Structural evidence for intermediates during O2 formation in photosystem II.

In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn4CaO5 cluster first stores four oxidizing equivalents, the S0 to S4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O-O bond formation chemistry1-3. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok's photosynthetic water oxidation cycle, the S3→[S4]→S0 transition where O2 is formed and Kok's water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn4CaO5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom Ox, which was introduced as a bridging ligand between Ca and Mn1 during the S2→S3 transition4-6, disappears or relocates in parallel with Yz reduction starting at approximately 700 µs after the third flash. The onset of O2 evolution, as indicated by the shortening of the Mn1-Mn4 distance, occurs at around 1,200 µs, signifying the presence of a reduced intermediate, possibly a bound peroxide.

Structures of the intermediates of Kok's photosynthetic water oxidation clock.

Inspired by the period-four oscillation in flash-induced oxygen evolution of photosystem II discovered by Joliot in 1969, Kok performed additional experiments and proposed a five-state kinetic model for photosynthetic oxygen evolution, known as Kok's S-state clock or cycle1,2. The model comprises four (meta)stable intermediates (S0, S1, S2 and S3) and one transient S4 state, which precedes dioxygen formation occurring in a concerted reaction from two water-derived oxygens bound at an oxo-bridged tetra manganese calcium (Mn4CaO5) cluster in the oxygen-evolving complex3-7. This reaction is coupled to the two-step reduction and protonation of the mobile plastoquinone QB at the acceptor side of PSII. Here, using serial femtosecond X-ray crystallography and simultaneous X-ray emission spectroscopy with multi-flash visible laser excitation at room temperature, we visualize all (meta)stable states of Kok's cycle as high-resolution structures (2.04-2.08 Å). In addition, we report structures of two transient states at 150 and 400 µs, revealing notable structural changes including the binding of one additional 'water', Ox, during the S2→S3 state transition. Our results suggest that one water ligand to calcium (W3) is directly involved in substrate delivery. The binding of the additional oxygen Ox in the S3 state between Ca and Mn1 supports O-O bond formation mechanisms involving O5 as one substrate, where Ox is either the other substrate oxygen or is perfectly positioned to refill the O5 position during O2 release. Thus, our results exclude peroxo-bond formation in the S3 state, and the nucleophilic attack of W3 onto W2 is unlikely.

In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121.

The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon-carbon (C-C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. We show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme-substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C-C bond coupling chemistry.

Room temperature X-ray absorption spectroscopy of metalloenzymes with drop-on-demand sample delivery at XFELs.

X-ray crystallography and X-ray spectroscopy using X-ray free electron lasers plays an important role in understanding the interplay of structural changes in the protein and the chemical changes at the metal active site of metalloenzymes through their catalytic cycles. As a part of such an effort, we report here our recent development of methods for X-ray absorption spectroscopy (XAS) at XFELs to study dilute biological samples, available in limited volumes. Our prime target is Photosystem II (PS II), a multi subunit membrane protein complex, that catalyzes the light-driven water oxidation reaction at the Mn4CaO5 cluster. This is an ideal system to investigate how to control multi-electron/proton chemistry, using the flexibility of metal redox states, in coordination with the protein and the water network. We describe the method that we have developed to collect XAS data using PS II samples with a Mn concentration of <1 mM, using a drop-on-demand sample delivery method.

Untangling the sequence of events during the S2 → S3 transition in photosystem II and implications for the water oxidation mechanism.

In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 → S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 → S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S2 → S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.

Inherent Spin-Polarization Coupling in a Magnetoelectric Vortex.

Solid-state materials are currently being explored as a platform for the manipulation of spins for spintronics and quantum information science. More broadly, a wide spectrum of ferroelectric materials, spanning from inorganic oxides to polymeric systems such as PVDF, present a different approach to explore quantum phenomena in which the spins are set and manipulated with electric fields. Using dilute Fe3+-doped ferroelectric PbTiO3-SrTiO3 superlattices as a model system, we demonstrate intrinsic spin-polarization control of spin directionality in complex ferroelectric vortices and skyrmions. Electron paramagnetic resonance (EPR) spectra show that the spins in the Fe3+ ion are strongly coupled to the local polarization and preferentially aligned perpendicular to the ferroelectric polar c axis in this complex vortex structure. The effect of polarization-spin directionality is corroborated by first-principles calculations, demonstrating the variation of the spin directionality with the polar texture and offering the potential for future quantum analogues of macroscopic magnetoelectric devices.

Structure of photosystem II and substrate binding at room temperature.

Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4), in which S1 is the dark-stable state and S3 is the last semi-stable state before O-O bond formation and O2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.

Mechanistic Investigation of the Iron-Catalyzed Azidation of Alkyl C(sp3)-H Bonds with Zhdankin's λ3-Azidoiodane.

An in-depth study of the mechanism of the azidation of C(sp3)-H bonds with Zhdankin's λ3-azidoiodane reagent catalyzed by iron(II)(pybox) complexes is reported. Previously, it was shown that tertiary and benzylic C(sp3)-H bonds of a range of complex molecules underwent highly site-selective azidation by reaction with a λ3-azidoiodane reagent and an iron(II)(pybox) catalyst under mild conditions. However, the mechanism of this reaction was unclear. Here, a series of mechanistic experiments are presented that reveal critical features responsible for the high selectivity and broad scope of this reaction. These experiments demonstrate the ability of the λ3-azidoiodane reagent to undergo I-N bond homolysis under mild conditions to form λ2-iodanyl and azidyl radicals that undergo highly site-selective and rate-limiting abstraction of a hydrogen atom from the substrate. The resultant alkyl radical then combines rapidly with a resting state iron(III)-azide complex, which is generated by the reaction of the λ3-azidoiodane with the iron(II)(pybox) complex, to form the C(sp3)-N3 bond. This mechanism is supported by the independent synthesis of well-defined iron complexes characterized by cyclic voltammetry, X-ray diffraction, and EPR spectroscopy, and by the reaction of the iron complexes with alkanes and the λ3-azidoiodane. Reaction monitoring and kinetic studies further reveal an unusual effect of the catalyst on the rate of formation of product and consumption of reactants and suggest a blueprint for the development of new processes leading to late-stage functionalization of C(sp3)-H bonds.

Effect of Spin-Orbit Coupling on Phonon-Mediated Magnetic Relaxation in a Series of Zero-Valent Vanadium, Niobium, and Tantalum Isocyanide Complexes.

Spin-vibronic coupling leads to spin relaxation in paramagnetic molecules, and an understanding of factors that contribute to this phenomenon is essential for designing next-generation spintronics technology, including single-molecule magnets and spin-based qubits, wherein long-lifetime magnetic ground states are desired. We report spectroscopic and magnetic characterization of the isoelectronic and isostructural series of homoleptic zerovalent transition metal triad M(CNDipp)6 (M = V, Nb, Ta; CNDipp = 2,6-diisopropylphenyl isocyanide) and show experimentally the significant increase in spin relaxation rate upon going from V to Nb to Ta. Correlated electronic calculations and first principle spin-phonon computations support the role of spin-orbit coupling in modulating spin-phonon relaxation. Our results provide experimental evidence that increasing magnetic anisotropy through spin-orbit coupling interactions leads to increased spin-vibronic relaxation, which is detrimental to long spin lifetime in paramagnetic molecules.

Defying Thermodynamics: Stabilization of Alane Within Covalent Triazine Frameworks for Reversible Hydrogen Storage.

The highly unfavorable thermodynamics of direct aluminum hydrogenation can be overcome by stabilizing alane within a nanoporous bipyridine-functionalized covalent triazine framework (AlH3 @CTF-bipyridine). This material and the counterpart AlH3 @CTF-biphenyl rapidly desorb H2 between 95 and 154 °C, with desorption complete at 250 °C. Sieverts measurements, 27 Al MAS NMR and 27 Al{1 H} REDOR experiments, and computational spectroscopy reveal that AlH3 @CTF-bipyridine dehydrogenation is reversible at 60 °C under 700 bar hydrogen, >10 times lower pressure than that required to hydrogenate bulk aluminum. DFT calculations and EPR measurements support an unconventional mechanism whereby strong AlH3 binding to bipyridine results in single-electron transfer to form AlH2 (AlH3 )n clusters. The resulting size-dependent charge redistribution alters the dehydrogenation/rehydrogenation thermochemistry, suggesting a novel strategy to enable reversibility in high-capacity metal hydrides.

Mixed-Valent Diiron µ-Carbyne, µ-Hydride Complexes: Implications for Nitrogenase.

Binding of N2 by the FeMo-cofactor of nitrogenase is believed to occur after transfer of 4 e- and 4 H+ equivalents to the active site. Although pulse EPR studies indicate the presence of two Fe-(µ-H)-Fe moieties, the structural and electronic features of this mixed valent intermediate remain poorly understood. Toward an improved understanding of this bioorganometallic cluster, we report herein that diiron µ-carbyne complex (P6ArC)Fe2(µ-H) can be oxidized and reduced, allowing for the first time spectral characterization of two EPR-active Fe(µ-C)(µ-H)Fe model complexes linked by a 2 e- transfer which bear some resemblance to a pair of En and En+2 states of nitrogenase. Both species populate S = 1/2 states at low temperatures, and the influence of valence (de)localization on the spectroscopic signature of the µ-hydride ligand was evaluated by pulse EPR studies. Compared to analogous data for the {Fe2(µ-H)}2 state of FeMoco (E4(4H)), the data and analysis presented herein suggest that the hydride ligands in E4(4H) bridge isovalent (most probably FeIII) metal centers. Although electron transfer involves metal-localized orbitals, investigations of [(P6ArC)Fe2(µ-H)]+1 and [(P6ArC)Fe2(µ-H)]-1 by pulse EPR revealed that redox chemistry induces significant changes in Fe-C covalency (-50% upon 2 e- reduction), a conclusion further supported by X-ray absorption spectroscopy, 57Fe Mössbauer studies, and DFT calculations. Combined, our studies demonstrate that changes in covalency buffer against the accumulation of excess charge density on the metals by partially redistributing it to the bridging carbon, thereby facilitating multielectron transformations.

S = 3 Ground State for a Tetranuclear MnIV4O4 Complex Mimicking the S3 State of the Oxygen-Evolving Complex.

The S3 state is currently the last observable intermediate prior to O-O bond formation at the oxygen-evolving complex (OEC) of Photosystem II, and its electronic structure has been assigned to a homovalent MnIV4 core with an S = 3 ground state. While structural interpretations based on the EPR spectroscopic features of the S3 state provide valuable mechanistic insight, corresponding synthetic and spectroscopic studies on tetranuclear complexes mirroring the Mn oxidation states of the S3 state remain rare. Herein, we report the synthesis and characterization by XAS and multifrequency EPR spectroscopy of a MnIV4O4 cuboidal complex as a spectroscopic model of the S3 state. Results show that this MnIV4O4 complex has an S = 3 ground state with isotropic 55Mn hyperfine coupling constants of -75, -88, -91, and 66 MHz. These parameters are consistent with an αααß spin topology approaching the trimer-monomer magnetic coupling model of pseudo-octahedral MnIV centers. Importantly, the spin ground state changes from S = 1/2 to S = 3 as the OEC is oxidized from the S2 state to the S3 state. This same spin state change is observed following oxidation of the previously reported MnIIIMnIV3O4 cuboidal complex to the MnIV4O4 complex described here. This sets a synthetic precedent for the observed low-spin to high-spin conversion in the OEC.

Metal-Ligand Cooperativity via Exchange Coupling Promotes Iron- Catalyzed Electrochemical CO2 Reduction at Low Overpotentials.

Biological and heterogeneous catalysts for the electrochemical CO2 reduction reaction (CO2RR) often exhibit a high degree of electronic delocalization that serves to minimize overpotential and maximize selectivity over the hydrogen evolution reaction (HER). Here, we report a molecular iron(II) system that captures this design concept in a homogeneous setting through the use of a redox non-innocent terpyridine-based pentapyridine ligand (tpyPY2Me). As a result of strong metal-ligand exchange coupling between the Fe(II) center and ligand, [Fe(tpyPY2Me)]2+ exhibits redox behavior at potentials 640 mV more positive than the isostructural [Zn(tpyPY2Me)]2+ analog containing the redox-inactive Zn(II) ion. This shift in redox potential is attributed to the requirement for both an open-shell metal ion and a redox non-innocent ligand. The metal-ligand cooperativity in [Fe(tpyPY2Me)]2+ drives the electrochemical reduction of CO2 to CO at low overpotentials with high selectivity for CO2RR (>90%) and turnover frequencies of 100 000 s-1 with no degradation over 20 h. The decrease in the thermodynamic barrier engendered by this coupling also enables homogeneous CO2 reduction catalysis in water without compromising selectivity or rates. Synthesis of the two-electron reduction product, [Fe(tpyPY2Me)]0, and characterization by X-ray crystallography, Mössbauer spectroscopy, X-ray absorption spectroscopy (XAS), variable temperature NMR, and density functional theory (DFT) calculations, support assignment of an open-shell singlet electronic structure that maintains a formal Fe(II) oxidation state with a doubly reduced ligand system. This work provides a starting point for the design of systems that exploit metal-ligand cooperativity for electrocatalysis where the electrochemical potential of redox non-innocent ligands can be tuned through secondary metal-dependent interactions.

Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers.

X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.

Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II.

We describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. We used the injector to analyze microcrystals of Geobacillus stearothermophilus thermolysin (2.2-Å structure), Thermosynechococcus elongatus photosystem II (<3-Å diffraction) and Thermus thermophilus small ribosomal subunit bound to the antibiotic paromomycin at ambient temperature (3.4-Å structure).

XANES and EXAFS of dilute solutions of transition metals at XFELs.

This work has demonstrated that X-ray absorption spectroscopy (XAS), both Mn XANES and EXAFS, of solutions with millimolar concentrations of metal is possible using the femtosecond X-ray pulses from XFELs. Mn XAS data were collected using two different sample delivery methods, a Rayleigh jet and a drop-on-demand setup, with varying concentrations of Mn. Here, a new method for normalization of XAS spectra based on solvent scattering that is compatible with data collection from a highly variable pulsed source is described. The measured XANES and EXAFS spectra of such dilute solution samples are in good agreement with data collected at synchrotron sources using traditional scanning protocols. The procedures described here will enable XFEL-based XAS on dilute biological samples, especially metalloproteins, with low sample consumption. Details of the experimental setup and data analysis methods used in this XANES and EXAFS study are presented. This method will also benefit XAS performed at high-repetition-rate XFELs such as the European XFEL, LCLS-II and LCLS-II-HE.

Structural isomers of the S2 state in photosystem II: do they exist at room temperature and are they important for function?

In nature, an oxo-bridged Mn4 CaO5 cluster embedded in photosystem II (PSII), a membrane-bound multi-subunit pigment protein complex, catalyzes the water oxidation reaction that is driven by light-induced charge separations in the reaction center of PSII. The Mn4 CaO5 cluster accumulates four oxidizing equivalents to enable the four-electron four-proton catalysis of two water molecules to one dioxygen molecule and cycles through five intermediate S-states, S0  - S4 in the Kok cycle. One important question related to the catalytic mechanism of the oxygen-evolving complex (OEC) that remains is, whether structural isomers are present in some of the intermediate S-states and if such equilibria are essential for the mechanism of the O-O bond formation. Here we compare results from electron paramagnetic resonance (EPR) and X-ray absorption spectroscopy (XAS) obtained at cryogenic temperatures for the S2 state of PSII with structural data collected of the S1 , S2 and S3 states by serial crystallography at neutral pH (∼6.5) using an X-ray free electron laser at room temperature. While the cryogenic data show the presence of at least two structural forms of the S2 state, the room temperature crystallography data can be well-described by just one S2 structure. We discuss the deviating results and outline experimental strategies for clarifying this mechanistically important question.

X-ray Emission Spectroscopy as an in Situ Diagnostic Tool for X-ray Crystallography of Metalloproteins Using an X-ray Free-Electron Laser.

Serial femtosecond crystallography (SFX) using the ultrashort X-ray pulses from a X-ray free-electron laser (XFEL) provides a new way of collecting structural data at room temperature that allows for following the reaction in real time after initiation. XFEL experiments are conducted in a shot-by-shot mode as the sample is destroyed and replenished after each X-ray pulse, and therefore, monitoring and controlling the data quality by using in situ diagnostic tools is critical. To study metalloenzymes, we developed the use of simultaneous collection of X-ray diffraction of crystals along with X-ray emission spectroscopy (XES) data that is used as a diagnostic tool for crystallography, by monitoring the chemical state of the metal catalytic center. We have optimized data analysis methods and sample delivery techniques for fast and active feedback to ensure the quality of each batch of samples and the turnover of the catalytic reaction caused by reaction triggering methods. Here, we describe this active in situ feedback system using Photosystem II as an example that catalyzes the oxidation of H2O to O2 at the Mn4CaO5 active site. We used the first moments of the Mn Kß1,3 emission spectra, which are sensitive to the oxidation state of Mn, as the primary diagnostics. This approach is applicable to different metalloproteins to determine the integrity of samples and follow changes in the chemical states of the reaction that can be initiated by light or activated by substrates and offers a metric for determining the diffraction images that are used for the final data sets.

Tetranuclear [MnIIIMn3IVO4] Complexes as Spectroscopic Models of the S2 State of the Oxygen Evolving Complex in Photosystem II.

Despite extensive biochemical, spectroscopic, and computational studies, the mechanism of biological water oxidation by the oxygen evolving complex (OEC) of Photosystem II remains a subject of significant debate. Mechanistic proposals are guided by the characterization of reaction intermediates such as the S2 state, which features two characteristic EPR signals at g = 2 and g = 4.1. Two nearly isoenergetic structural isomers have been proposed as the source of these distinct signals, but relevant structure-electronic structure studies remain rare. Herein, we report the synthesis, crystal structure, electrochemistry, XAS, magnetic susceptibility, variable temperature CW-EPR, and pulse EPR data for a series of [MnIIIMn3IVO4] cuboidal complexes as spectroscopic models of the S2 state of the OEC. Resembling the oxidation state and EPR spectra of the S2 state of the OEC, these model complexes show two EPR signals, a broad low field signal and a multiline signal, that are remarkably similar to the biological system. The effect of systematic changes in the nature of the bridging ligands on spectroscopy were studied. Results show that the electronic structure of tetranuclear Mn complexes is highly sensitive to even small geometric changes and the nature of the bridging ligands. Our model studies suggest that the spectroscopic properties of the OEC may also react very sensitively to small changes in structure; the effect of protonation state and other reorganization processes need to be carefully assessed.