A Practical Guide to High-resolution X-ray Spectroscopic Measurements and their Applications in Bioinorganic Chemistry

Integrated Experimental and Theoretical Investigation of Copper Active Site Properties of a Lytic Polysaccharide Monooxygenase from Serratia marcescens

In this paper, we employed a multidisciplinary approach, combining experimental techniques and density functional theory (DFT) calculations to elucidate key features of the copper coordination environment of the bacterial lytic polysaccharide monooxygenase (LPMO) from Serratia marcescens (SmAA10). The structure of the holo-enzyme was successfully obtained by X-ray crystallography. We then determined the copper(II) binding affinity using competing ligands and observed that the affinity of the histidine brace ligands for copper is significantly higher than previously described. UV-vis, advanced electron paramagnetic resonance (EPR), and X-ray absorption spectroscopy (XAS) techniques, including high-energy resolution fluorescence detected (HERFD) XAS, were further used to gain insight into the copper environment in both the Cu(II) and Cu(I) redox states. The experimental data were successfully rationalized by DFT models, offering valuable information on the electronic structure and coordination geometry of the copper center. Finally, the Cu(II)/Cu(I) redox potential was determined using two different methods at ca. 350 mV vs NHE and rationalized by DFT calculations. This integrated approach not only advances our knowledge of the active site properties of SmAA10 but also establishes a robust framework for future studies of similar enzymatic systems.

PINK: a tender X-ray beamline for X-ray emission spectroscopy

A high-flux beamline optimized for non-resonant X-ray emission spectroscopy (XES) in the tender X-ray energy range has been constructed at the BESSY II synchrotron source. The beamline utilizes a cryogenically cooled undulator that provides X-rays over the energy range 2.1 keV to 9.5 keV. This energy range provides access to XES [and in the future X-ray absorption spectroscopy (XAS)] studies of transition metals ranging from Ti to Cu (Kα, Kβ lines) and Zr to Ag (Lα, Lβ), as well as light elements including P, S, Cl, K and Ca (Kα, Kβ). The beamline can be operated in two modes. In PINK mode, a multilayer monochromator (E/ΔE ≃ 30-80) provides a high photon flux (1014 photons s-1 at 6 keV and 300 mA ring current), allowing non-resonant XES measurements of dilute substances. This mode is currently available for general user operation. X-ray absorption near-edge structure and resonant XAS techniques will be available after the second stage of the PINK commissioning, when a high monochromatic mode (E/ΔE ≃ 10000-40000) will be facilitated by a double-crystal monochromator. At present, the beamline incorporates two von Hamos spectrometers, enabling time-resolved XES experiments with time scales down to 0.1 s and the possibility of two-color XES experiments. This paper describes the optical scheme of the PINK beamline and the endstation. The design of the two von Hamos dispersive spectrometers and sample environment are discussed here in detail. To illustrate, XES spectra of phosphorus complexes, KCl, TiO2 and Co3O4 measured using the PINK setup are presented.

Gauging Iron-Sulfur Cubane Reactivity from Covalency: Trends with Oxidation State

We investigated room-temperature metal and ligand K-edge X-ray absorption (XAS) spectra of a complete redox series of cubane-type iron-sulfur clusters. The Fe K-edge position provides a qualitative but convenient alternative to the traditional spectroscopic descriptors used to identify oxidation states in these systems, which we demonstrate by providing a calibration curve based on two analytic methods. Furthermore, high energy resolution fluorescence detected XAS (HERFD-XAS) at the S K-edge was used to measure Fe-S bond covalencies and record their variation with the average valence of the Fe atoms. While the Fe-S(thiolate) covalency evolves linearly, gaining 11 ± 0.4% per bond and hole, the Fe-S(μ3) covalency evolves asystematically, reflecting changes in the magnetic exchange mechanism. A strong discontinuity manifested for superoxidation to the all-ferric state, distinguishing its electronic structure and its potential (bio)chemical role from those of its redox congeners. We highlight the functional implications of these trends for the reactivity of iron-sulfur cubanes.

Kβ X-ray Emission Spectroscopy of Cu(I)-Lytic Polysaccharide Monooxygenase: Direct Observation of the Frontier Molecular Orbital for H2O2 Activation

Lytic polysaccharide monooxygenases (LPMOs) catalyze the degradation of recalcitrant carbohydrate polysaccharide substrates. These enzymes are characterized by a mononuclear Cu(I) active site with a three-coordinate T-shaped "His-brace" configuration including the N-terminal histidine and its amine group as ligands. This study explicitly investigates the electronic structure of the d10 Cu(I) active site in a LPMO using Kβ X-ray emission spectroscopy (XES). The lack of inversion symmetry in the His-brace site enables the 3d/p mixing required for intensity in the Kβ valence-to-core (VtC) XES spectrum of Cu(I)-LPMO. These Kβ XES data are correlated to density functional theory (DFT) calculations to define the bonding, and in particular, the frontier molecular orbital (FMO) of the Cu(I) site. These experimentally validated DFT calculations are used to evaluate the reaction coordinate for homolytic cleavage of the H2O2 O-O bond and understand the contribution of this FMO to the low barrier of this reaction and how the geometric and electronic structure of the Cu(I)-LPMO site is activated for rapid reactivity with H2O2.

Electrochemical Sodiation Mechanism in Magnetite Nanoparticle-Based Anodes: Understanding of Nanoionics-Based Sodium Ion Storage Behavior of Fe3O4

Electrochemical ion storage behaviors of Fe₃O₄ nanoparticles, as a representative transition metal oxide for an environmentally benign and low-cost anode for a sodium-ion battery, are thoroughly investigated through a combination of electrochemical analysis and diagnostics of Fe₃O₄ electrode cells, X-ray-based and spectroscopic analysis of material structure evolution as functions of depth of discharge (DoD) and state of charge (SoC), and first principle modeling. The gravimetric capacity is found to be 50 mA h/g for bulk Fe₃O₄ (50 nm average crystallite size) and 100 mA h/g─about a tenth of the theoretical prediction for complete conversion─for Fe₃O₄ nanoparticles (8.7 nm average particle size), respectively. A fundamental and mechanistic study of material evolution as functions of DoD and SoC shows that Fe₃O₄ does not allow electrochemical incorporation of Na⁺ ions into the empty cation positions of the inverse spinel structure, leading to our assertion that electrochemical intercalation of Na⁺ ions to conversion of the Fe₃O₄ anode in sodium-ion batteries is nonviable. A density functional theory investigation points to the impracticality of the intercalation of Na⁺ ions into Fe₃O₄ and further validates our experimental findings. We propose several possible mechanisms corresponding to the observed low capacity, including formation of solid electrolyte interphases with unfavorable properties and adsorption of Na⁺ ions onto surfaces of nanoparticles and/or at heterointerfaces in Fe₃O₄ composite electrodes in a NaPF₆-based electrolyte system.

Determination of the iron(IV) local spin states of the Q intermediate of soluble methane monooxygenase by Kβ X-ray emission spectroscopy

Soluble methane monooxygenase (sMMO) facilitates the conversion of methane to methanol at a non-heme Fe^IV₂ intermediate MMOH_Q, which is formed in the active site of the sMMO hydroxylase component (MMOH) during the catalytic cycle. Other biological systems also employ high-valent Fe^IV sites in catalysis; however, MMOH_Q is unique as Nature’s only identified Fe^IV₂ intermediate. Previous ⁵⁷Fe Mössbauer spectroscopic studies have shown that MMOH_Q employs antiferromagnetic coupling of the two Fe^IV sites to yield a diamagnetic cluster. Unfortunately, this lack of net spin prevents the determination of the local spin state (S_loc) of each of the irons by most spectroscopic techniques. Here, we use Fe Kβ X-ray emission spectroscopy (XES) to characterize the local spin states of the key intermediates of the sMMO catalytic cycle, including MMOH_Q trapped by rapid-freeze-quench techniques. A pure XES spectrum of MMOH_Q is obtained by subtraction of the contributions from other reaction cycle intermediates with the aid of Mössbauer quantification. Comparisons of the MMOH_Q spectrum with those of known S_loc = 1 and S_loc = 2 Fe^IV sites in chemical and biological models reveal that MMOH_Q possesses S_loc = 2 iron sites. This experimental determination of the local spin state will help guide future computational and mechanistic studies of sMMO catalysis.

A Combined Spectroscopic and Computational Study on the Mechanism of Iron-Catalyzed Aminofunctionalization of Olefins Using Hydroxylamine Derived N-O Reagent as the "Amino" Source and "Oxidant"

Herein, we study the mechanism of iron-catalyzed direct synthesis of unprotected aminoethers from olefins by a hydroxyl amine derived reagent using a wide range of analytical and spectroscopic techniques (Mössbauer, Electron Paramagnetic Resonance, Ultra-Violet Visible Spectroscopy, X-ray Absorption, Nuclear Resonance Vibrational Spectroscopy, and resonance Raman) along with high-level quantum chemical calculations. The hydroxyl amine derived triflic acid salt acts as the “oxidant” as well as “amino” group donor. It activates the high-spin Fe(II) (S_t = 2) catalyst [Fe(acac)₂(H₂O)₂] (1) to generate a high-spin (S_t = 5/2) intermediate (Int I), which decays to a second intermediate (Int II) with S_t = 2. The analysis of spectroscopic and computational data leads to the formulation of Int I as [Fe(III)(acac)₂-N-acyloxy] (an alkyl-peroxo-Fe(III) analogue). Furthermore, Int II is formed by N–O bond homolysis. However, it does not generate a high-valent Fe(IV)(NH) species (a Fe(IV)(O) analogue), but instead a high-spin Fe(III) center which is strongly antiferromagnetically coupled (J = −524 cm^–1) to an iminyl radical, [Fe(III)(acac)₂-NH·], giving S_t = 2. Though Fe(NH) complexes as isoelectronic surrogates to Fe(O) functionalities are known, detection of a high-spin Fe(III)-N-acyloxy intermediate (Int I), which undergoes N–O bond cleavage to generate the active iron–nitrogen intermediate (Int II), is unprecedented. Relative to Fe(IV)(O) centers, Int II features a weak elongated Fe–N bond which, together with the unpaired electron density along the Fe–N bond vector, helps to rationalize its propensity for N-transfer reactions onto styrenyl olefins, resulting in the overall formation of aminoethers. This study thus demonstrates the potential of utilizing the iron-coordinated nitrogen-centered radicals as powerful reactive intermediates in catalysis.

Structural Elucidation, Aggregation, and Dynamic Behaviour of N,N,N,N ‐Copper(I) Schiff Base Complexes in Solid and in Solution: A Combined NMR, X‐ray Spectroscopic and Crystallographic Investigation

A series of Cu(I) complexes of bidentate or tetradentate Schiff base ligands bearing either 1‐H‐imidazole or pyridine moieties were synthesized. The complexes were studied by a combination of NMR and X‐ray spectroscopic techniques. The differences between the imidazole‐ and pyridine‐based ligands were examined by ¹H, ¹³C and ¹⁵N NMR spectroscopy. The magnitude of the ¹⁵N_imine coordination shifts was found to be strongly affected by the nature of the heterocycle in the complexes. These trends showed good correlation with the obtained Cu−N_imine bond lengths from single‐crystal X‐ray diffraction measurements. Variable‐temperature NMR experiments, in combination with diffusion ordered spectroscopy (DOSY) revealed that one of the complexes underwent a temperature‐dependent interconversion between a monomer, a dimer and a higher aggregate. The complexes bearing tetradentate imidazole ligands were further studied using Cu K‐edge XAS and VtC XES, where DFT‐assisted assignment of spectral features suggested that these complexes may form polynuclear oligomers in solid state. Additionally, the Cu(II) analogue of one of the complexes was incorporated into a metal‐organic framework (MOF) as a way to obtain discrete, mononuclear complexes in the solid state.

Probing Physical Oxidation State by Resonant X-ray Emission Spectroscopy: Applications to Iron Model Complexes and Nitrogenase

The ability of resonant X-ray emission spectroscopy (XES) to recover physical oxidation state information, which may often be ambiguous in conventional X-ray spectroscopy, is demonstrated. By combining Kβ XES with resonant excitation in the XAS pre-edge region, resonant Kβ XES (or 1s3p RXES) data are obtained, which probe the 3dn+1 final-state configuration. Comparison of the non-resonant and resonant XES for a series of high-spin ferrous and ferric complexes shows that oxidation state assignments that were previously unclear are now easily made. The present study spans iron tetrachlorides, iron sulfur clusters, and the MoFe protein of nitrogenase. While 1s3p RXES studies have previously been reported, to our knowledge, 1s3p RXES has not been previously utilized to resolve questions of metal valency in highly covalent systems. As such, the approach presented herein provides chemists with means to more rigorously and quantitatively address challenging electronic-structure questions.

XABOOM: An X-ray Absorption Benchmark of Organic Molecules Based on Carbon, Nitrogen, and Oxygen 1s → π* Transitions

The performance of several standard and popular approaches for calculating X-ray absorption spectra at the carbon, nitrogen, and oxygen K-edges of 40 primarily organic molecules up to the size of guanine has been evaluated, focusing on the low-energy and intense 1s → π* transitions. Using results obtained with CVS-ADC(2)-x and fc-CVS-EOM-CCSD as benchmark references, we investigate the performance of CC2, ADC(2), ADC(3/2), and commonly adopted density functional theory (DFT)-based approaches. Here, focus is on precision rather than on accuracy of transition energies and intensities-in other words, we target relative energies and intensities and the spread thereof, rather than absolute values. The use of exchange-correlation functionals tailored for time-dependent DFT calculations of core excitations leads to error spreads similar to those seen for more standard functionals, despite yielding superior absolute energies. Long-range corrected functionals are shown to perform particularly well compared to our reference data, showing error spreads in energy and intensity of 0.2-0.3 eV and ∼10%, respectively, as compared to 0.3-0.6 eV and ∼20% for a typical pure hybrid. In comparing intensities, state mixing can complicate matters, and techniques to avoid this issue are discussed. Furthermore, the influence of basis sets in high-level ab initio calculations is investigated, showing that reasonably accurate results are obtained with the use of 6-311++G**. We name this benchmark suite as XABOOM (X-ray absorption benchmark of organic molecules) and provide molecular structures and ground-state self-consistent field energies and spectroscopic data. We believe that it provides a good assessment of electronic structure theory methods for calculating X-ray absorption spectra and will become useful for future developments in this field.

Quantification of Ni-N-O Bond Angles and NO Activation by X-ray Emission Spectroscopy

A series of β-diketiminate Ni-NO complexes with a range of NO binding modes and oxidation states were studied by X-ray emission spectroscopy (XES). The results demonstrate that XES can directly probe and distinguish end-on vs side-on NO coordination modes as well as one-electron NO reduction. Density functional theory (DFT) calculations show that the transition from the NO 2s2s σ* orbital has higher intensity for end-on NO coordination than for side-on NO coordination, whereas the 2s2s σ orbital has lower intensity. XES calculations in which the Ni-N-O bond angle was fixed over the range from 80° to 176° suggest that differences in NO coordination angles of ∼10° could be experimentally distinguished. Calculations of Cu nitrite reductase (NiR) demonstrate the utility of XES for characterizing NO intermediates in metalloenzymes. This work shows the capability of XES to distinguish NO coordination modes and oxidation states at Ni and highlights applications in quantifying small molecule activation in enzymes.

The five-analyzer point-to-point scanning crystal spectrometer at ESRF ID26

X-ray emission spectroscopy in a point-to-point focusing geometry using instruments that employ more than one analyzer crystal poses challenges with respect to mechanical design and performance. This work discusses various options for positioning the components and provides the formulas for calculating their relative placement. Ray-tracing calculations were used to determine the geometrical contributions to the energy broadening including the source volume as given by the beam footprint on the sample. The alignment of the instrument is described and examples are given for the performance.

Probing a Silent Metal: A Combined X-ray Absorption and Emission Spectroscopic Study of Biologically Relevant Zinc Complexes

As the second most common transition metal in the human body, zinc is of great interest to research but has few viable routes for its direct structural study in biological systems. Herein, Zn valence-to-core X-ray emission spectroscopy (VtC XES) and Zn K-edge X-ray absorption spectroscopy (XAS) are presented as a means to understand the local structure of zinc in biological systems through the application of these methods to a series of biologically relevant molecular model complexes. Taken together, the Zn K-edge XAS and VtC XES provide a means to establish the ligand identity, local geometry, and metal-ligand bond lengths. Experimental results are supported by correlation with density-functional-theory-based calculations. Combining these theoretical and experimental approaches will enable future applications to protein systems in a predictive manner.

In situ X-ray emission and high-resolution X-ray absorption spectroscopy applied to Ni-based bimetallic dry methane reforming catalysts

The promoting effect of cobalt on the catalytic activity of a NiCoO Dry Methane Reforming (DMR) catalyst was studied by a combination of in situ Kβ X-ray Emission Spectroscopy (XES) and Kβ-detected High Energy Resolution Fluorescence Detected X-ray absorption spectroscopy (HERFD XAS). Following the calcination process, Ni XES and Kβ-detected HERFD XAS data revealed that the NiO coordination in the NiCoO catalyst has a higher degree of symmetry and is different than that of pure NiO/γ-Al₂O₃. Following the reductive activation, it was found that the NiCoO/γ-Al₂O₃ catalyst required a relatively higher temperature compared to the monometallic NiO/γ-Al₂O₃ catalyst. This finding suggests that Co is hampering the reduction of Ni in the NiCoO catalyst by modulation of its electronic structure. It has also been previously shown that the addition of Co enhances the DMR activity. Further, the Kβ XES spectrum of the partly reduced catalysts at 450 °C reveals that the Ni sites in the NiCoO catalyst are electronically different from the NiO catalyst. The in situ X-ray spectroscopic study demonstrates that reduced metallic Co and Ni are the primary species present after reduction and are preserved under DMR conditions. However, the NiCo catalyst appears to always be somewhat more oxidized than the Ni-only species, suggesting that the presence of cobalt modulates the Ni electronic structure. The electronic structural modulations resulting from the presence of Co may be the key to the increased activity of the NiCo catalyst relative to the Ni-only catalyst. This study emphasizes the potential of in situ X-ray spectroscopy experiments for probing the electronic structure of catalytic materials during activation and under operating conditions.

The Spectroscopy of Nitrogenases

Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.

High-resolution iron X-ray absorption spectroscopic and computational studies of non-heme diiron peroxo intermediates

Ferritin-like carboxylate-bridged non-heme diiron enzymes activate O₂ for a variety of difficult reactions throughout nature. These reactions often begin by abstraction of hydrogen from strong CH bonds. The enzymes activate O₂ at their diferrous cofactors to form canonical diferric peroxo intermediates, with a range of possible coordination modes. Herein, we explore the ability of high-energy resolution fluorescence detected X-ray absorption spectroscopy (HERFD XAS) to provide insight into the nature of peroxo level intermediates in non-heme diiron proteins. Freeze quenched (FQ) peroxo intermediates from p-aminobenzoate N-oxygenase (AurF), aldehyde-deformylating oxygenase (ADO), and the β subunit of class Ia ribonucleotide reductase from Escherichia coli (Ecβ) are investigated. All three intermediates are proposed to adopt different peroxo binding modes, and each exhibit different Fe Kα HERFD XAS pre-edge features and intensities. As these FQ-trapped samples consist of multiple species, deconvolution of HERFD XAS spectra based on speciation, as determined by Mössbauer spectroscopy, is also necessitated - yielding 'pure' diferric peroxo HERFD XAS spectra from dilute protein samples. Finally, the impact of a given peroxo coordination mode on the HERFD XAS pre-edge energy and intensity is evaluated through time-dependent density functional theory (TDDFT) calculations of the XAS spectra on a series of hypothetical model complexes, which span a full range of possible peroxo coordination modes to a diferric core. The utility of HERFD XAS for future studies of enzymatic intermediates is discussed.

Localized Electronic Structure of Nitrogenase FeMoco Revealed by Selenium K-Edge High Resolution X-ray Absorption Spectroscopy

The size and complexity of Mo-dependent nitrogenase, a multicomponent enzyme capable of reducing dinitrogen to ammonia, have made a detailed understanding of the FeMo cofactor (FeMoco) active site electronic structure an ongoing challenge. Selective substitution of sulfur by selenium in FeMoco affords a unique probe wherein local Fe-Se interactions can be directly interrogated via high-energy resolution fluorescence detected X-ray absorption spectroscopic (HERFD XAS) and extended X-ray absorption fine structure (EXAFS) studies. These studies reveal a significant asymmetry in the electronic distribution of the FeMoco, suggesting a more localized electronic structure picture than is typically assumed for iron-sulfur clusters. Supported by experimental small molecule model data in combination with time dependent density functional theory (TDDFT) calculations, the HERFD XAS data is consistent with an assignment of Fe2/Fe6 as an antiferromagnetically coupled diferric pair. HERFD XAS and EXAFS have also been applied to Se-substituted CO-inhibited MoFe protein, demonstrating the ability of these methods to reveal electronic and structural changes that occur upon substrate binding. These results emphasize the utility of Se HERFD XAS and EXAFS for selectively probing the local electronic and geometric structure of FeMoco.

X-ray Magnetic Circular Dichroism Spectroscopy Applied to Nitrogenase and Related Models: Experimental Evidence for a Spin-Coupled Molybdenum(III) Center

Nitrogenase enzymes catalyze the reduction of atmospheric dinitrogen to ammonia utilizing a Mo‐7Fe‐9S‐C active site, the so‐called FeMoco cluster. FeMoco and an analogous small‐molecule (Et₄N)[(Tp)MoFe₃S₄Cl₃] cubane have both been proposed to contain unusual spin‐coupled Mo^III sites with an S(Mo)=1/2 non‐Hund configuration at the Mo atom. Herein, we present Fe and Mo L₃‐edge X‐ray magnetic circular dichroism (XMCD) spectroscopy of the (Et₄N)[(Tp)MoFe₃S₄Cl₃] cubane and Fe L_2,3‐edge XMCD spectroscopy of the MoFe protein (containing both FeMoco and the 8Fe‐7S P‐cluster active sites). As the P‐clusters of MoFe protein have an S=0 total spin, these are effectively XMCD‐silent at low temperature and high magnetic field, allowing for FeMoco to be selectively probed by Fe L_2,3‐edge XMCD within the intact MoFe protein. Further, Mo L₃‐edge XMCD spectroscopy of the cubane model has provided experimental support for a local S(Mo)=1/2 configuration, demonstrating the power and selectivity of XMCD.

X-Ray Absorption Spectroscopy Measurements of Cu-ProIAPP Complexes at Physiological Concentrations

The amyloidogenic islet amyloid polypeptide (IAPP) and the associated pro-peptide ProIAPP1–48 are involved in cell death in type 2 diabetes mellitus. It has been observed that interactions of this peptide with metal ions have an impact on the cytotoxicity of the peptides as well as on their deposition in the form of amyloid fibrils. In particular, Cu(II) seems to inhibit amyloid fibril formation, thus suggesting that Cu homeostasis imbalance may be involved in the pathogenesis of type 2 diabetes mellitus. We performed X-ray Absorption Spectroscopy (XAS) measurements of Cu(II)-ProIAPP complexes under near-physiological (10 μM), equimolar concentrations of Cu(II) and peptide. Such low concentrations were made accessible to XAS measurements owing to the use of the High Energy Resolved Fluorescence Detection XAS facility recently installed at the ESRF beamline BM16 (FAME-UHD). Our preliminary data show that XAS measurements at micromolar concentrations are feasible and confirm that ProIAPP1–48-Cu(II) binding at near-physiological conditions can be detected.

Sub-ppm level high energy resolution fluorescence detected X-ray absorption spectroscopy of selenium in articular cartilage

Selenium speciation down to 400 ppb within articular cartilage was demonstrated through high energy resolution fluorescence detected X-ray absorption spectroscopy coupled to an array of crystal analyzers.

High-Resolution Extended X-ray Absorption Fine Structure Analysis Provides Evidence for a Longer Fe···Fe Distance in the Q Intermediate of Methane Monooxygenase

Despite decades of intense research, the core structure of the methane C-H bond breaking diiron(IV) intermediate, Q, of soluble methane monooxygenase remains controversial, with conflicting reports supporting either a "diamond" diiron core structure or an open core structure. Early extended X-ray absorption fine structure (EXAFS) data assigned a short 2.46 Å Fe-Fe distance to Q (Shu et al. Science 1997, 275, 515 ) that is inconsistent with several theoretical studies and in conflict with our recent high-resolution Fe K-edge X-ray absorption spectroscopy (XAS) studies (Castillo et al. J. Am. Chem. Soc. 2017, 139, 18024 ). Herein, we revisit the EXAFS of Q using high-energy resolution fluorescence-detected extended X-ray absorption fine structure (HERFD-EXAFS) studies. The present data show no evidence for a short Fe-Fe distance, but rather a long 3.4 Å diiron distance, as observed in open core synthetic model complexes. The previously reported 2.46 Å feature plausibly arises from a background metallic iron contribution from the experimental setup, which is eliminated in HERFD-EXAFS due to the increased selectivity. Herein, we explore the origin of the short diiron feature in partial-fluorescent yield EXAFS measurements and discuss the diagnostic features of background metallic scattering contribution to the EXAFS of dilute biological samples. Lastly, differences in sample preparation and resultant sample inhomogeneity in rapid-freeze quenched samples for EXAFS analysis are discussed. The presented approaches have broad implications for EXAFS studies of all dilute iron-containing samples.

Rhodium Oxide Surface-Loaded Gas Sensors

In order to increase their stability and tune-sensing characteristics, metal oxides are often surface-loaded with noble metals. Although a great deal of empirical work shows that surface-loading with noble metals drastically changes sensing characteristics, little information exists on the mechanism. Here, a systematic study of sensors based on rhodium-loaded WO₃, SnO₂, and In₂O₃-examined using X-ray diffraction, high-resolution scanning transmission electron microscopy, direct current (DC) resistance measurements, operando diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy, and operando X-ray absorption spectroscopy-is presented. Under normal sensing conditions, the rhodium clusters were oxidized. Significant evidence is provided that, in this case, the sensing is dominated by a Fermi-level pinning mechanism, i.e., the reaction with the target gas takes place on the noble-metal cluster, changing its oxidation state. As a result, the heterojunction between the oxidized rhodium clusters and the base metal oxide was altered and a change in the resistance was detected. Through measurements done in low-oxygen background, it was possible to induce a mechanism switch by reducing the clusters to their metallic state. At this point, there was a significant drop in the overall resistance, and the reaction between the target gas and the base material was again visible. For decades, noble metal loading was used to change the characteristics of metal-oxide-based sensors. The study presented here is an attempt to clarify the mechanism responsible for the change. Generalities are shown between the sensing mechanisms of different supporting materials loaded with rhodium, and sample-specific aspects that must be considered are identified.

Trends and Advances in the Characterization of Gas Sensing Materials Based on Semiconducting Oxides

The understanding of the fundamental properties and processes of chemoresistive gas sensors based on semiconducting metal oxides is driven by the available characterization techniques and sophisticated approaches used to identify structure-function-relationships. This article summarizes trends and advances in the characterization of gas sensing materials based on semiconducting metal oxides, giving a unique overview of the state of the art methodology used in this field. The focus is set on spectroscopic techniques, but the presented concepts apply to other characterization methods, such as electronic, imaging or diffraction-based techniques. The presented concepts are relevant for academic research as well as for improving R&D approaches in industry.

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 Kβ_1,3 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.

High-Energy-Resolution Fluorescence-Detected X-ray Absorption of the Q Intermediate of Soluble Methane Monooxygenase

Kα high-energy-resolution fluorescence detected X-ray absorption spectroscopy (HERFD XAS) provides a powerful tool for overcoming the limitations of conventional XAS to identify the electronic structure and coordination environment of metalloprotein active sites. Herein, Fe Kα HERFD XAS is applied to the diiron active site of soluble methane monooxygenase (sMMO) and to a series of high-valent diiron model complexes, including diamond-core [FeIV2(μ-O)2(L)2](ClO4)4] (3) and open-core [(O═FeIV-O-FeIV(OH)(L)2](ClO4)3 (4) models (where, L = tris(3,5-dimethyl-4-methoxypyridyl-2-methyl)amine) (TPA*)). Pronounced differences in the HERFD XAS pre-edge energies and intensities are observed for the open versus closed Fe2O2 cores in the model compounds. These differences are reproduced by time-dependent density functional theory (TDDFT) calculations and allow for the pre-edge energies and intensity to be directly correlated with the local active site geometric and electronic structure. A comparison of the model complex HERFD XAS data to that of MMOHQ (the key intermediate in methane oxidation) is supportive of an open-core structure. Specifically, the large pre-edge area observed for MMOHQ may be rationalized by invoking an open-core structure with a terminal FeIV═O motif, though further modulations of the core structure due to the protein environment cannot be ruled out. The present study thus motivates the need for additional experimental and theoretical studies to unambiguously assess the active site conformation of MMOHQ.

Advanced X-ray Spectroscopic Methods for Studying Iron-Sulfur-Containing Proteins and Model Complexes

In this chapter, a brief overview of X-ray spectroscopic methods that may be utilized to obtain insight into the geometric and electronic structure of iron-sulfur proteins is provided. These methods include conventional methods, such as metal and ligand K-edge X-ray absorption, as well as more advanced methods including nonresonant and resonant X-ray emission. In each section, the basic information content of the spectra is highlighted and important experimental considerations are discussed. Throughout the chapter, recent applications to iron-sulfur-containing models and proteins are highlighted.

High-Energy Resolution Fluorescence Detected X-Ray Absorption Spectroscopy: A Powerful New Structural Tool in Environmental Biogeochemistry Sciences

The study of the speciation of highly diluted elements by X-ray absorption spectroscopy (XAS) is extremely challenging, especially in environmental biogeochemistry sciences. Here we present an innovative synchrotron spectroscopy technique: high-energy resolution fluorescence detected XAS (HERFD-XAS). With this approach, measurement of the XAS signal in fluorescence mode using a crystal analyzer spectrometer with a ∼1-eV energy resolution helps to overcome restrictions on sample concentrations that can be typically measured with a solid-state detector. We briefly describe the method, from both an instrumental and spectroscopic point of view, and emphasize the effects of energy resolution on the XAS measurements. We then illustrate the positive impact of this technique in terms of detection limit with two examples dealing with Ce in ecologically relevant organisms and with Hg species in natural environments. The sharp and well-marked features of the HERFD-X-ray absorption near-edge structure spectra obtained enable us to determine unambiguously and with greater precision the speciation of the probed elements. This is a major technological advance, with strong benefits for the study of highly diluted elements using XAS. It also opens new possibilities to explore the speciation of a target chemical element at natural concentration levels, which is critical in the fields of environmental and biogeochemistry sciences.

Comparative electronic structures of nitrogenase FeMoco and FeVco

An investigation of the active site cofactors of the molybdenum and vanadium nitrogenases (FeMoco and FeVco) was performed using high-resolution X-ray spectroscopy. Synthetic heterometallic iron-sulfur cluster models and density functional theory calculations complement the study of the MoFe and VFe holoproteins using both non-resonant and resonant X-ray emission spectroscopy. Spectroscopic data show the presence of direct iron-heterometal bonds, which are found to be weaker in FeVco. Furthermore, the interstitial carbide is found to perturb the electronic structures of the cofactors through highly covalent Fe-C bonding. The implications of these conclusions are discussed in light of the differential reactivity of the molybdenum and vanadium nitrogenases towards various substrates. Possible functional roles for both the heterometal and the interstitial carbide are detailed.