Analysis Of X-ray Absorption Spectroscopy Data Research Articles

Iterative Bragg peak removal on X-ray absorption spectra with automatic intensity correction.

This study introduces a novel iterative Bragg peak removal with automatic intensity correction (IBR-AIC) methodology for X-ray absorption spectroscopy (XAS), specifically addressing the challenge of Bragg peak interference in the analysis of crystalline materials. The approach integrates experimental adjustments and sophisticated post-processing, including an iterative algorithm for robust calculation of the scaling factor of the absorption coefficients and efficient elimination of the Bragg peaks, a common obstacle in accurately interpreting XAS data, particularly in crystalline samples. The method was thoroughly evaluated on dilute catalysts and thin films, with fluorescence mode and large-angle rotation. The results underscore the technique's effectiveness, adaptability and substantial potential in improving the precision of XAS data analysis. While demonstrating significant promise, the method does have limitations related to signal-to-noise ratio sensitivity and the necessity for meticulous angle selection during experimentation. Overall, IBR-AIC represents a significant advancement in XAS, offering a pragmatic solution to Bragg peak contamination challenges, thereby expanding the applications of XAS in understanding complex materials under diverse experimental conditions.

ProSPyX: software for post-processing images of X-ray ptychography with spectral capabilities.

X-ray ptychography is a coherent diffraction imaging technique based on acquiring multiple diffraction patterns obtained through the illumination of the sample at different partially overlapping probe positions. The diffraction patterns collected are used to retrieve the complex transmittivity function of the sample and the probe using a phase retrieval algorithm. Absorption or phase contrast images of the sample as well as the real and imaginary parts of the probe function can be obtained. Furthermore, X-ray ptychography can also provide spectral information of the sample from absorption or phase shift images by capturing multiple ptychographic projections at varying energies around the resonant energy of the element of interest. However, post-processing of the images is required to extract the spectra. To facilitate this, ProSPyX, a Python package that offers the analysis tools and a graphical user interface required to process spectral ptychography datasets, is presented. Using the PyQt5 Python open-source module for development and design, the software facilitates extraction of absorption and phase spectral information from spectral ptychographic datasets. It also saves the spectra in file formats compatible with other X-ray absorption spectroscopy data analysis software tools, streamlining integration into existing spectroscopic data analysis pipelines. To illustrate its capabilities, ProSPyX was applied to process the spectral ptychography dataset recently acquired on a nickel wire at the SWING beamline of the SOLEIL synchrotron.

Probing the Local Structure of Na in NaNO3-Promoted, MgO-Based CO2 Sorbents via X-ray Absorption Spectroscopy.

This work provides insight into the local structure of Na in MgO-based CO2 sorbents that are promoted with NaNO3. To this end, we use X-ray absorption spectroscopy (XAS) at the Na K-edge to interrogate the local structure of Na during the CO2 capture (MgO + CO2 ↔ MgCO3). The analysis of Na K-edge XAS data shows that the local environment of Na is altered upon MgO carbonation when compared to that of NaNO3 in the as-prepared sorbent. We attribute the changes observed in the carbonated sorbent to an alteration in the local structure of Na at the NaNO3/MgCO3 interfaces and/or in the vicinity of [Mg2+···CO32-] ionic pairs that are trapped in the cooled NaNO3 melt. The changes observed are reversible, i.e., the local environment of NaNO3 was restored after a regeneration treatment to decompose MgCO3 to MgO. The ex situ Na K-edge XAS experiments were complemented by ex situ magic-angle spinning 23Na nuclear magnetic resonance (MAS 23Na NMR), Mg K-edge XAS and X-ray powder diffraction (XRD). These additional experiments support our interpretation of the Na K-edge XAS data. Furthermore, we develop in situ Na (and Mg) K-edge XAS experiments during the carbonation of the sorbent (NaNO3 is molten under the conditions of the in situ experiments). These in situ Na K-edge XANES spectra of molten NaNO3 open new opportunities to investigate the atomic scale structure of CO2 sorbents modified with Na-based molten salts by using XAS.

Bridging the Gap between the X-ray Absorption Spectroscopy and the Computational Catalysis Communities in Heterogeneous Catalysis: A Perspective on the Current and Future Research Directions

X-ray absorption spectroscopy (XAS) [extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES)] is a key technique within the heterogeneous catalysis community to probe the structure and properties of the active site(s) for a diverse range of catalytic materials. However, the interpretation of the raw experimental data to derive an atomistic picture of the catalyst requires modeling and analysis; the EXAFS data are compared to a model, and a goodness of fit parameter is used to judge the best fit. This EXAFS modeling can often be nontrivial and time-consuming; overcoming or improving these limitations remains a central challenge for the community. Considering these limitations, this Perspective highlights how recent developments in analysis software, increased availability of reliable computational models, and application of data science tools can be used to improve the speed, accuracy, and reliability of EXAFS interpretation. In particular, we emphasize the advantages of combining theory and EXAFS as a unified technique that should be treated as a standard (when applicable) to identify catalytic sites and not two separate complementary methods. Building on the recent trends in the computational catalysis community, we also present a community-driven approach to adopt FAIR Guiding Principles for the collection, analysis, dissemination, and storage of XAS data. Written with both the experimental and theory audience in mind, we provide a unified roadmap to foster collaborations between the two communities.

Multivariate curve resolution analysis of operando XAS data for the investigation of the lithiation mechanisms in high entropy oxides

Transition metal-based high entropy oxides (TM-HEO) have recently been gaining interest for their potential use as anodes in next-generation Li-ion batteries. In such systems, however, the lithiation/delithiation mechanisms remain a matter of ongoing investigation. In this work we demonstrate the suitability of Multivariate Curve Resolution (MCR) of operando X-ray absorption spectroscopy (XAS) data to study the lithiation mechanisms in the TM-HEO (Mg0.2Co0.2Ni0.2Cu0.2Zn0.2)O. Through the MCR analysis, the number, nature and concentration evolution as a function of stored charge of all Cu-, Ni- and Co-related active species present during the first lithiation cycle is obtained.

Nano-polycrystalline diamond anvils: key devices for XAS at extreme conditions: their use, scientific impact, present status and future needs

ABSTRACTNano-polycrystalline diamonds (NPDs) have become fundamental tools for cutting-edge X-ray absorption spectroscopy (XAS) studies at high P/T conditions that opened up new research directions by overcoming previous limitations. Indeed, NPDs yield a continuous and weak X-ray background signal which enables the collection of high-quality XAS data of materials compressed in diamond anvil cells. This is a critical advantage over the classically used single-crystal diamonds that generate strong parasitic signals (glitches) which render the analysis of XAS data in many cases impossible. In this contribution we give an overview of the impact and the scientific opportunities that NPDs opened up for extreme condition XAS spectroscopy at the European Synchrotron Radiation Facility and discuss future needs.

Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin.

We present a detailed analysis of the X-ray absorption near-edge structure (XANES) data on the Fe K-edge of CO Myoglobin based on a combined procedure of Molecular Dynamics (MD) calculations and MXAN (Minuit XANes) data analysis that we call D-MXAN. The ability of performing quantitative XANES data analysis allows us to refine classical force field MD parameters, thus obtaining a reliable tool for the atomic investigation of this important model system for biological macromolecules. The iterative procedure here applied corrects the greatest part of the structural discrepancy between classical MD sampling and experimental determinations. Our procedure, moreover, is able to discriminate between different heme conformational basins visited during the MD simulation, thus demonstrating the necessity of a sampling on the order of tens of nanoseconds, even for an application such X-ray absorption spectroscopy data analysis.

Design of efficient Pt-based electrocatalysts through characterization by X-ray absorption spectroscopy

A method is described to determine the internal structure of electrocatalyst nanoparticles by in situ X-ray absorption spectroscopy (XAS). The nondestructive spectroscopic technique typically utilizing synchrotron radiation as the source measures changes in the X-ray absorption coefficient as a function of energy. The bulk technique has found its use for materials characterization in all scientific areas, including nanomaterials. The analysis of the internal structure of nanoparticles reveals interatomic distances and coordination numbers for each element, and their values and mutual relations indicate whether the elements form a homogeneous or heterogeneous mixture. The core-shell heterogeneous structure in which certain elements are predominantly located in the core, and others form the encapsulating shell is of particular importance in catalysis and electrocatalysis because it may reduce the amount of precious metals in nanoparticles by replacing the atoms in the core of nanoparticles with more abundant and cheaper alternatives. The examples of nanoparticle structures designed in the laboratory and the approach to model efficient catalysts through systematic analysis of XAS data in electrochemical systems consisting of two and three metals are also demonstrated.

Cerium sequestration and accumulation in fractured crystalline bedrock: The role of Mn-Fe (hydr-)oxides and clay minerals

This study focuses on the mechanisms of Ce sequestration and accumulation in the fracture network of the upper kilometer of the granitoid bedrock of the Baltic Shield in southeast Sweden (Laxemar area, Sweden). The material includes 81 specimens of bulk secondary mineral precipitates (“fracture coatings”) collected on fracture walls identified in 17 drill cores, and 66 groundwater samples collected from 21 deep boreholes with equipment designed for retrieval of representative groundwater at controlled depths. The concentrations of Ce in the fracture coatings, although varying considerably (10–90th percentiles: 67–438mgkg−1), were frequently higher than those of the wall rock (10–90th percentiles: 70–118mgkg−1). Linear combination fitting analysis of Ce LIII-edge X-ray absorption near-edge structure (XANES) spectra, obtained for 19 fracture coatings with relatively high Ce concentrations (⩾145mgkg−1) and a wide range of Ce-anomaly values, revealed that Ce(IV) occurs frequently in the upper 10m of the fracture network (Ce(IV)/Cetotal=0.06–1.00 in 8 out of 11 specimens) and is mainly associated with Mn oxides (modeled as Ce oxidatively scavenged by birnessite). These features are in line with the strong oxidative and sorptive capacities of Mn oxide as demonstrated by previous studies, and abundant todorokite and birnessite-like Mn oxides identified in 3 out of 4 specimens analyzed by Mn K-edge X-ray absorption spectroscopy (XAS) in the upper parts of the fracture network (down to 5m). For a specimen with very high Ce concentration (1430mgkg−1) and NASC-normalized Ce anomaly (3.63), the analysis of Ce XANES and Mn XAS data revealed (i) a predominance of Ce oxide in addition to Ce scavenged by Mn oxide; and (ii) a large fraction of poorly-crystalline hexagonal birnessite and aqueous Mn2+, suggesting a recent or on-going oxidation of Mn2+ in this fracture. In addition, the Ce oxide precipitates on this fracture observed by in situ SEM-EDS contained considerable amounts of Mn. These spectroscopic and microscopic features led us to suggest that the remarkable accumulation of Ce(IV) in this fracture is a result of repeated formation and dissolution of Mn oxides, that is, formation of Mn oxide followed by oxidative scavenging of Ce as Ce oxide nanoparticles, which largely remained during the subsequent reductive dissolution of the Mn oxides. In addition, the XANES data indicate that goethite has the capability to oxidize Ce at near-neutral pH under our experimental conditions (goethite reacted with 0.001M Ce for 48h in a glove box with O2 <1ppm). This previously unrecognized Ce oxidation pathway also seems to contribute to a minor extent to the oxidative scavenging of Ce in the fracture network. Trivalent Ce in the fracture coatings, in particular below 2.5m, is mainly sorbed as inner-sphere complexes on clay minerals. Taking into account the facts that Ce in the present groundwater is scarce and modeled to be largely complexed with humic substance, it is argued that the inner-sphere complexes were mainly formed from past (Paleozoic) hydrothermal fluids.

Revisiting pressure-induced phase transition in silicon clathrates using Ge substitution

$\mathrm{B}{\mathrm{a}}_{8}\mathrm{S}{\mathrm{i}}_{39}\mathrm{G}{\mathrm{e}}_{7}$ and $\mathrm{B}{\mathrm{a}}_{8}\mathrm{S}{\mathrm{i}}_{29}\mathrm{G}{\mathrm{e}}_{17}$ have been studied at high pressure using x-ray diffraction and x-ray absorption spectroscopy (XAS) at the Ge $K$ edge. In $\mathrm{B}{\mathrm{a}}_{8}\mathrm{S}{\mathrm{i}}_{39}\mathrm{G}{\mathrm{e}}_{7}$, a transition is observed similar to the one in $\mathrm{B}{\mathrm{a}}_{8}\mathrm{S}{\mathrm{i}}_{46}$, apparently isostructural. However, the XAS data analysis shows that the transformation is related to the off-centering of the Ba atoms. A theoretical model based on a Landau potential suggests that this transition is second order, with a symmetry-breaking mechanism related to the Ba displacement probably initiated by the vacancy creation or local distortion predicted theoretically. This analysis gives a coherent picture of the phase transition mechanism. In the case of $\mathrm{B}{\mathrm{a}}_{8}\mathrm{S}{\mathrm{i}}_{29}\mathrm{G}{\mathrm{e}}_{17}$, such phase transition is not observed as the Ba atoms appear already off-center at ambient pressure.

Local Structure Studies of Ti for SrTi16O3 and SrTi18O3 by Advanced X-ray Absorption Spectroscopy Data Analysis

Strontium titanate is a model quantum paraelectric in which in the region of dominating quantum statistics the ferroelectric instability is inhibited due to nearly complete compensation of the harmonic contribution into ferroelectric soft mode frequency by the zero-point motion contribution. The enhancement of atomic masses by the substitution of 18O for 16O decreases the zero-point atomic motion and low-T ferroelectricity in SrTi18O3 is realized. In this study we report on the local structure of Ti in SrTi16O3 and SrTi18O3 by Ti K-edge extended x-ray absorption fine structure measurements in temperature range 6 – 300 K.

Short-range order of compressed amorphous GeSe2.

The structure of amorphous GeSe2 (a-GeSe2) has been studied by means of a combination of two-edges X-ray absorption spectroscopy (XAS) and angle-dispersive X-ray diffraction under pressures up to about 30 GPa. Multiple-edge XAS data-analysis of a-GeSe2 at ambient conditions allowed us to reconstruct and compare the first-neighbor distribution function with previous results obtained by neutron diffraction with isotopic substitution. GeSe2 is found to remain amorphous up to the highest pressures attained, and a reversible 1.5 eV red-shift of the Ge K-edge energy indicating metallization, occurs between 10 GPa and 15 GPa. Two compression stages are identified by XAS structure refinement. First, a decrease of the first-neighbor distances up to about 10 GPa, in the same pressure region of a previously observed breakdown of the intermediate-range order. Second, an increase of the Ge-Se distances, bond disorder, and of the coordination number. This stage is related to a reversible non-isostructural transition involving a gradual conversion from tetra- to octa-hedral geometry which is not yet fully completed at 30 GPa.

The five-to-six-coordination transition of ferric human serum heme-albumin is allosterically-modulated by ibuprofen and warfarin: a combined XAS and MD study.

Human serum albumin (HSA) is involved physiologically in heme scavenging; in turn, heme-albumin (HSA-heme-Fe) displays globin-like properties. Here, the allosteric effect of ibuprofen and warfarin on the local atomic structure around the ferric heme-Fe (heme-Fe(III)) atom of HSA-heme-Fe (HSA-heme-Fe(III)) has been probed by Fe-K edge X-ray absorption spectroscopy (XAS). The quantitative analysis of the Fe-K edge extended X-ray absorption fine structure (EXAFS) signals and modeling of the near edge (XANES) spectral features demonstrated that warfarin and ibuprofen binding modify the local structure of the heme-Fe(III). Combined XAS data analysis and targeted molecular dynamics (MD) simulations provided atomic resolution insights of protein structural rearrangements required to accommodate the heme-Fe(III) upon ibuprofen and warfarin binding. In the absence of drugs, the heme-Fe(III) atom is penta-coordinated having distorted 4+1 configuration made by the nitrogen atoms of the porphyrin ring and the oxygen phenoxy atom of the Tyr161 residue. MD simulations show that ibuprofen and warfarin association to the secondary fatty acid (FA) binding site 2 (FA2) induces a reorientation of domain I of HSA-heme-Fe(III), this leads to the redirection of the His146 residue providing an additional bond to the heme-Fe(III) atom, providing the 5+1 configuration. The comparison of Fe-K edge XANES spectra calculated using MD structures with those obtained experimentally confirms the reliability of the proposed structural model. As a whole, combining XAS and MD simulations it has been possible to provide a reliable model of the heme-Fe(III) atom coordination state and to understand the complex allosteric transition occurring in HSA-heme-Fe(III) upon ibuprofen and warfarin binding.

Origin of saturated green emission from europium in zinc thiogallate

Europium doped zinc thiogallate, ZnGa2S4:Eu2+, has been reported as a saturated green emitting phosphor, suitable as conversion phosphor in white LEDs for lighting or displays. Up to now, no direct proof for the incorporation of Eu2+ in ZnGa2S4 has been given. We combined X-ray diffraction (XRD), cathodoluminescence in electron microscopy (SEM-CL) and X-ray absorption spectroscopy (XAS) to study the incorporation of the europium ions in the host material. The previously reported green luminescence was found to originate from small amounts of unintentionally formed EuGa2S4, and not from europium ions incorporated into ZnGa2S4. EuGa2S4 has a low quantum efficiency (< 20%) and shows strong thermal quenching, already below room temperature. The XAS data analysis suggests that a certain amount of europium might occupy octahedral voids inside the zinc thiogallate lattice in a divalent state. The zinc ion next to these interstitial dopants is then removed for charge compensation. Notwithstanding the possible, but limited, incorporation of Eu2+ in ZnGa2S4, these ions do not activate any luminescence as was shown with SEM-CL.

High resolution scanning tunnelling microscopy and extended x-ray-absorption fine structure study of the (5 × 3) silicide structure on Cu(001)

Using low energy electron diffraction (LEED), scanning tunnelling microscopy (STM), and x-ray absorption spectroscopy (XAS) techniques, we have studied the first steps of silicon adsorption onto Cu (001) single crystal substrate. For low coverage (∼0.5 ML) and after annealing at 100 °C, STM images and LEED patterns reveal the formation of an ordered quasi commensurate (5×3) superstructure. From a quantitative analysis of XAS data, we extract the Si-Cu distance and detail the local atomic arrangement of the (5×3) structure.

Nanostructured calcite precipitated under hydrothermal conditions in the presence of organic and inorganic selenium

Selenium is an important trace metalloid, whose global cycle is controlled by fluid–rock interactions in the Earth's upper crust, interactions with bio-molecules in soils and living systems, and atmospheric transport in ashes. The cycling of selenium is often intimately associated with carbonate phases, with Se being generally incorporated as an impurity in calcite crystals or adsorbed on carbonate nanoparticles. In order to better understand the interaction of aqueous selenium species with carbonates, we studied the precipitation of calcite under hydrothermal conditions (30–90°C, 25–90bar) in a CO2–H2O–Ca(OH)2 medium in the presence of aqueous inorganic and organic selenium compounds. Aqueous carbonation reactions in the presence of selenium at elevated temperatures and pressures, relevant for long-term CO2 sequestration in reservoirs and other natural geological systems, have until now not been investigated to the best of our knowledge. Electron microscopy (FESEM and TEM) and synchrotron X-ray absorption spectroscopy (XAS) were used in a complementary manner to investigate crystal size, structural order (crystallinity), morphology of crystal faces, crystal organization, and selenium speciation in the calcite samples. XAS data analysis showed clear evidence for the incorporation of selenite oxyanion (SeO32−) into the calcite crystal structure. At low Se content (1.3mg/g calcite), a single site was observed with Se surrounded by six Ca atoms, whereas additional sites, probably corresponding to surface sorption sites, were found with increasing Se content. XAS also showed that seleno-L-cystine (Secys) was chemically fragmented during carbonation, and the solid phase contained elemental and oxidized Se, in hexagonal or amorphous form depending on the experimental conditions, with a minor proportion of Se(IV). Moreover, FESEM and TEM measurements revealed a very complex effect of Secys on the particle size and aggregation/agglomeration process, leading to the following calcite morphologies: rhombohedra, elongated rhombohedra (c-axis elongation), scalenohedra, star-like and shell-like crystal aggregates, and irregular calcite polycrystals. The aggregates and irregular polycrystals, which we designate as nanostructured calcite material, were constituted of nanometer-sized calcite crystallites (<100nm). The star and shell-like crystal aggregates, which were observed only in the presence of Secys, may be due to crystal growth in the presence of associated secondary organic compounds due to a simultaneous chemical fragmentation of Secys. Overall, the results from this study show that selenium (of biotic or abiotic origin) can be integrated into the crystallographic structure of calcite under hydrothermal conditions. This has relevance for geological processes in diverse environments, such as hydrothermal systems along mid-ocean ridges, or underground reservoirs associated with massive injection of CO2 for long-term geological sequestration.

Advanced methods for the analysis of x-ray absorption spectroscopy data applied to semiconductors

X-ray absorption spectroscopy (XAS) is an ideal technique for the investigation of the local structure in materials and in particular around dopant species in semiconducting crystals. This experimental technique permits the quantitative determination of structural parameters such as the bond distances and number of neighbors that are fundamental for understanding the incorporation site of the dopant in the matrix. The use of ab initio advanced methods for the simulation of atomic structures or XAS spectra has recently permitted a more complete interpretation of experimental data. Examples on the use of joint theoretical/experimental methods are given here as well as some perspectives for the future development of XAS data analysis.

Structural characterization of vanadium oxide catalysts supported on nanostructured silica SBA-15 using X-ray absorption spectroscopy

The local structure of vanadium oxide supported on nanostructured SiO2 (VxOy/SBA-15) was investigated by in situ X-ray absorption spectroscopy (XAS). Because the number of potential parameters in XAS data analysis often exceeds the number of "independent" parameters, evaluating the reliability and significance of a particular fitting procedure is mandatory. The number of independent parameters (Nyquist) may not be sufficient. Hence, in addition to the number of independent parameters, a novel approach to evaluate the significance of structural fitting parameters in XAS data analysis is introduced. Three samples with different V loadings (i.e. 2.7 wt %, 5.4 wt %, and 10.8 wt %) were employed. Thermal treatment in air at 623 K resulted in characteristic structural changes of the V oxide species. Independent of the V loading, the local structure around V centers in dehydrated VxOy/SBA-15 corresponded to an ordered arrangement of adjacent V2O7 units. Moreover, the V2O7 units were found to persist under selective oxidation reaction conditions.

Towards a black-box for biological EXAFS data analysis. II.Automatic BioXAS Refinement and Analysis(ABRA)

In biological systems, X-ray absorption spectroscopy (XAS) can determine structural details of metal binding sites with high resolution. Here a method enabling an automated analysis of the corresponding EXAFS data is presented, utilizing in addition to least-squares refinement the prior knowledge about structural details and important fit parameters. A metal binding motif is characterized by the type of donor atoms and their bond lengths. These fit results are compared by bond valance sum analysis and target distances with established structures of metal binding sites. Other parameters such as the Debye-Waller factor and shift of the Fermi energy provide further insights into the quality of a fit. The introduction of mathematical criteria, their combination and calibration allows an automated analysis of XAS data as demonstrated for a number of examples. This presents a starting point for future applications to all kinds of systems studied by XAS and allows the algorithm to be transferred to data analysis in other fields.

Pressure-induced phase transitions in amorphous and metastable crystalline germanium by Raman scattering, x-ray spectroscopy, andab initiocalculations

A detailed study of the pressure-induced phase transitions in amorphous Ge $(a\text{-Ge})$ up to 17 GPa is reported combining Raman scattering, x-ray absorption spectroscopy (XAS) measurements, and density-functional theory calculations. $a\text{-Ge}$ samples were films obtained by evaporation and characterized by different density of voids. Specific and reproducible phase transitions (interpreted as disorder-disorder, disorder-order, and order-disorder) are observed on pressurization and depressurization, depending on the initial density of voids. Details of the structural and vibrational properties of the various phases have been obtained by XAS and Raman-scattering data analysis. Samples showing a low density of voids transform first into a metallic disordered phase (8 GPa) and to GeII at higher pressures while those with higher density of voids transform directly to the GeII phase (10.6 GPa). Upon depressurization, the first nucleates into the GeIII metastable phase in the 7.2--2.3 GPa pressure range, while the others return to the amorphous state below 5 GPa. The behavior upon depressurization shows that the initial morphology determines the transitions experienced by the pressurized sample down to ambient pressure.