On the structure of the manganese complex of photosystem II: extended-range EXAFS data and specific atomic-resolution models for four S-states

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-O bond formation

This paper reviews our historical developments of broken-symmetry (BS) and beyond BS methods that are applicable for theoretical investigations of metalloenzymes such as OEC in PSII. The BS hybrid DFT (HDFT) calculations starting from high-resolution (HR) XRD structure in the most stable S1 state have been performed to elucidate structure and bonding of whole possible intermediates of the CaMn4Ox cluster (1) in the Si (i = 0 ~ 4) 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(T0) 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 1 embedded in protein matrix, indicating the participations of the Ca(H2O)n ion and tyrosine(Yz)-O radical as a one-electron acceptor for the O-O bond formation. The Ca-assisted Yz-coupled O-O bond formation mechanisms for water oxidation are consistent with recent XES and very recent time-resolved SFX XFEL and FTIR results.

Development of serial X-ray fluorescence holography for radiation-sensitive protein crystals

X-ray fluorescence holography (XFH) is a powerful atomic resolution technique capable of directly imaging the local atomic structure around atoms of a target element within a material. Although it is theoretically possible to use XFH to study the local structures of metal clusters in large protein crystals, the experiment has proven difficult to perform, especially on radiation-sensitive proteins. Here, the development of serial X-ray fluorescence holography to allow the direct recording of hologram patterns before the onset of radiation damage is reported. By combining a 2D hybrid detector and the serial data collection used in serial protein crystallography, the X-ray fluorescence hologram can be directly recorded in a fraction of the measurement time needed for conventional XFH measurements. This approach was demonstrated by obtaining the Mn Kα hologram pattern from the protein crystal Photosystem II without any X-ray-induced reduction of the Mn clusters. Furthermore, a method to interpret the fluorescence patterns as real-space projections of the atoms surrounding the Mn emitters has been developed, where the surrounding atoms produce large dark dips along the emitter-scatterer bond directions. This new technique paves the way for future experiments on protein crystals that aim to clarify the local atomic structures of their functional metal clusters, and for other related XFH experiments such as valence-selective XFH or time-resolved XFH.

Water oxidation in oxygenic photosynthesis studied by magnetic resonance techniques

The understanding of light-induced biological water oxidation in oxygenic photosynthesis is of great importance both for biology and (bio)technological applications. The chemically difficult multistep reaction takes place at a unique protein-bound tetra-manganese/calcium cluster in photosystem II whose structure has been elucidated by X-ray crystallography (Umena et al. Nature 2011, 473, 55). The cluster moves through several intermediate states in the catalytic cycle. A detailed understanding of these intermediates requires information about the spatial and electronic structure of the Mn₄ Ca complex; the latter is only available from spectroscopic techniques. Here, the important role of Electron Paramagnetic Resonance (EPR) and related double resonance techniques (ENDOR, EDNMR), complemented by quantum chemical calculations, is described. This has led to the elucidation of the cluster's redox and protonation states, the valence and spin states of the manganese ions and the interactions between them, and contributed substantially to the understanding of the role of the protein surrounding, as well as the binding and processing of the substrate water molecules, the O-O bond formation and dioxygen release. Based on these data, models for the water oxidation cycle are developed.

Mimicking the Oxygen-Evolving Center in Photosynthesis

The oxygen-evolving center (OEC) in photosystem II (PSII) of oxygenic photosynthetic organisms is a unique heterometallic-oxide Mn₄CaO₅-cluster that catalyzes water splitting into electrons, protons, and molecular oxygen through a five-state cycle (S_n, n = 0 ~ 4). It serves as the blueprint for the developing of the man-made water-splitting catalysts to generate solar fuel in artificial photosynthesis. Understanding the structure-function relationship of this natural catalyst is a great challenge and a long-standing issue, which is severely restricted by the lack of a precise chemical model for this heterometallic-oxide cluster. However, it is a great challenge for chemists to precisely mimic the OEC in a laboratory. Recently, significant advances have been achieved and a series of artificial Mn₄XO₄-clusters (X = Ca/Y/Gd) have been reported, which closely mimic both the geometric structure and the electronic structure, as well as the redox property of the OEC. These new advances provide a structurally well-defined molecular platform to study the structure-function relationship of the OEC and shed new light on the design of efficient catalysts for the water-splitting reaction in artificial photosynthesis.

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.

Structural and dynamic insights into Mn4Ca cluster-depleted Photosystem II

In the first steps of natural oxygenic photosynthesis, sunlight is used to oxidize water molecules to protons, electrons and molecular oxygen. This reaction takes place on the Mn₄Ca cluster located in the reaction centre of Photosystem II (PSII), where the cluster is assembled and continuously repaired through a process known as photoactivation. Understanding the molecular details of such a process has important implications in different fields, in particular inspiring synthesis and repair strategies for artificial photosynthesis devices. In this regard, a detailed structural and dynamic characterization of Photosystem II lacking a Mn₄Ca cluster, namely apo PSII, is a prerequisite for the full comprehension of the photoactivation. Recently, the structure of the apo PSII was resolved at 2.55 Å resolution [Zhang et al., eLife, 2017, 6, e26933], suggesting a pre-organized structure of the protein cavity hosting the cluster. Anyway, the question of whether these findings are a feature of the method used remains open. Here, by means of classical Molecular Dynamics simulations, we characterized the structural and dynamic features of the apo PSII for different protonation states of the cluster cavity. Albeit an overall conformational stability common to all investigated systems, we found significant deviations in the conformation of the side chains of the active site with respect to the X-ray positions. Our findings suggest that not all residues acting as Mn ligands are pre-organized prior to the Mn₄Ca formation and previous local conformational changes are required in order to bind the first Mn ion in the high-affinity binding site.

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.

Ligand Radical Mediated Water Oxidation by a Family of Copper o-Phenylene Bis-oxamidate Complexes

Understanding the reactivity landscape for the activation of water until the formation of the O-O bond and O₂ release in molecular chemistry is a decisive step in guiding the elaboration of cost-effective catalysts for the oxygen-evolving reaction (OER). Copper(II) complexes have recently caught the attention of chemists as catalysts for the 4e^-/4H⁺ water oxidation process. While a copper(IV) intermediate has been proposed as the reactive intermediate species, no spectroscopic signature has been reported so far. Copper(III) ligand radical species have also been formulated and supported by theoretical studies. We found, herein, that the reactivity sequence for the water oxidation with a family of Copper(II) o-phenylene bis-oxamidate complexes is a function of the substitution pattern on the periphery of the aromatic ring. In-situ EPR, FTIR, and rR spectroelectrochemical studies helped to sequence the elementary electrochemical and chemical events leading toward the O₂ formation selectively at the copper center. EPR and FTIR spectroelectrochemistry suggests that ligand-centered oxidations are preferred over metal-centered oxidations. rR spectroelectrochemical study revealed the accumulation of a bis-imine bound copper(II) superoxide species, as the reactive intermediate, under catalytic turnover, which provides the evidence for the O-O bond formation during OER.

On the Origin of the OER Activity of Ultrathin Manganese Oxide Films

There is an urgent need for cheap, stable, and abundant catalyst materials for photoelectrochemical water splitting. Manganese oxide is an interesting candidate as an oxygen evolution reaction (OER) catalyst, but the minimum thickness above which MnO_x thin films become OER-active has not yet been established. In this work, ultrathin (<10 nm) manganese oxide films are grown on silicon by atomic layer deposition to study the origin of OER activity under alkaline conditions. We found that MnO_x films thinner than 1.5 nm are not OER-active. X-ray photoelectron spectroscopy shows that this is due to electrostatic catalyst-support interactions that prevent the electrochemical oxidation of the manganese ions close to the interface with the support, while in thicker films, Mn^III and Mn^IV oxide layers appear as OER-active catalysts after oxidation and electrochemical treatment. From our investigations, it can be concluded that one Mn^III,IV-O monolayer is sufficient to establish oxygen evolution under alkaline conditions. The results of this study provide important new design criteria for ultrathin manganese oxide oxygen evolution catalysts.

Current Understanding of the Mechanism of Water Oxidation in Photosystem II and Its Relation to XFEL Data

The investigation of water oxidation in photosynthesis has remained a central topic in biochemical research for the last few decades due to the importance of this catalytic process for technological applications. Significant progress has been made following the 2011 report of a high-resolution X-ray crystallographic structure resolving the site of catalysis, a protein-bound Mn4CaOxcomplex, which passes through ≥5 intermediate states in the water-splitting cycle. Spectroscopic techniques complemented by quantum chemical calculations aided in understanding the electronic structure of the cofactor in all (detectable) states of the enzymatic process. Together with isotope labeling, these techniques also revealed the binding of the two substrate water molecules to the cluster. These results are described in the context of recent progress using X-ray crystallography with free-electron lasers on these intermediates. The data are instrumental for developing a model for the biological water oxidation cycle.

Mimicking the Catalytic Center for the Water-Splitting Reaction in Photosystem II

The oxygen-evolving center (OEC) in photosystem II (PSII) of plants, algae and cyanobacteria is a unique natural catalyst that splits water into electrons, protons and dioxygen. The crystallographic studies of PSII have revealed that the OEC is an asymmetric Mn4CaO5-cluster. The understanding of the structure-function relationship of this natural Mn4CaO5-cluster is impeded mainly due to the complexity of the protein environment and lack of a rational chemical model as a reference. Although it has been a great challenge for chemists to synthesize the OEC in the laboratory, significant advances have been achieved recently. Different artificial complexes have been reported, especially a series of artificial Mn4CaO4-clusters that closely mimic both the geometric and electronic structures of the OEC in PSII, which provides a structurally well-defined chemical model to investigate the structure-function relationship of the natural Mn4CaO5-cluster. The deep investigations on this artificial Mn4CaO4-cluster could provide new insights into the mechanism of the water-splitting reaction in natural photosynthesis and may help the development of efficient catalysts for the water-splitting reaction in artificial photosynthesis.

On the comparison between differential vibrational spectroscopy spectra and theoretical data in the carboxyl region of photosystem II

Understanding the structural modification experienced by the Mn₄ CaO₅ oxygen-evolving complex of photosystem II along the Kok-Joliot's cycle has been a challenge for both theory and experiments since many decades. In particular, differential infrared spectroscopy was extensively used to probe the surroundings of the reaction center, to catch spectral changes between different S-states along the catalytic cycle. Because of the complexity of the signals, only a limited quantity of identified peaks have been assigned so far, also because of the difficulty of a direct comparison with theoretical calculations. In the present work, we critically reconsider the comparison between differential vibrational spectroscopy and theoretical calculations performed on the structural models of the photosystem II active site and an inorganic structural mimic. Several factors are currently limiting the reliability of a quantitative comparison, such as intrinsic errors associated to theoretical methods, and most of all, the uncertainty attributed to the lack of knowledge about the localization of the underlying structural changes. Critical points in this comparison are extensively discussed. Comparing several computational data of differential S₂ /S₁ infrared spectroscopy, we have identified weak and strong points in their interpretation when compared with experimental spectra.

Theoretical and computational investigations of geometrical, electronic and spin structures of the CaMn4 OX (X = 5, 6) cluster in the Kok cycle Si (i = 0-3) of oxygen evolving complex of photosystem II

The optimized geometries of the CaMn₄ O_X (X = 5, 6) cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) by large-scale quantum mechanics (QM) and molecular mechanics (MM) calculations are compared with recent serial femtosecond crystallography (SFX) results for the S_i (i = 0-3) states. The valence states of four Mn ions by the QM/MM calculations are also examined in relation to the experimental results by the X-ray emission spectroscopy (XES) for the S_i intermediates. Geometrical and valence structures of right-opened Mn-hydroxide, Mn-oxo and Mn-peroxide intermediates in the S₃ state are investigated in detail in relation to recent SFX and XES experiments for the S₃ state. Interplay between theory and experiment indicates that the Mn-oxo intermediate is a new possible candidate for the S₃ state. Implications of the computational results are discussed in relation to possible mechanisms of the oxygenoxygen bond formation for water oxidation in OEC of PSII.

Thermodynamics of the S2-to-S3 state transition of the oxygen-evolving complex of photosystem II

The S₂ to S₃ transition in the OEC of PSII changes the structure of the Mn cluster. Monte Carlo sampling finds a Ca terminal water moves to form a bridge to Mn4 and the Mn1 ligand E189 can be replaced with a hydroxyl as a proton is lost.

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.

Resolving Ambiguous Protonation and Oxidation States in the Oxygen Evolving Complex of Photosystem II

Photosystem II (PSII) of photosynthetic organisms converts light energy into chemical energy by oxidizing water to dioxygen at the Mn₄CaO₅ oxygen-evolving complex (OEC). Extensive structural data have been collected on the resting dark state (nominally S₁ in the standard Kok nomenclature) from crystal diffraction and EXAFS studies but the protonation and Mn oxidation states are still uncertain. A "high-oxidation" model assigns the S₁ state to have the formal Mn oxidation level of (III, IV, IV, III), whereas the "low-oxidation" model posits two additional electrons. Generally, additional protons are expected to be associated with the low-oxidation model and were not fully investigated until now. Here we consider structural features of the S₀ and S₁ states using a quantum mechanics/molecular mechanics (QM/MM) method. We systematically alter the hydrogen-bonding network and the protonation states of bridging and terminal oxygens and His337 to investigate how they influence Mn-Mn and Mn-O distances, relative energetics, and the internal distribution of Mn oxidation states, in both high and low-oxidation state paradigms. The bridging oxygens (O1, O2, O3, O4) all need to be deprotonated (O^2-) to be compatible with available structural data, whereas the position of O5 (bridging Mn3, Mn4, and Ca) in the XFEL structure is more consistent with an OH^- under the low paradigm. We show that structures with two short Mn-Mn distances, which are sometimes argued to be diagnostic of a high oxidation state paradigm, can also arise in low oxidation-state models. We conclude that the low Mn oxidation state proposal for the OEC can closely fit all of the available structural data at accessible energies in a straightforward manner. Modeling at the 4 H⁺ protonation level of S₁ under the high paradigm predicts rearrangement of bidentate D1-Asp170 to H-bond to O5 (OH^-), a geometry found in artificial OEC catalysts.

Photosynthetic water splitting by the Mn4Ca2+OX catalyst of photosystem II: its structure, robustness and mechanism

The biological energy cycle of our planet is driven by photosynthesis whereby sunlight is absorbed by chlorophyll and other accessory pigments. The excitation energy is then efficiently transferred to a reaction centre where charge separation occurs in a few picoseconds. In the case of photosystem II (PSII), the energy of the charge transfer state is used to split water into oxygen and reducing equivalents. This is accomplished by the relatively low energy content of four photons of visible light. PSII is a large multi-subunit membrane protein complex embedded in the lipid environment of the thylakoid membranes of plants, algae and cyanobacteria. Four high energy electrons, together with four protons (4H+), are used to reduce plastoquinone (PQ), the terminal electron acceptor of PSII, to plastoquinol (PQH2). PQH2 passes its reducing equivalents to an electron transfer chain which feeds into photosystem I (PSI) where they gain additional reducing potential from a second light reaction which is necessary to drive CO2 reduction. The catalytic centre of PSII consists of a cluster of four Mn ions and a Ca2+ linked by oxo bonds. In addition, there are seven amino acid ligands. In this Article, I discuss the structure of this metal cluster, its stability and the probability that an acid-base (nucleophilic-electrophilic) mechanism catalyses the water splitting reaction on the surface of the metal-cluster. Evidence for this mechanism is presented from studies on water splitting catalysts consisting of organo-complexes of ruthenium and manganese and also by comparison with the enzymology of carbon monoxide dehydrogenase (CODH). Finally the relevance of our understanding of PSII is discussed in terms of artificial photosynthesis with emphasis on inorganic water splitting catalysts as oxygen generating photoelectrodes.

Optimizing Crystal Size of Photosystem II by Macroseeding: Toward Neutron Protein Crystallography

Photosystem II (PSII) catalyzes the photo-oxidation of water to molecular oxygen and protons. The water splitting reaction occurs inside the oxygen-evolving complex (OEC) via a Mn₄CaO₅ cluster. To elucidate the reaction mechanism, detailed structural information for each intermediate state of the OEC is required. Despite the current high-resolution crystal structure of PSII at 1.85 Å and other efforts to follow the structural changes of the Mn₄CaO₅ cluster using X-ray free electron laser (XFEL) crystallography in addition to spectroscopic methods, many details about the reaction mechanism and conformational changes in the catalytic site during water oxidation still remain elusive. In this study, we present a rarely found successful application of the conventional macroseeding method to a large membrane protein like the dimeric PSII core complex (dPSIIcc). Combining microseeding with macroseeding crystallization techniques allowed us to reproducibly grow large dPSIIcc crystals with a size of ~3 mm. These large crystals will help improve the data collected from spectroscopic methods like polarized extended X-ray absorption fine structure (EXAFS) and single crystal electron paramagnetic resonance (EPR) techniques and are a prerequisite for determining a three-dimensional structure using neutron diffraction.

Mixed valency in ligand-bridged diruthenium frameworks: divergences and perspectives

Emerging fundamental issues involving intramolecular electron transfer at the mixed valent diruthenium frameworks and its application prospects have been highlighted.

Crystallographic Data Support the Carousel Mechanism of Water Supply to the Oxygen-Evolving Complex of Photosystem II

Photosystem II (PSII) oxidizes water to produce oxygen through a four-step photocatalytic cycle. Understanding PSII structure-function relations is important for the development of biomimetic photocatalytic systems. The quantum mechanics/molecular mechanics (QM/MM) analysis of substrate water binding to the oxygen-evolving complex (OEC) has suggested a rearrangement of water ligands in a carousel mechanism around a key Mn center. Here, we find that the most recently reported X-ray free-electron laser (XFEL) crystallographic data obtained for the dark-stable S₁ state and the doubly flashed S₃ state at 2.25 Å resolution support the carousel mechanism. The features in the XFEL data and QM/MM model-simulated difference Fourier maps suggest that water displacement may occur from the so-called "narrow" channel, resulting in binding of a new water molecule to the OEC, and thus provide new insights into the nature of rearrangements of water ligands along the catalytic cycle before O=O bond formation.

A DFT/B3LYP study of the mechanisms of the O2 formation reaction catalyzed by the [(terpy)(H2O)MnIII(O)2MnIV(OH2)(terpy)](NO3)3 complex: A paradigm for photosystem II

We present a theoretical study of the reaction pathway for dioxygen molecular formation catalyzed by the [(terpy)(H₂O)Mn^III(O)₂Mn^IV(OH₂) (terpy)](NO₃)₃ (terpy=2,2':6',2″-terpyridine) complex based on DFT-B3LYP calculations. In the initial state of the reaction, a partial oxido radical (0.44 spins) is formed ligated to Mn. This radical is involved in a nucleophylic attack by bulk water in the OO bond reaction formation step, in which the oxido fractional unpaired electron is delocalized toward the outermost Mn of the μ-oxo bridge, instead of the ligated Mn center. The reaction then follows with a series of proton-coupled electron transfer steps, in which the oxidation state, as well as the bond strength of the OO moiety increase, while the OOMn(1) bond gets weaker until O₂ is released. In this model, basic acetate ions from the buffer solution capture protons in the proton-transfer steps. In each step there is reduction of the OOMn(1) binding strength, with concomitant increase of the OO bond strength, which culminates with the release of O₂ in the last step. This last step is entropy driven, while formation of hydroperoxide and superoxide moieties is enthalpy driven. According with experiments, the rate-limiting step is the double oxidation of Mn(IV,III) or peroxymonosulfate binding, which occur prior to the OO bond formation step. This supports our findings that the barriers of all intermediate steps are below the experimental barrier of 19-21kcal/mol. The implications of these findings for understanding photosynthetic water-splitting catalysis are also discussed.

Two Different Structures of the Oxygen-Evolving Complex in the Same Polypeptide Frameworks of Photosystem II

The oxygen-evolving complex (OEC) forms the heart of photosystem II (PSII) in photosynthesis. The crystal structure of PSII from Thermosynechococcus vulcanus has been reported at a resolution of 1.9 Å and at an averaged X-ray dose of 0.43 MGy. The OEC structure is suggested to be partially reduced to Mn(II) by EXAFS and DFT computational studies. Recently, the "radiation-damage-free" structures have been published at 1.95 Å resolution using XFEL, but reports continued to appear that the OEC is reduced to the S₀-state of the Kok cycle. To elucidate much more precise structure of the OEC, in this study two structures were determined at extremely low X-ray doses of 0.03 and 0.12 MGy using conventional synchrotron radiation source. The results indicated that the X-ray reduction effects on the OEC were very small in the low dose region below 0.12 MGy, that is, a threshold existed for the OEC structural changes caused by X-ray exposure. The OEC structures of the two identical monomers in the crystal were clearly different under the threshold of the radiation dose, although the surrounding polypeptide frameworks of PSII were the same. The assumption that the OECs in the crystal were in the dark-stable S₁-state of the Kok cycle should be re-evaluated.

The O2-Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data

Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn₄O₅ inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage "S" states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves through the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O₂ evolution. The structure of the dark-stable S₁ state has been a target for X-ray crystallography for the past 15 years. However, traditional X-ray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S₁ state. However, the atom positions in this crystal structure are still not consistent with high-resolution EXAFS spectroscopy, partially due to the poorly resolved oxygen positions next to Mn centers and partial reduction due to extended dark adaptation of the sample. These inconsistencies led to the new models of the OEC with an alternative low oxidation state and raised questions on the protonation state of the cluster, especially the O5 μ-oxo bridge. This Account summarizes the most recent models of the OEC that emerged from QM/MM, EXAFS and femtosecond X-ray crystallography methods. When PSII in the S₁ state is exposed to light, the S₁ state is advanced to the higher oxidation states and eventually binds substrate water molecules. Identifying the substrate waters is of paramount importance for establishing the water-oxidation mechanism but is complicated by a large number of spectroscopically similar waters. Water analogues can, therefore, be helpful because they serve as spectroscopic markers that help to track the motion of the substrate waters. Due to a close structural and electronic similarity to water, ammonia has been of particular interest. We review three competing hypotheses on substrate water/ammonia binding and compile theoretical and experimental evidence to support them. Binding of ammonia as a sixth ligand to Mn4 during the S₁ → S₂ transition seems to satisfy most of the criteria, especially the most compelling recent EPR data on D1-D61A mutated PSII. Such a binding mode suggests delivery of water from the "narrow" channel through a "carousel" rearrangement of waters around Mn4 upon the S₂ → S₃ transition. An alternative hypothesis suggests water delivery through the "large" channel on the Ca side. However, both water delivery paths lead to a similar S₃ structure, seemingly reaching consensus on the nature of the last detectable S-state intermediate in the Kok cycle before O₂ evolution.

Theoretical study of the EPR spectrum of the S3TyrZ• metalloradical intermediate state of the O2-evolving complex of photosystem II

The intermediates trapped during the transitions between the consecutive S-states of the oxygen-evolving complex (OEC) of photosystem II (PSII) contain the free radical TyrZ^• interacting magnetically with the Mn-cluster (Mn₄Ca). In this paper, we present a theoretical study of the EPR spectrum of the S₃TyrZ^• metalloradical intermediate state, which has been recently detected in MeOH-containing PSII preparations. For this analysis, we use two different approximations: the first, simpler one, is the point-dipole approach, where the two interacting spins are the S = 1/2 of TyrZ^• and the ground spin state of S = 3 of the OEC being in the S₃ state. The second approximation is based on previous proposals indicating that the ground spin state (S _G = 3) of the S₃ state arises from an antiferromagnetic exchange coupling between the S = 9/2 of the Mn(IV)₃CaO₄ and the S = 3/2 of the external Mn(IV) of the OEC. Under the above assumption, the second approximation involves three interacting spins, denoted S _A(Mn(IV)₃Ca) = 9/2, S _B(Mn(IV)) = 3/2 and S _C(TyrZ^•) = 1/2. Accordingly, the tyrosine radical is exposed to dipolar interactions with both fragments of the OEC, while an antiferromagnetic exchange coupling within the "3 + 1" structural motif of the OEC is also considered. By application of the first-point-dipole approach, the inter-spin distance that simulates the experimental spectrum is not consistent with the theoretical models that were recently reported for the OEC in the S₃ state. Instead, the recent models are consistent with the results of the analysis that is performed by using the second, more detailed, approach.

'Photosystem II: the water splitting enzyme of photosynthesis and the origin of oxygen in our atmosphere'

About 3 billion years ago an enzyme emerged which would dramatically change the chemical composition of our planet and set in motion an unprecedented explosion in biological activity. This enzyme used solar energy to power the thermodynamically and chemically demanding reaction of water splitting. In so doing it provided biology with an unlimited supply of reducing equivalents needed to convert carbon dioxide into the organic molecules of life while at the same time produced oxygen to transform our planetary atmosphere from an anaerobic to an aerobic state. The enzyme which facilitates this reaction and therefore underpins virtually all life on our planet is known as Photosystem II (PSII). It is a pigment-binding, multisubunit protein complex embedded in the lipid environment of the thylakoid membranes of plants, algae and cyanobacteria. Today we have detailed understanding of the structure and functioning of this key and unique enzyme. The journey to this level of knowledge can be traced back to the discovery of oxygen itself in the 18th-century. Since then there has been a sequence of mile stone discoveries which makes a fascinating story, stretching over 200 years. But it is the last few years that have provided the level of detail necessary to reveal the chemistry of water oxidation and O-O bond formation. In particular, the crystal structure of the isolated PSII enzyme has been reported with ever increasing improvement in resolution. Thus the organisational and structural details of its many subunits and cofactors are now well understood. The water splitting site was revealed as a cluster of four Mn ions and a Ca ion surrounded by amino-acid side chains, of which seven provide direct ligands to the metals. The metal cluster is organised as a cubane structure composed of three Mn ions and a Ca2+ linked by oxo-bonds with the fourth Mn ion attached to the cubane. This structure has now been synthesised in a non-protein environment suggesting that it is a totally inorganic precursor for the evolution of the photosynthetic oxygen-evolving complex. In summary, the overall structure of the catalytic site has given a framework on which to build a mechanistic scheme for photosynthetic dioxygen generation and at the same time provide a blue-print and incentive to develop catalysts for artificial photo-electrochemical systems to split water and generate renewable solar fuels.

Room-Temperature Energy-Sampling Kβ X-ray Emission Spectroscopy of the Mn4Ca Complex of Photosynthesis Reveals Three Manganese-Centered Oxidation Steps and Suggests a Coordination Change Prior to O2 Formation

In oxygenic photosynthesis, water is oxidized and dioxygen is produced at a Mn4Ca complex bound to the proteins of photosystem II (PSII). Valence and coordination changes in its catalytic S-state cycle are of great interest. In room-temperature (in situ) experiments, time-resolved energy-sampling X-ray emission spectroscopy of the Mn Kβ1,3 line after laser-flash excitation of PSII membrane particles was applied to characterize the redox transitions in the S-state cycle. The Kβ1,3 line energies suggest a high-valence configuration of the Mn4Ca complex with Mn(III)3Mn(IV) in S0, Mn(III)2Mn(IV)2 in S1, Mn(III)Mn(IV)3 in S2, and Mn(IV)4 in S3 and, thus, manganese oxidation in each of the three accessible oxidizing transitions of the water-oxidizing complex. There are no indications of formation of a ligand radical, thus rendering partial water oxidation before reaching the S4 state unlikely. The difference spectra of both manganese Kβ1,3 emission and K-edge X-ray absorption display different shapes for Mn(III) oxidation in the S2 → S3 transition when compared to Mn(III) oxidation in the S1 → S2 transition. Comparison to spectra of manganese compounds with known structures and oxidation states and varying metal coordination environments suggests a change in the manganese ligand environment in the S2 → S3 transition, which could be oxidation of five-coordinated Mn(III) to six-coordinated Mn(IV). Conceivable options for the rearrangement of (substrate) water species and metal-ligand bonding patterns at the Mn4Ca complex in the S2 → S3 transition are discussed.

The MOD-QM/MM Method: Applications to Studies of Photosystem II and DNA G-Quadruplexes

Quantum mechanics/molecular mechanics (QM/MM) hybrid methods are currently the most powerful computational tools for studies of structure/function relations and catalytic sites embedded in macrobiomolecules (eg, proteins and nucleic acids). QM/MM methodologies are highly efficient since they implement quantum chemistry methods for modeling only the portion of the system involving bond-breaking/forming processes (QM layer), as influenced by the surrounding molecular environment described in terms of molecular mechanics force fields (MM layer). Some of the limitations of QM/MM methods when polarization effects are not explicitly considered include the approximate treatment of electrostatic interactions between QM and MM layers. Here, we review recent advances in the development of computational protocols that allow for rigorous modeling of electrostatic interactions in biomacromolecules and structural refinement, beyond the common limitations of QM/MM hybrid methods. We focus on photosystem II (PSII) with emphasis on the description of the oxygen-evolving complex (OEC) and its high-resolution extended X-ray absorption fine structure spectra (EXAFS) in conjunction with Monte Carlo structural refinement. Furthermore, we review QM/MM structural refinement studies of DNA G4 quadruplexes with embedded monovalent cations and direct comparisons to NMR data.

Electrosynthesis of Biomimetic Manganese-Calcium Oxides for Water Oxidation Catalysis--Atomic Structure and Functionality

Water-oxidizing calcium-manganese oxides, which mimic the inorganic core of the biological catalyst, were synthesized and structurally characterized by X-ray absorption spectroscopy at the manganese and calcium K edges. The amorphous, birnesite-type oxides are obtained through a simple protocol that involves electrodeposition followed by active-site creation through annealing at moderate temperatures. Calcium ions are inessential, but tune the electrocatalytic properties. For increasing calcium/manganese molar ratios, both Tafel slopes and exchange current densities decrease gradually, resulting in optimal catalytic performance at calcium/manganese molar ratios of close to 10 %. Tracking UV/Vis absorption changes during electrochemical operation suggests that inactive oxides reach their highest, all-Mn(IV) oxidation state at comparably low electrode potentials. The ability to undergo redox transitions and the presence of a minor fraction of Mn(III) ions at catalytic potentials is identified as a prerequisite for catalytic activity.

Mechanism of Water Delivery to the Active Site of Photosystem II along the S(2) to S(3) Transition

The two water molecules serving as substrate for the oxygen evolution in Photosystem II are already bound in the S2 state of the Kok-Joliot's cycle. Nevertheless, an additional water molecule is supposed to bind the cluster during the transition between the S2 and S3 states, which has been recently revealed to have the Mn4CaO5 catalytic cluster arranged in an open cubane fashion. In this Letter, by means of ab initio calculations, we investigated the possible pathways for the binding of the upcoming water molecule. Upon the four different possibilities checked in our calculations, the binding of the crystallographic water molecule, originally located nearby the Cl(-) binding site, showed the lowest activation energy barrier. Our findings therefore support the view in which the W2 hydroxyl group and the O5 oxygen act as substrates for the oxygen evolution. Within this framework the role of the open and closed Mn4CaO5 conformers is clarified as well as the exact mechanistic events occurring along the S2 to S3 transition.