A five-coordinate Mn(iv) intermediate in biological water oxidation: spectroscopic signature and a pivot mechanism for water binding

Abstract

Among the four photo-driven transitions of the water-oxidizing tetramanganese-calcium cofactor of biological photosynthesis, the second-last step of the catalytic cycle, that is the S₂ to S₃ state transition, is the crucial step that poises the catalyst for the final O-O bond formation. This transition, whose intermediates are not yet fully understood, is a multi-step process that involves the redox-active tyrosine residue and includes oxidation and deprotonation of the catalytic cluster, as well as the binding of a water molecule. Spectroscopic data has the potential to shed light on the sequence of events that comprise this catalytic step, which still lacks a structural interpretation. In this work the S₂-S₃ state transition is studied and a key intermediate species is characterized: it contains a Mn₃O₄Ca cubane subunit linked to a five-coordinate Mn(iv) ion that adopts an approximately trigonal bipyramidal ligand field. It is shown using high-level density functional and multireference wave function calculations that this species accounts for the near-infrared absorption and electron paramagnetic resonance observations on metastable S₂-S₃ intermediates. The results confirm that deprotonation and Mn oxidation of the cofactor must precede the coordination of a water molecule, and lead to identification of a novel low-energy water binding mode that has important implications for the identity of the substrates in the mechanism of biological water oxidation.

Fig. 1. (a) A view of the Mn₄Ca cluster and its environment, according to one of the S₁-state XFEL crystallographic models of Suga et al. (monomer A of dataset 4UB6). (b) Schematic depiction and labeling scheme for the inorganic core of the OEC. (c) The catalytic cycle with spectroscopically consistent models of the inorganic core and their spin states, adapted from ref. 9. In the present work we focus on the multi-step S₂–S₃ transition.

Fig. 2. Schematic depiction of two major suggestions for water binding during the S₂–S₃ transition. Top: A model involving water binding to the Mn1 ion of an SA2-type conformer. Bottom: A model involving the shift of a Ca-bound water to the Mn4 ion of an SB2-type conformer.

Fig. 3. Relative acidities of titratable groups for the S₂ and S₂Y_Z˙ species indicated by color: green for the most favorable site, orange for relative energies in the range 10–20 kcal mol^–1, and red for more than 20 kcal mol^–1.

Fig. 4. The progression of the open-cubane SA2 and closed-cubane SB2 structures during the S₂–S₃ transition of the Kok cycle. The deprotonated form of SA(–)2Y_Z˙ is stable and cannot progress any further by Mn oxidation. A low-barrier open/closed-cubane rearrangement however induces intramolecular electron transfer (with or without direct involvement of an unstable SB(–)2Y_Z˙ species as transient intermediate) and formation of the stabilized SB3Y_Z state. Two conceivable progression pathways that converge to the same closed-cubane SB3 species are indicated with the green and blue arrows, the latter being the one favored by the present computational results.

Fig. 5. Depiction of the inorganic core of the SB3 species and geometric parameters (Å and degrees) of its Mn4 center.

Fig. 6. (a) CASSCF d orbitals on the Mn4 center of SB3. Symmetry labels correspond to idealized local C_2v point group symmetry (intermediate between D_3h trigonal bipyramidal and C_4v square pyramidal). (b) The dominant natural transition orbital pair for the first excited state obtained from TD-DFT calculations (n indicates the contribution of the pair to the overall transition). (c) The corresponding CASSCF orbitals, where n indicates the weight of the Mn4 configuration in the first excited state.

Fig. 7. Dependence of the local zero-field splitting parameter D for the Mn4 ion of SB3 on the O4–Mn4–W1 angle.

Fig. 8. The Mn₄O₅Ca core of the optimized SB3 model showing the two possible pathways for water delivery to the five-coordinate Mn4 site: (a) “internal”-side delivery through the water channel associated with Ca, and (b) “external”-side delivery through the water channel terminating close to O4. Potential movement of water molecules is indicated with the light blue arrows.

Fig. 9. Schematic diagram for the binding of a water molecule (W_new) to the Mn4 of a reduced-size model of SB3 (coordinating amino acids are omitted for clarity). Relative energies in kcal mol^–1.