outcomes of the secondary coordination sphere is to develop chelating ligands that can provide H-bond donors/accepts around the Mn–OH unit. Toward this goal, tripodal ligand [H 2 pout] 3- was designed to accommodate three intramolecular H-bond to the hydroxido ligand.…”

Evolution from S3 to S4 States of the Oxygen‐Evolving Complex in Photosystem II Monitored by Quantum Mechanics/Molecular Mechanics (QM/MM) Dynamics

“…[16][17][18][19][20][21][22] Computational studies also revealed the presence of intermediate states within the catalytic cycle of PSII, which suggested the presence of different isomers representative of the S 1 , [23,24] S 2 [24][25][26] and S 3 states. [24,[27][28][29][30] In particular, for the S 3 state, experimental evidence demonstrates that the Mn 4 Ca cluster is arrangedi nao pen cubane fashion, [31] with the possible presence of an additional hydroxyl group bound to the Mn1 ion. [15] This conformation is also suggested by computational studies, which additionally support the presence of ah ydroxyl group bound to the Mn1 ion (see also Figure 1).…”