X-ray Emission Spectroscopy Spectra Research Articles

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.

Enhancing Performances of the VOXES Bragg Spectrometer for XES Investigations

Utilizing a dispersive crystal for X-ray Emission Spectroscopy (XES) significantly enhances the energy resolution when compared with spectroscopy performed with just silicon drift detectors. This high resolution is particularly valuable for studying metals, as it offers essential insights into their electronic structures and chemical environments. Conducting such experiments in the laboratory, as opposed to synchrotron light sources, presents challenges due to the reduced intensities of X-ray tubes and, consequently, low signal rates, with the effect of increasing the acquisition time. In this study, we demonstrate that XES spectra can be acquired within a few hours for a CuNiZn metallic sample alloy while still maintaining a good energy resolution and a large dynamic range. This is achieved with the VOXES spectrometer, developed at INFN National Laboratories of Frascati (LNF), along with a background reduction procedure that enhances the signal from emission lines under study. This study is a showcase for improving the efficiency of XES in tabletop setup experiments.

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.

Oriented sp2 bonded carbon structure of hydrogenated amorphous carbon films

Hydrogenated amorphous carbon films consist of sp 2 or sp 3 bonded carbon networks and hydrogen terminations, and their structure are often determined in terms of sp 2 / sp 3 ratio and the hydrogen contents. Although sp 3 bonded carbon structure is isotropic, sp 2 bonded carbon structure has structural anisotropy. To detect the orientation of extremely small the sp 2 bonded carbon network structure in hydrogenated amorphous carbon film, X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES) measurements using synchrotron radiation X-rays with different incident angles were performed. On all prepared films from three types of hydrocarbon source, and the oriented sp 2 bonded carbon networks were detected from their incident angle dependence on XAS and XES spectra. The continuity of these oriented sp 2 carbon bonded structures was small and formed extremely small clusters, and the orientation distribution and direction of the sp 2 carbon structure depended on the source material. Some films have different sp 2 orientations on the surface and inside the film. The orientation of this sp 2 bonded carbon structure in the film was also an important factor and may affect several other film properties. • There is hydrogenated amorphous carbon films with sp 2 oriented structure. • The sp 2 oriented structure could be estimated by angle dependence of XAS and XES. • The sp 2 orientation angle is depend on deposition condition of the films. • The orientation of sp 2 bonded carbon structure affects film properties.

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 FeIV2 intermediate MMOHQ, which is formed in the active site of the sMMO hydroxylase component (MMOH) during the catalytic cycle. Other biological systems also employ high-valent FeIV sites in catalysis; however, MMOHQ is unique as Nature’s only identified FeIV2 intermediate. Previous 57Fe Mössbauer spectroscopic studies have shown that MMOHQ employs antiferromagnetic coupling of the two FeIV sites to yield a diamagnetic cluster. Unfortunately, this lack of net spin prevents the determination of the local spin state (Sloc) 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 MMOHQ trapped by rapid-freeze-quench techniques. A pure XES spectrum of MMOHQ is obtained by subtraction of the contributions from other reaction cycle intermediates with the aid of Mössbauer quantification. Comparisons of the MMOHQ spectrum with those of known Sloc = 1 and Sloc = 2 FeIV sites in chemical and biological models reveal that MMOHQ possesses Sloc = 2 iron sites. This experimental determination of the local spin state will help guide future computational and mechanistic studies of sMMO catalysis.Graphical abstract

AXEAP: a software package for X-ray emission data analysis using unsupervised machine learning.

The Argonne X-ray Emission Analysis Package (AXEAP) has been developed to calibrate and process X-ray emission spectroscopy (XES) data collected with a two-dimensional (2D) position-sensitive detector. AXEAP is designed to convert a 2D XES image into an XES spectrum in real time using both calculations and unsupervised machine learning. AXEAP is capable of making this transformation at a rate similar to data collection, allowing real-time comparisons during data collection, reducing the amount of data stored from gigabyte-sized image files to kilobyte-sized text files. With a user-friendly interface, AXEAP includes data processing for non-resonant and resonant XES images from multiple edges and elements. AXEAP is written in MATLAB and can run on common operating systems, including Linux, Windows, and MacOS.

Interpretation of the X-Ray Emission Spectra of Liquid Water through Temperature and Isotope Dependence.

The interpretation of x-ray emission spectroscopy (XES) spectra in terms of their sensitivity to the hydrogen bonding and the consequent microheterogeneity in liquid water has been debated over a decade. To shed a light on this problem, we report the theoretical reproduction of the debated 1b_{1} peaks observed in the XES spectra of liquid water using semiclassical Kramers-Heisenberg formula. The essence of the temperature and isotope dependence of the 1b_{1} double peaks is explained by molecular dynamics simulations including full vibrational (O─H stretching, bending, and) modes, rotational combined with the density functional theory and core-hole induced dynamics. Some inconsistencies exist with the experimental XES profile, which illustrates the need to employ a more precise theoretical calculations for both geometry sampling and electronic structure using a more sophisticated procedure.

Effects of x-ray free-electron laser pulse intensity on the Mn K β 1,3 x-ray emission spectrum in photosystem II-A case study for metalloprotein crystals and solutions.

In the last ten years, x-ray free-electron lasers (XFELs) have been successfully employed to characterize metalloproteins at room temperature using various techniques including x-ray diffraction, scattering, and spectroscopy. The approach has been to outrun the radiation damage by using femtosecond (fs) x-ray pulses. An example of an important and damage sensitive active metal center is the Mn4CaO5 cluster in photosystem II (PS II), the catalytic site of photosynthetic water oxidation. The combination of serial femtosecond x-ray crystallography and Kβ x-ray emission spectroscopy (XES) has proven to be a powerful multimodal approach for simultaneously probing the overall protein structure and the electronic state of the Mn4CaO5 cluster throughout the catalytic (Kok) cycle. As the observed spectral changes in the Mn4CaO5 cluster are very subtle, it is critical to consider the potential effects of the intense XFEL pulses on the Kβ XES signal. We report here a systematic study of the effects of XFEL peak power, beam focus, and dose on the Mn Kβ1,3 XES spectra in PS II over a wide range of pulse parameters collected over seven different experimental runs using both microcrystal and solution PS II samples. Our findings show that for beam intensities ranging from ∼5 × 1015 to 5 × 1017 W/cm2 at a pulse length of ∼35 fs, the spectral effects are small compared to those observed between S-states in the Kok cycle. Our results provide a benchmark for other XFEL-based XES studies on metalloproteins, confirming the viability of this approach.

Sulfate Speciation Analysis Using Soft X-ray Emission Spectroscopy.

The chemical and electronic structures of 15 different sulfates are studied using S L2,3 soft X-ray emission spectroscopy (XES). Sulfur L2,3 XES spectra of sulfates are distinctively different from those of other sulfur compounds, which makes XES a powerful technique for sulfate detection. Furthermore, subtle but distinct differences between the spectra of sulfates with different cations are observed, which allow a further differentiation of the specific compound. Most prominently, the position and width of the emission from "S 3s" derived bands systematically vary for different compounds, which can be understood with electronic structure and spectral calculations based on density functional theory.

Kβ X-ray Emission Spectroscopy as a Probe of Cu(I) Sites: Application to the Cu(I) Site in Preprocessed Galactose Oxidase.

Cu(I) active sites in metalloproteins are involved in O2 activation, but their O2 reactivity is difficult to study due to the Cu(I) d10 closed shell which precludes the use of conventional spectroscopic methods. Kβ X-ray emission spectroscopy (XES) is a promising technique for investigating Cu(I) sites as it detects photons emitted by electronic transitions from occupied orbitals. Here, we demonstrate the utility of Kβ XES in probing Cu(I) sites in model complexes and a metalloprotein. Using Cu(I)Cl, emission features from double-ionization (DI) states are identified using varying incident X-ray photon energies, and a reasonable method to correct the data to remove DI contributions is presented. Kβ XES spectra of Cu(I) model complexes, having biologically relevant N/S ligands and different coordination numbers, are compared and analyzed, with the aid of density functional theory (DFT) calculations, to evaluate the sensitivity of the spectral features to the ligand environment. While the low-energy Kβ2,5 emission feature reflects the ionization energy of ligand np valence orbitals, the high-energy Kβ2,5 emission feature corresponds to transitions from molecular orbitals (MOs) having mainly Cu 3d character with the intensities determined by ligand-mediated d-p mixing. A Kβ XES spectrum of the Cu(I) site in preprocessed galactose oxidase (GOpre) supports the 1Tyr/2His structural model that was determined by our previous X-ray absorption spectroscopy and DFT study. The high-energy Kβ2,5 emission feature in the Cu(I)-GOpre data has information about the MO containing mostly Cu 3dx2-y2 character that is the frontier molecular orbital (FMO) for O2 activation, which shows the potential of Kβ XES in probing the Cu(I) FMO associated with small-molecule activation in metalloproteins.

Spin Transitions and Compressibility of ε‐Fe7N3 and γ′‐Fe4N: Implications for Iron Alloys in Terrestrial Planet Cores

AbstractIron nitrides are possible constituents of the cores of Earth and other terrestrial planets. Pressure‐induced magnetic changes in iron nitrides and effects on compressibility remain poorly understood. Here we report synchrotron X‐ray emission spectroscopy (XES) and X‐ray diffraction (XRD) results for ε‐Fe7N3 and γ′‐Fe4N up to 60 GPa at 300 K. The XES spectra reveal completion of high‐ to low‐spin transition in ε‐Fe7N3 and γ′‐Fe4N at 43 and 34 GPa, respectively. The completion of the spin transition induces stiffening in bulk modulus of ε‐Fe7N3 by 22% at ~40 GPa, but has no resolvable effect on the compression behavior of γ′‐Fe4N. Fitting pressure‐volume data to the Birch‐Murnaghan equation of state yields V0 = 83.29 ± 0.03 (Å3), K0 = 232 ± 9 GPa, K0′ = 4.1 ± 0.5 for nonmagnetic ε‐Fe7N3 above the spin transition completion pressure, and V0 = 54.82 ± 0.02 (Å3), K0 = 152 ± 2 GPa, K0′ = 4.0 ± 0.1 for γ′‐Fe4N over the studied pressure range. By reexamining evidence for spin transition and effects on compressibility of other candidate components of terrestrial planet cores, Fe3S, Fe3P, Fe7C3, and Fe3C based on previous XES and XRD measurements, we located the completion of high‐ to low‐spin transition at ~67, 38, 50, and 30 GPa at 300 K, respectively. The completion of spin transitions of Fe3S, Fe3P, and Fe3C induces elastic stiffening, whereas that of Fe7C3 induces elastic softening. Changes in compressibility at completion of spin transitions in iron‐light element alloys may influence the properties of Earth's and planetary cores.

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.

A portable on-axis laser-heating system for near-90° X-ray spectroscopy: application to ferropericlase and iron silicide.

A portable IR fiber laser-heating system, optimized for X-ray emission spectroscopy (XES) and nuclear inelastic scattering (NIS) spectroscopy with signal collection through the radial opening of diamond anvil cells near 90°with respect to the incident X-ray beam, is presented. The system offers double-sided on-axis heating by a single laser source and zero attenuation of incoming X-rays other than by the high-pressure environment. A description of the system, which has been tested for pressures above 100 GPa and temperatures up to 3000 K, is given. The XES spectra of laser-heated Mg0.67Fe0.33O demonstrate the potential to map the iron spin state in the pressure-temperature range of the Earth's lower mantle, and the NIS spectra of laser-heated FeSi give access to the sound velocity of this candidate of a phase inside the Earth's core. This portable system represents one of the few bridges across the gap between laser heating and high-resolution X-ray spectroscopies with signal collection near 90°.

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.

Ab initio simulations of x-ray emission spectroscopy with the GW+ Bethe-Salpeter equation method

In order to calculate x-ray emission spectroscopy (XES) spectra, we apply the $GW+$Bethe-Salpeter equation ($\mathrm{GW}+\mathrm{BSE}$) method on a basis of extended quasiparticle theory, which enables one to treat an arbitrary excited state as an initial state, because the initial state in the XES process is a highly excited state with a core hole. Compared to the preexisting experimental data of XES fluorescence photon energy, the calculated $\mathrm{GW}+\mathrm{BSE}$ results give values with about 1-eV accuracy, which is comparable to the previous results using the time-dependent density functional theory with the short-range corrected exchange-correlation functional, the equation of motion-coupled cluster single and double, and delta self-consistent field methods. Our $\mathrm{GW}+\mathrm{BSE}$ results reproduce corresponding experimental XES spectra without missing any peak. The method can assign the excitonic configuration of each peak in XES spectra with the quasiparticle levels. As a result, the analysis of excitonic structure for each peak gives obvious interpretation concerning the relation between excitonic states and valence states.

Evolution of electronic and magnetic properties of nominal magnetite nanoparticles at high pressure probed by x-ray absorption and emission techniques

We present a study of electronic and magnetic properties of nominal magnetite nanoparticles (NPs) (~6 nm) at high pressure in the presence of silicon pressure medium using x-ray absorption near edge structure (XANES), x-ray magnetic circular dichroism (XMCD) and non-resonant x-ray emission spectroscopy (XES). XANES data show a reduction of Fe charge state, a change in local environment around Fe at tetrahedral sites, and a reduced occupation of Fe 4p  orbitals, not seen in previous pressure studies of bulk magnetite. XMCD data show a continuous magnetic moment reduction of ~50% between ambient pressure and 20 GPa, similar to what was observed in previous bulk magnetite studies. XES spectra of NPs indicate a gradual change in spin configuration away from the high-spin state consistent with a postulated charge transfer from Fe 4p  to 3d states and the observed reduction in XMCD signal. Taken together, the results point to substantial differences in the response of electronic and magnetic properties of the nano-counterparts of bulk magnetite at high pressure.

Cu 2p-1s x-ray emission spectroscopy of mineral tetrahedrite Cu12Sb4S13

The electronic structure of mineral tetrahedrite Cu12Sb4S13 showing a metal-semiconductor transition (MST) at TMST = 85 K has been investigated by means of Cu 1s x-ray absorption spectroscopy with the partial fluorescence yield mode (PFY-XAS) and Cu 2p-1s x-ray emission spectroscopy (XES). Remarkable changes are detected in both the PFY-XAS and XES spectra on cooling across TMST. The changes in the spectra indicate that the unoccupied Cu 3d and 4p densities of states (DOS) shift away from the Fermi energy (EF). We conclude that the MST of Cu12Sb4S13 is associated with the decrease of the Cu 3d DOS at EF.

Manganese speciation in Mn-rich CaCO3: A density functional theory study

The manganese content of aragonitic bivalve shells is a potential archival indicator of temporal Mn bioavailability in aquatic environments. The Mn speciation mechanism in biogenic aragonite minerals remains elusive because the analog is challenging to synthesize, and the metastable phase has yet to be fully resolved experimentally. In this study, we performed density functional theory (DFT) computations of hypothetical Mn-doped aragonite to examine its local coordination structure and thermodynamic and electronic properties. Our DFT calculations reproduced the experimental crystal structures and solubility product constants (Ksp) of Mn-doped calcite. The magnetic moment of Mn was close to 5 μB in both Mn-doped calcite and Mn-doped aragonite (Ca1−xMnxCO3). The calculated Ksp of Mn-doped aragonite was higher than that of Mn-doped calcite and increased with Mn content, indicative of the unfavorable coprecipitation of Mn with the aragonite phase. We found that the incorporation of a small mole fraction of Mn into aragonite created significant structural distortion around the Mn site, resulting in mixed coordination numbers of Mn (mainly five and seven). Valence-to-core X-ray emission spectroscopy (XES) measurements are useful in determining the coordination environment of Mn complexes. We calculated theoretical XES spectra, with a 1s core hole in Mn, for Mn-doped calcite and four versions of Mn-doped aragonite. The Boltzmann-averaged spectrum for different coordination numbers in Mn-doped aragonite was akin to an experimental XES spectrum of aragonitic bivalve shells. The energy position of the Kβ2,5 band was calculated to be insensitive to Mn speciation in CaCO3; however, the band intensity was relatively sensitive to Mn speciation. The XES spectrum intensity decreased exponentially with increasing Mn–O distance. This quantitative XES relationship we report can reduce uncertainties in the spectral interpretation due to the absence of an Mn-doped aragonite reference spectrum.

Mn 2p resonant X-ray emission clarifies the redox reaction and charge-transfer effects in LiMn2O4.

High-energy-resolution soft X-ray emission spectroscopy (XES) was applied to understand the changes in the electronic structure of LiMn2O4 upon Li-ion extraction/insertion. Mn 2p-3d-2p resonant XES spectra were analyzed by configuration-interaction full-multiplet (CIFM) calculations, which reproduced both dd and charge-transfer (CT) excitations. From the resonant XES spectra it is found that Mn3+ and Mn4+ coexist in the initial state, while this changes into Mn4+ in the charged-state. For the discharged-state, the Mn3+ component appears again although the dd excitations are slightly modified from those for the initial state. Furthermore, negative CT energy is expected for the Mn4+ configuration, which suggests very strong hybridization between the Mn 3d and O 2p orbitals. The large difference in the CT effect between the Mn4+ and Mn3+ states should give mechanical stress to the Mn-O bond during charge-discharge cycling, leading to capacity fading.

Rapid evolution of the Photosystem II electronic structure during water splitting.

Photosynthetic water oxidation is a fundamental process that sustains the biosphere. A Mn4Ca cluster embedded in the photosystem II protein environment is responsible for the production of atmospheric oxygen. Here, time-resolved x-ray emission spectroscopy (XES) was used to observe the process of oxygen formation in real time. These experiments reveal that the oxygen evolution step, initiated by three sequential laser flashes, is accompanied by rapid (within 50 μs) changes to the Mn Kβ XES spectrum. However, no oxidation of the Mn4Ca core above the all MnIV state was detected to precede O-O bond formation, and the observed changes were therefore assigned to O-O bond formation dynamics. We propose that O-O bond formation occurs prior to the transfer of the final (4th) electron from the Mn4Ca cluster to the oxidized tyrosine YZ residue. This model resolves the kinetic limitations associated with O-O bond formation, and suggests an evolutionary adaptation to avoid releasing of harmful peroxide species.