Comparison between Experimental and Broken Symmetry Density Functional Theory (BS-DFT) Calculated Electron Paramagnetic Resonance (EPR) Parameters of the S2 State of the Oxygen-Evolving Complex of Photosystem II in Its Native (Calcium) and Strontium-Substituted Form

Water Ligands Regulate the Redox Leveling Mechanism of the Oxygen-Evolving Complex of the Photosystem II

Understanding how water ligands regulate the conformational changes and functionality of the oxygen-evolving complex (OEC) in photosystem II (PSII) throughout the catalytic cycle of oxygen evolution remains a highly intriguing and unresolved challenge. In this study, we investigate the effect of water insertion (WI) on the redox state of the OEC by using the molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) hybrid methods. We find that water binding significantly reduces the free energy change for proton-coupled electron transfer (PCET) from Mn to YZ•, underscoring the important regulatory role of water binding, which is essential for enabling the OEC redox-leveling mechanism along the catalytic cycle. We propose a water binding mechanism in which WI is thermodynamically favored by the closed-cubane form of the OEC, with water delivery mediated by Ca2+ ligand exchange. Isomerization from the closed- to open-cubane conformation at three post-WI states highlights the importance of the location of the MnIII center in the OEC and the orientation of its Jahn-Teller axis to conformational changes of the OEC, which might be critical for the formation of the O-O bond. These findings reveal a complex interplay between conformational changes in the OEC and the ligand environment during the activation of the OEC by YZ•. Analogous regulatory effects due to water ligand binding are expected to be important for a wide range of catalysts activated by redox state transitions in aqueous environments.

A Reappraisal of the S2 State of Nature's Water Oxidizing Complex in Its Low and High Spin Forms

Density functional theory calculated 14N hyperfine couplings are obtained for the Mn1 ligated π-N of residue His332 of the photosystem 2 water oxidizing complex. An open cubane, O4H, model closely matches the experimental coupling obtained for the high spin S = 5/2 form of the S2 state, supporting an open cubane structure for this state. We also investigate the unusual geometric features for the S2 state obtained by X-ray free electron laser structure determinations and rationalize it as an equilibrium occurring at room temperature between W1/O4 deprotonated and protonated forms of the open cubane structure.

Protonation structure of the closed-cubane conformation of the O2-evolving complex in photosystem II

In photosystem II (PSII), one-electron oxidation of the most stable state of the oxygen-evolving Mn₄CaO₅ cluster (S₁) leads to the S₂ state formation, Mn1(III)Mn2(IV)Mn3(IV)Mn4(IV) (open-cubane S₂) or Mn1(IV)Mn2(IV)Mn3(IV)Mn4(III) (closed-cubane S₂). In electron paramagnetic resonance (EPR) spectroscopy, the g = 4.1 signal is not observed in cyanobacterial PSII but in plant PSII, whereas the g = 4.8 signal is observed in cyanobacterial PSII and extrinsic-subunit-depleted plant PSII. Here, we investigated the closed-cubane S₂ conformation, a candidate for a higher spin configuration that accounts for g > 4.1 EPR signal, considering all pairwise exchange couplings in the PSII protein environment (i.e. instead of considering only a single exchange coupling between the [Mn₃(CaO₄)] cubane region and the dangling Mn4 site). Only when a ligand water molecule that forms an H-bond with D1-Asp61 (W1) is deprotonated at dangling Mn4(IV), the g = 4.1 EPR spectra can be reproduced using the cyanobacterial PSII crystal structure. The closed-cubane S₂ is less stable than the open-cubane S₂ in cyanobacterial PSII, which may explain why the g = 4.1 EPR signal is absent in cyanobacterial PSII.

Pulsed Multifrequency Electron Paramagnetic Resonance Spectroscopy Reveals Key Branch Points for One- vs Two-Electron Reactivity in Mn/Fe Proteins

Traditionally, the ferritin-like superfamily of proteins was thought to exclusively use a diiron active site in catalyzing a diverse array of oxygen-dependent reactions. In recent years, novel redox-active cofactors featuring heterobimetallic Mn/Fe active sites have been discovered in both the radical-generating R2 subunit of class Ic (R2c) ribonucleotide reductases (RNRs) and the related R2-like ligand-binding oxidases (R2lox). However, the protein-specific factors that differentiate the radical reactivity of R2c from the C-H activation reactions of R2lox remain unknown. In this work, multifrequency pulsed electron paramagnetic resonance (EPR) spectroscopy and ligand hyperfine techniques in conjunction with broken-symmetry density functional theory calculations are used to characterize the molecular and electronic structures of two EPR-active intermediates trapped during aerobic assembly of the R2lox Mn/Fe cofactor. A Mn^III(μ-O)(μ-OH)Fe^III species is identified as the first EPR-active species and represents a common state between the two classes of redox-active Mn/Fe proteins. The species downstream from the Mn^III(μ-O)(μ-OH)Fe^III state exhibits unique EPR properties, including unprecedented spectral breadth and isotope-dependent g-tensors, which are attributed to a weakly coupled, hydrogen-bonded Mn^III(μ-OH)Fe^III species. This final intermediate precedes formation of the Mn^III/Fe^III resting state and is suggested to be relevant to understanding the endogenous reactivity of R2lox.

Binding of the substrate analog methanol in the oxygen-evolving complex of photosystem II in the D1-N87A genetic variant of cyanobacteria

The solar water-splitting protein complex, photosystem II (PSII), catalyzes one of the most energetically demanding reactions in nature by using light energy to drive a catalyst capable of oxidizing water. The water oxidation reaction is catalyzed at the Mn₄Ca-oxo cluster in the oxygen-evolving complex (OEC), which cycles through five light-driven S-state intermediates (S₀-S₄). A detailed mechanism of the reaction remains elusive as it requires knowledge of the delivery and binding of substrate water in the higher S-state intermediates. In this study, we use two-dimensional (2D) hyperfine sublevel correlation spectroscopy, in conjunction with quantum mechanics/molecular mechanics (QM/MM) and density functional theory (DFT), to probe the binding of the substrate analog, methanol, in the S₂ state of the D1-N87A variant of PSII from Synechocystis sp. PCC 6803. The results indicate that the size and specificity of the "narrow" channel is altered in D1-N87A PSII, allowing for the binding of deprotonated ¹³C-labeled methanol at the Mn4(IV) ion of the catalytic cluster in the S₂ state. This has important implications on the mechanistic models for water oxidation in PSII.

S3 State Models of Nature's Water Oxidizing Complex: Analysis of Bonding and Magnetic Exchange Pathways, Assessment of Experimental Electron Paramagnetic Resonance Data, and Implications for the Water Oxidation Mechanism

Broken symmetry density functional theory (BS-DFT) calculations on large models of Nature's water oxidizing complex (WOC) are used to investigate the electronic structure and associated magnetic interactions of this key intermediate state. The electronic origins of the ferromagnetic and antiferromagnetic couplings between neighboring Mn ions are investigated and illustrated by using corresponding orbital transformations. Protonation of the O4 and/or O6 atoms leads to large variation in the distribution of spin around the complex with associated changes in its magnetic resonance properties. Models for Sr²⁺ exchange and methanol addition indicate minor perturbations reflected in slightly altered spin projection coefficients for the Mn₁ and Mn₂ ions. These are shown to account for the observed changes observed experimentally via electron paramagnetic resonance methods and suggest a reinterpretation of the experimental findings. By comparison with experimental determinations, we show that the spin projections and resulting calculated ⁵⁵Mn hyperfine couplings support the open cubane form of an oxo (O5)-hydroxo (O6) cluster in all cases with no need to invoke a closed cubane intermediate. The implications of these findings for the water oxidation mechanism are discussed.

Mechanism of Oxygen Evolution and Mn4CaO5 Cluster Restoration in the Natural Water-Oxidizing Catalyst

Water oxidation occurring in the first steps of natural oxygenic photosynthesis is catalyzed by the pigment/protein complex Photosystem II. This process takes place on the Mn₄Ca cluster located in the core of Photosystem II and proceeds along the five steps (S₀-S₄) of the so-called Kok-Joliot cycle until the release of molecular oxygen. The catalytic cycle can therefore be started afresh through insertion of a new water molecule. Here, combining quantum mechanics/molecular mechanics simulations and minimum energy path calculations, we characterized on different spin surfaces the events occurring in the last sector of the catalytic cycle from structural, electronic, and thermodynamic points of view. We found that the process of oxygen evolution and water insertion can be described well by a two-step mechanism, with oxygen release being the rate-limiting step of the process. Moreover, our results allow us to identify the upcoming water molecule required to regenerate the initial structure of the Mn₄Ca cluster in the S₀ state. The insertion of the water molecule was found to be coupled with the transfer of a proton to a neighboring hydroxide ion, thus resulting in the reconstitution of the most widely accepted model of the S₀ state.

Bonding and Magnetic Exchange Pathways in Nature's Water-Oxidizing Complex

The nature of the bonding and magnetic exchange pathways of the water-oxidizing complex of photosystem 2 is explored using broken symmetry density functional theory. The electronic structure and superexchange pathways are illustrated and analyzed using corresponding orbitals and intrinsic bond orbitals. These demonstrate a dominating influence on the bonding and magnetic interactions by both the geometrical structure of the Mn₄CaO₅ core complex and the ionic interactions of the oxo bridges with the neighboring Ca²⁺ ion. The demonstrated ionic nature of the Ca²⁺ bonds is proposed to contribute to the stabilization of the oxygen atoms participating in O-O bond formation.

Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research

Overview of the rich and diverse contributions of quantum chemistry to understanding the structure and function of the biological archetypes for solar fuel research, photosystem II and hydrogenases.

How accurate is density functional theory in predicting spin density? An insight from the prediction of hyperfine coupling constants

Electron paramagnetic resonance (EPR) spectroscopy has been proven to be an important technique for studying paramagnetic systems. Probably, the most accessible EPR parameter and the one that provides a significant amount of information about molecular structure and spin density is the hyperfine coupling constant (HFCC). Hence, accurate quantum-chemical modeling of HFCCs is frequently essential to the adequate interpretation of EPR spectra. It requires the precise spin density, which is the difference between the densities of α- and β-electrons, and thus, its quality is expected to reflect the quality of the total electron density. The question of which approximate exchange-correlation density functional yields sufficiently accurate HFCCs, and thus, the spin density remains open. To assess the performance of well-established density functionals for calculating HFCCs, we used a series of 26 small paramagnetic species and compared the obtained results to the CCSD reference values. The performance of DFT was also tested on EPR-studied o-semiquinone radical interacting with water molecules and Mg²⁺ cation. The HFCCs were additionally calculated by the DLPNO-CCSD method, and this wave function-based technique was found superior to all functionals we tested. Although some functionals were found, on average, to be fairly efficient, we found that the most accurate functional is system-dependent, and therefore, the DLPNO-CCSD method should be preferred for theoretical investigations of the HFCCs and spin density.

Proton Isomers Rationalize the High- and Low-Spin Forms of the S2 State Intermediate in the Water-Oxidizing Reaction of Photosystem II

A new paradigm for the high- and low-spin forms of the S₂ state of nature's water-oxidizing complex in Photosystem II is found. Broken symmetry density functional theory calculations combined with Heisenberg-Dirac-van Vleck spin ladder calculations show that an open cubane form of the water-oxidizing complex changes from a low-spin, S = 1/2, to a high-spin, S = 5/2, form on protonation of the bridging O4 oxo. We show that such models are fully compatible with structural determinations of the S₂ state by X-ray free-electron laser crystallography and extended X-ray absorption fine structure and provide a clear rationale for the effect of various treatments on the relative populations of each form observed experimentally in electron paramagnetic resonance studies.

Assessment of Double-Hybrid Density Functional Theory for Magnetic Exchange Coupling in Manganese Complexes

Molecular systems containing magnetically interacting (exchange-coupled) manganese ions are important in catalysis, biomimetic chemistry, and molecular magnetism. The reliable prediction of exchange coupling constants with quantum chemical methods is key for tracing the relationships between structure and magnetic properties in these systems. Density functional theory (DFT) in the broken-symmetry approach has been employed extensively for this purpose and hybrid functionals with moderate levels of Hartree–Fock exchange admixture have often been shown to perform adequately. Double-hybrid density functionals that introduce a second-order perturbational contribution to the Kohn–Sham energy are generally regarded as a superior approach for most molecular properties, but their performance remains unexplored for exchange-coupled manganese systems. An assessment of various double-hybrid functionals for the prediction of exchange coupling constants is presented here using a set of experimentally characterized dinuclear manganese complexes that cover a wide range of exchange coupling situations. Double-hybrid functionals perform more uniformly compared to conventional DFT methods, but they fail to deliver improved accuracy or reliability in the prediction of exchange coupling constants. Reparametrized double-hybrid density functionals (DHDFs) perform no better, and most often worse, than the original B2-PLYP double-hybrid method. All DHDFs are surpassed by the hybrid-meta-generalized gradient approximation (GGA) TPSSh functional. Possible directions for future methodological developments are discussed.

Microsolvation of the Redox-Active Tyrosine-D in Photosystem II: Correlation of Energetics with EPR Spectroscopy and Oxidation-Induced Proton Transfer

Photosystem II (PSII) of oxygenic photosynthesis captures sunlight to drive the catalytic oxidation of water and the reduction of plastoquinone. Among the several redox-active cofactors that participate in intricate electron transfer pathways there are two tyrosine residues, YZ and YD. They are situated in symmetry-related electron transfer branches but have different environments and play distinct roles. YZ is the immediate oxidant of the oxygen-evolving Mn4CaO5 cluster, whereas YD serves regulatory and protective functions. The protonation states and hydrogen-bond network in the environment of YD remain debated, while the role of microsolvation in stabilizing different redox states of YD and facilitating oxidation or mediating deprotonation, as well the fate of the phenolic proton, is unclear. Here we present detailed structural models of YD and its environment using large-scale quantum mechanical models and all-atom molecular dynamics of a complete PSII monomer. The energetics of water distribution within a hydrophobic cavity adjacent to YD are shown to correlate directly with electron paramagnetic resonance (EPR) parameters such as the tyrosyl g-tensor, allowing us to map the correspondence between specific structural models and available experimental observations. EPR spectra obtained under different conditions are explained with respect to the mode of interaction of the proximal water with the tyrosyl radical and the position of the phenolic proton within the cavity. Our results revise previous models of the energetics and build a detailed view of the role of confined water in the oxidation and deprotonation of YD. Finally, the model of microsolvation developed in the present work rationalizes in a straightforward way the biphasic oxidation kinetics of YD, offering new structural insights regarding the function of the radical in biological photosynthesis.

Reconciling Structural and Spectroscopic Fingerprints of the Oxygen-Evolving Complex of Photosystem II: A Computational Study of the S2 State

The catalytic cycle of photosynthetic water oxidation occurs at the Mn₄CaO₅ oxygen-evolving complex (OEC) of photosystem II. Extensive spectroscopic data have been collected on the intermediates, especially the S₂ (Kok) state, although the proton and electron inventories (Mn oxidation states) are still uncertain. The "high oxidation" paradigm assigns S₂ Mn oxidation level (III, IV, IV, IV) or (IV, IV, IV, III), whereas a "low oxidation" paradigm posits two additional electrons. Here, we investigate the geometric (X-ray diffraction, extended X-ray absorption fine structure) and spectroscopic (electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR)) properties of the S₂ state using quantum chemical density functional theory calculations, focusing on the neglected low paradigm. Two interconvertible electronic spin configurations are predicted as ground states, producing multiline ( S = 1/2) and broad ( S = 5/2) EPR signals in the low paradigm oxidation state (III, IV, III, III) and with W2 as OH^- and O5 as OH^-. They have "open" ( S = 5/2) and "closed" ( S = 1/2) Mn₃CaO₄-cubane geometries. Other energetically accessible isomers with ground spin states 1/2, 7/2, 9/2, or 11/2 can be obtained through perturbations of hydrogen-bonding networks (e.g., H⁺ from His337 to O3 or W2), consistent with experimental observations. Conformers with the low oxidation state configuration (III, IV, IV, II) also become energetically accessible when the protonation states are O5 (OH^-), W2 (H₂O), and neutral His337. The configuration with (III, IV, III, III) agrees well with earlier low-temperature EPR and ENDOR interpretations, whereas the Mn^II-containing configuration agrees partially with recent ENDOR data. However, the low oxidation paradigm does not yield isotropic ligand hyperfine interactions in good agreement with observed values. We conclude that the low Mn oxidation state proposal for the OEC can closely fit most of the available structural and electronic data for S₂ at accessible energies.

Evidence of O-O Bond Formation in the Final Metastable S3 State of Nature's Water Oxidizing Complex Implying a Novel Mechanism of Water Oxidation

A novel mechanism for the final stages of Nature's photosynthetic water oxidation to molecular oxygen is proposed. This is based on a comparison of experimental and broken symmetry density functional theory (BS-DFT) calculated geometries and magnetic resonance properties of water oxidizing complex models in the final metastable oxidation state, S₃. We show that peroxo models of the S₃ state are in vastly superior agreement with the current experimental structural determinations compared with oxo-hydroxo models. Comparison of experimental and BS-DFT calculated ⁵⁵Mn hyperfine couplings for the electron paramagnetic resonance (EPR) visible form shows better agreement for the oxo-hydroxo model. An equilibrium between oxo-hydroxo and peroxo models is proposed for the S₃ state and the major implications for the final steps in the water oxidation mechanism are analyzed and discussed.