Evidence from in situ X-ray absorption spectroscopy for the involvement of terminal disulfide in the reduction of protons by an amorphous molybdenum sulfide electrocatalyst

The reduction of protons into dihydrogen is important because of its potential use in a wide range of energy applications. The preparation of efficient and cheap catalysts for this reaction is one of the issues that need to be tackled to allow the widespread use of hydrogen as an energy carrier. In this paper, we report the study of an amorphous molybdenum sulfide (MoSx) proton reducing electrocatalyst under functional conditions, using in situ X-ray absorption spectroscopy. We probed the local and electronic structures of both the molybdenum and sulfur elements for the as prepared material as well as the precatalytic and catalytic states. The as prepared material is very similar to MoS3 and remains unmodified under functional conditions (pH = 2 aqueous HNO3) in the precatalytic state (+0.3 V vs RHE). In its catalytic state (-0.3 V vs RHE), the film is reduced to an amorphous form of MoS2 and shows spectroscopic features that indicate the presence of terminal disulfide units. These units are formed concomitantly with the release of hydrogen, and we suggest that the rate-limiting step of the HER is the reduction and protonation of these disulfide units. These results show the implication of terminal disulfide chemical motifs into HER driven by transition-metal sulfides and provide insight into their reaction mechanism.

Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy

The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O-O bond formation, coupled to Mn reduction, does not yet occur within 250 μs after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 Å. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.

Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.

The protonation states of oxo-bridged Mn(IV) dimers resolved by experimental and computational Mn K pre-edge X-ray absorption spectroscopy

In nature, the protonation of oxo bridges is a commonly encountered mechanism for fine-tuning chemical properties and reaction pathways. Often, however, the protonation states are difficult to establish experimentally. This is of particular importance in the oxygen evolving complex of photosystem II, where identification of the bridging oxo protonation states is one of the essential requirements toward unraveling the mechanism. In order to establish a combined experimental and theoretical protocol for the determination of protonation states, we have systematically investigated a series of Mn model complexes by Mn K pre-edge X-ray absorption spectroscopy. An ideal test case for selective bis-μ-oxo-bridge protonation in a Mn dimer is represented by the system [Mn(IV)2(salpn)2(μ-OHn)2](n+). Although the three species [Mn(IV)2(salpn)2(μ-O)2], [Mn(IV)2(salpn)2(μ-O)(μ-OH)](+) and [Mn(IV)2(salpn)2(μ-OH)2](2+) differ only in the protonation of the oxo bridges, they exhibit distinct differences in the pre-edge region while maintaining the same edge energy. The experimental spectra are correlated in detail to theoretically calculated spectra. A time-dependent density functional theory approach for calculating the pre-edge spectra of molecules with multiple metal centers is presented, using both high spin (HS) and broken symmetry (BS) electronic structure solutions. The most intense pre-edge transitions correspond to an excitation of the Mn 1s core electrons into the unoccupied orbitals of local e(g) character (d(z)(2) and d(xy) based in the chosen coordinate system). The lowest energy experimental feature is dominated by excitations of 1s-α electrons, and the second observed feature is primarily attributed to 1s-β electron excitations. The observed energetic separation is due to spin polarization effects in spin-unrestricted density functional theory and models final state multiplet effects. The effects of spin polarization on the calculated Mn K pre-edge spectra, in both the HS and BS solutions, are discussed in terms of the strength of the antiferromagnetic coupling and associated changes in the covalency of Mn-O bonds. The information presented in this paper is complemented with the X-ray emission spectra of the same compounds published in an accompanying paper. Taken together, the two studies provide the foundation for a better understanding of the X-ray spectroscopic data of the oxygen evolving complex (OEC) in photosystem II.

Experimental and computational X-ray emission spectroscopy as a direct probe of protonation states in oxo-bridged Mn(IV) dimers relevant to redox-active metalloproteins

The protonation state of oxo bridges in nature is of profound importance for a variety of enzymes, including the Mn4CaO5 cluster of photosystem II and the Mn2O2 cluster in Mn catalase. A set of dinuclear bis-μ-oxo-bridged Mn(IV) complexes in different protonation states was studied by Kβ emission spectroscopy to form the foundation for unraveling the protonation states in the native complex. The valence-to-core regions (valence-to-core XES) of the spectra show significant changes in intensity and peak position upon protonation. DFT calculations were performed to simulate the valence-to-core XES spectra and to assign the spectral features to specific transitions. The Kβ(2,5) peaks arise primarily from the ligand 2p to Mn 1s transitions, with a characteristic low energy shoulder appearing upon oxo-bridge protonation. The satellite Kβ" peak provides a more direct signature of the protonation state change, since the transitions originating from the 2s orbitals of protonated and unprotonated μ-oxo bridges dominate this spectral region. The energies of the Kβ" features differ by ~3 eV and thus are well resolved in the experimental spectra. Additionally, our work explores the chemical resolution limits of the method, namely, whether a mixed (μ-O)(μ-OH2) motif can be distinguished from a symmetric (μ-OH)2 one. The results reported here highlight the sensitivity of Kβ valence-to-core XES to single protonation state changes of bridging ligands, and form the basis for further studies of oxo-bridged polymetallic complexes and metalloenzyme active sites. In a complementary paper, the results from X-ray absorption spectroscopy of the same Mn(IV) dimer series are discussed.

Effect of Al3+ co-doping on the dopant local structure, optical properties, and exciton dynamics in Cu+-doped ZnSe nanocrystals

The dopant local structure and optical properties of Cu-doped ZnSe (ZnSe:Cu) and Cu and Al co-doped ZnSe (ZnSe:Cu,Al) nanocrystals (NCs) were studied with an emphasis on understanding the impact of introducing Al as a co-dopant. Quantum-confined NCs with zinc blende crystal structure and particle size of 6 ± 0.6 Å were synthesized using a wet chemical route. The local structure of the Cu dopant, studied by extended X-ray absorption fine structure, indicated that Cu in ZnSe:Cu NCs occupies a site that is neither substitutional nor interstitial and is adjacent to a Se vacancy. Additionally, we estimated that approximately 25 ± 8% of Cu was located on the surface of the NC. Al(3+) co-doping aids in Cu doping by accounting for the charge imbalance originated by Cu(+) doping and consequently reduces surface Cu doping. The Cu ions remain distorted from the center of the tetrahedron to one of the triangular faces. The lifetime of the dopant-related photoluminescence was found to increase from 550 ± 60 to 700 ± 60 ns after Al co-doping. DFT calculations were used to obtain the density of states of a model system to help explain the optical properties and dynamics processes observed. This study demonstrates that co-doping using different cations with complementary oxidation states is an effective method to enhance optical properties of doped semiconductor NCs of interest for various photonics applications.

L-Edge X-ray Absorption Spectroscopy of Dilute Systems Relevant to Metalloproteins Using an X-ray Free-Electron Laser

L-edge spectroscopy of 3d transition metals provides important electronic structure information and has been used in many fields. However, the use of this method for studying dilute aqueous systems, such as metalloenzymes, has not been prevalent because of severe radiation damage and the lack of suitable detection systems. Here we present spectra from a dilute Mn aqueous solution using a high-transmission zone-plate spectrometer at the Linac Coherent Light Source (LCLS). The spectrometer has been optimized for discriminating the Mn L-edge signal from the overwhelming O K-edge background that arises from water and protein itself, and the ultrashort LCLS X-ray pulses can outrun X-ray induced damage. We show that the deviations of the partial-fluorescence yield-detected spectra from the true absorption can be well modeled using the state-dependence of the fluorescence yield, and discuss implications for the application of our concept to biological samples.

In situ X-ray absorption spectroscopy investigation of a bifunctional manganese oxide catalyst with high activity for electrochemical water oxidation and oxygen reduction

In situ X-ray absorption spectroscopy (XAS) is a powerful technique that can be applied to electrochemical systems, with the ability to elucidate the chemical nature of electrocatalysts under reaction conditions. In this study, we perform in situ XAS measurements on a bifunctional manganese oxide (MnOx) catalyst with high electrochemical activity for the oxygen reduction reaction (ORR) and the oxygen evolution reaction (OER). Using X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS), we find that exposure to an ORR-relevant potential of 0.7 V vs RHE produces a disordered Mn3(II,III,III)O4 phase with negligible contributions from other phases. After the potential is increased to a highly anodic value of 1.8 V vs RHE, relevant to the OER, we observe an oxidation of approximately 80% of the catalytic thin film to form a mixed Mn(III,IV) oxide, while the remaining 20% of the film consists of a less oxidized phase, likely corresponding to unchanged Mn3(II,III,III)O4. XAS and electrochemical characterization of two thin film catalysts with different MnOx thicknesses reveals no significant influence of thickness on the measured oxidation states, at either ORR or OER potentials, but demonstrates that the OER activity scales with film thickness. This result suggests that the films have porous structure, which does not restrict electrocatalysis to the top geometric layer of the film. As the portion of the catalyst film that is most likely to be oxidized at the high potentials necessary for the OER is that which is closest to the electrolyte interface, we hypothesize that the Mn(III,IV) oxide, rather than Mn3(II,III,III)O4, is the phase pertinent to the observed OER activity.

Electronic structural changes of Mn in the oxygen-evolving complex of photosystem II during the catalytic cycle

The oxygen-evolving complex (OEC) in photosystem II (PS II) was studied in the S0 through S3 states using 1s2p resonant inelastic X-ray scattering spectroscopy. The spectral changes of the OEC during the S-state transitions are subtle, indicating that the electrons are strongly delocalized throughout the cluster. The result suggests that, in addition to the Mn ions, ligands are also playing an important role in the redox reactions. A series of Mn(IV) coordination complexes were compared, particularly with the PS II S3 state spectrum to understand its oxidation state. We find strong variations of the electronic structure within the series of Mn(IV) model systems. The spectrum of the S3 state best resembles those of the Mn(IV) complexes Mn3(IV)Ca2 and saplnMn2(IV)(OH)2. The current result emphasizes that the assignment of formal oxidation states alone is not sufficient for understanding the detailed electronic structural changes that govern the catalytic reaction in the OEC.

Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature

Intense femtosecond x-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) of microcrystals of photosystem II (PS II) at room temperature. This method probes the overall protein structure and the electronic structure of the Mn4CaO5 cluster in the oxygen-evolving complex of PS II. XRD data are presented from both the dark state (S1) and the first illuminated state (S2) of PS II. Our simultaneous XRD-XES study shows that the PS II crystals are intact during our measurements at the LCLS, not only with respect to the structure of PS II, but also with regard to the electronic structure of the highly radiation-sensitive Mn4CaO5 cluster, opening new directions for future dynamics studies.

Nanoflow electrospinning serial femtosecond crystallography

An electrospun liquid microjet has been developed that delivers protein microcrystal suspensions at flow rates of 0.14-3.1 µl min(-1) to perform serial femtosecond crystallography (SFX) studies with X-ray lasers. Thermolysin microcrystals flowed at 0.17 µl min(-1) and diffracted to beyond 4 Å resolution, producing 14,000 indexable diffraction patterns, or four per second, from 140 µg of protein. Nanoflow electrospinning extends SFX to biological samples that necessitate minimal sample consumption.

A multi-crystal wavelength dispersive x-ray spectrometer

A multi-crystal wavelength dispersive hard x-ray spectrometer with high-energy resolution and large solid angle collection is described. The instrument is specifically designed for time-resolved applications of x-ray emission spectroscopy (XES) and x-ray Raman scattering (XRS) at X-ray Free Electron Lasers (XFEL) and synchrotron radiation facilities. It also simplifies resonant inelastic x-ray scattering (RIXS) studies of the whole 2d RIXS plane. The spectrometer is based on the Von Hamos geometry. This dispersive setup enables an XES or XRS spectrum to be measured in a single-shot mode, overcoming the scanning needs of the Rowland circle spectrometers. In conjunction with the XFEL temporal profile and high-flux, it is a powerful tool for studying the dynamics of time-dependent systems. Photo-induced processes and fast catalytic reaction kinetics, ranging from femtoseconds to milliseconds, will be resolvable in a wide array of systems circumventing radiation damage.

Preparation and properties of a monomeric high-spin Mn(V)-oxo complex

Oxomanganese(V) species have been implicated in a variety of biological and synthetic processes, including their role as a key reactive center within the oxygen-evolving complex in photosynthesis. Nearly all mononuclear Mn(V)-oxo complexes have tetragonal symmetry, producing low-spin species. A new high-spin Mn(V)-oxo complex that was prepared from a well-characterized oxomanganese(III) complex having trigonal symmetry is now reported. Oxidation experiments with [FeCp(2)](+) were monitored with optical and electron paramagnetic resonance (EPR) spectroscopies and support a high-spin oxomanganese(V) complex formulation. The parallel-mode EPR spectrum has a distinctive S = 1 signal at g = 4.01 with a six-line hyperfine pattern having A(z) = 113 MHz. The presence of an oxo ligand was supported by resonance Raman spectroscopy, which revealed O-isotope-sensitive peaks at 737 and 754 cm(-1) assigned as a Fermi doublet centered at 746 cm(-1)(Δ(18)O = 31 cm(-1)). Mn Kβ X-ray emission spectra showed Kβ' and Kβ(1,3) bands at 6475.92 and 6490.50 eV, respectively, which are characteristic of a high-spin Mn(V) center.

Calcium in the oxygen-evolving complex: structural and mechanistic role determined by X-ray spectroscopy

This review describes the results from X-ray Absorption Spectroscopy studies that have contributed to an understanding of the role of Ca in the photosynthetic water-oxidation reaction. The results include the first Mn, Ca and Sr X-ray spectroscopy studies using Ca or Sr-substituted PS II samples that established the presence of a MnCa heteronuclear structure and its orientation, and the most recent Sr X-ray spectroscopy study using biosynthetically prepared Sr-containing PS II in the various S-states that provide important insights into the requirement for Ca in the mechanism of the Mn(4)Ca catalytic center.

Altered structure of the Mn4Ca cluster in the oxygen-evolving complex of photosystem II by a histidine ligand mutation

The effect of replacing a histidine ligand on the properties of the oxygen-evolving complex (OEC) and the structure of the Mn(4)Ca cluster in Photosystem II (PSII) is studied by x-ray absorption spectroscopy using PSII core complexes from the Synechocystis sp. PCC 6803 D1 polypeptide mutant H332E. In the x-ray crystallographic structures of PSII, D1-His(332) has been assigned as a direct ligand of a manganese ion, and the mutation of this histidine ligand to glutamate has been reported to prevent the advancement of the OEC beyond the S(2)Yz(•) intermediate state. The manganese K-edge (1s core electron to 4p) absorption spectrum of D1-H332E shifts to a lower energy compared with that of the native WT samples, suggesting that the electronic structure of the manganese cluster is affected by the presence of the additional negative charge on the OEC of the mutant. The extended x-ray absorption spectrum shows that the geometric structure of the cluster is altered substantially from that of the native WT state, resulting in an elongation of manganese-ligand and manganese-manganese interactions in the mutant. The strontium-H332E mutant, in which calcium is substituted by strontium, confirms that strontium (calcium) is a part of the altered cluster. The structural perturbations caused by the D1-H332E mutation are much larger than those produced by any biochemical treatment or mutation examined previously with x-ray absorption spectroscopy. The substantial structural changes provide an explanation not only for the altered properties of the D1-H332E mutant but also the importance of the histidine ligand for proper assembly of the Mn(4)Ca cluster.

Activation of a water molecule using a mononuclear Mn complex: from Mn-aquo, to Mn-hydroxo, to Mn-oxyl via charge compensation

Activation of a water molecule by the electrochemical oxidation of a Mn-aquo complex accompanied by the loss of protons is reported. The sequential (2 × 1 electron/1 proton) and direct (2 electron/2 proton) proton-coupled electrochemical oxidation of a non-porphyrinic six-coordinated Mn(II)OH2 complex into a mononuclear Mn(O) complex is described. The intermediate Mn(III)OH2 and Mn(III)OH complexes are electrochemically prepared and analysed. Complete deprotonation of the coordinated water molecule in the Mn(O) complex is confirmed by electrochemical data while the analysis of EXAFS data reveals a gradual shortening of an Mn-O bond upon oxidation from Mn(II)OH2 to Mn(III)OH and Mn(O). Reactivity experiments, DFT calculations and XANES pre-edge features provide strong evidence that the bonding in Mn(O) is best characterized by a Mn(III)-oxyl description. Such oxyl species could play a crucial role in natural and artificial water splitting reactions. We provide here a synthetic example for such species, obtained by electrochemical activation of a water ligand.

X-ray emission spectroscopy to study ligand valence orbitals in Mn coordination complexes

We discuss a spectroscopic method to determine the character of chemical bonding and for the identification of metal ligands in coordination and bioinorganic chemistry. It is based on the analysis of satellite lines in X-ray emission spectra that arise from transitions between valence orbitals and the metal ion 1s level (valence-to-core XES). The spectra, in connection with calculations based on density functional theory (DFT), provide information that is complementary to other spectroscopic techniques, in particular X-ray absorption (XANES and EXAFS). The spectral shape is sensitive to protonation of ligands and allows ligands, which differ only slightly in atomic number (e.g., C, N, O...), to be distinguished. A theoretical discussion of the main spectral features is presented in terms of molecular orbitals for a series of Mn model systems: [Mn(H(2)O)(6)](2+), [Mn(H(2)O)(5)OH](+), and [Mn(H(2)O)(5)NH(3)](2+). An application of the method, with comparison between theory and experiment, is presented for the solvated Mn(2+) ion in water and three Mn coordination complexes, namely [LMn(acac)N(3)]BPh(4), [LMn(B(2)O(3)Ph(2))(ClO(4))], and [LMn(acac)N]BPh(4), where L represents 1,4,7-trimethyl-1,4,7-triazacyclononane, acac stands for the 2,4-pentanedionate anion, and B(2)O(3)Ph(2) represents the 1,3-diphenyl-1,3-dibora-2-oxapropane-1,3-diolato dianion.

X-ray absorption spectroscopy

This review gives a brief description of the theory and application of X-ray absorption spectroscopy, both X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS), especially, pertaining to photosynthesis. The advantages and limitations of the methods are discussed. Recent advances in extended EXAFS and polarized EXAFS using oriented membranes and single crystals are explained. Developments in theory in understanding the XANES spectra are described. The application of X-ray absorption spectroscopy to the study of the Mn(4)Ca cluster in Photosystem II is presented.

Carbon-Centered Free Radicals in Particulate Matter Emissions from Wood and Coal Combustion

Electron paramagnetic resonance (EPR) spectroscopy was used to measure the free radicals in the particulate matter (PM) emissions from wood and coal combustion. The intensity of radicals in PM dropped linearly within two months of sample storage and stabilized after that. This factor of storage time was adjusted when comparing radical intensities among different PM samples. An inverse relationship between coal rank and free radical intensities in PM emissions was observed, which was in contrast with the pattern of radical intensities in the source coals. The strong correlation between intensities of free radical and elemental carbon in PM emissions suggests that the radical species may be carbon-centered. The increased g-factors, 2.0029-2.0039, over that of purely carbon-centered radicals may indicate the presence of vicinal oxygen heteroatom. The redox and biology activities of these carbon-centered radicals are worthy of evaluation.