Blueprint XAS: a Matlab‐based toolbox for the fitting and analysis of XAS spectra

Blueprint XAS is a new Matlab‐based program developed to fit and analyse X‐ray absorption spectroscopy (XAS) data, most specifically in the near‐edge region of the spectrum. The program is based on a methodology that introduces a novel background model into the complete fit model and that is capable of generating any number of independent fits with minimal introduction of user bias [Delgado‐Jaime & Kennepohl (2010), J. Synchrotron Rad. 17 , 119–128]. The functions and settings on the five panels of its graphical user interface are designed to suit the needs of near‐edge XAS data analyzers. A batch function allows for the setting of multiple jobs to be run with Matlab in the background. A unique statistics panel allows the user to analyse a family of independent fits, to evaluate fit models and to draw statistically supported conclusions. The version introduced here (v0.2) is currently a toolbox for Matlab. Future stand‐alone versions of the program will also incorporate several other new features to create a full package of tools for XAS data processing.     

Trace element analysis of hairs in patients with dementia

The trace elements of scalp hair samples from ≥60‐year‐old dementia patients and normal persons have been studied by X‐ray absorption near‐edge spectroscopy (XANES) in fluorescent mode and wavelength‐dispersive X‐ray fluorescence spectrometry. Comparisons of hair trace element levels of age‐matched dementia patients and normal persons revealed significantly elevated amounts of calcium, chlorine and phosphorus in dementia patients relative to normal persons. The results of XANES measurements identify the chemical forms of deposited calcium and phosphorus in the hair samples of both dementia patients and normal persons to be calcium chloride (CaCl₂) and phosphate (PO₄^3?), respectively. The amount of sulfur in hairs of dementia patients was found to be not significantly different from that in normal persons. The sulfur K‐edge XANES spectra, however, show significantly higher accumulations of sulfur in the sulfate (SO₄^2?) form in hairs of Alzheimer's disease and Parkinson's disease dementia patients. This study presents the possible roles of calcium, chlorine, phosphorus and sulfur in the etiology of dementia in elderly patients.     

SUT‐NANOTEC‐SLRI beamline for X‐ray absorption spectroscopy

The SUT‐NANOTEC‐SLRI beamline was constructed in 2012 as the flagship of the SUT‐NANOTEC‐SLRI Joint Research Facility for Synchrotron Utilization, co‐established by Suranaree University of Technology (SUT), National Nanotechnology Center (NANOTEC) and Synchrotron Light Research Institute (SLRI). It is an intermediate‐energy X‐ray absorption spectroscopy (XAS) beamline at SLRI. The beamline delivers an unfocused monochromatic X‐ray beam of tunable photon energy (1.25–10 keV). The maximum normal incident beam size is 13 mm (width) × 1 mm (height) with a photon flux of 3 × 10⁸ to 2 × 10¹⁰ photons s^?1 (100 mA)^?1 varying across photon energies. Details of the beamline and XAS instrumentation are described. To demonstrate the beamline performance, K‐edge XANES spectra of MgO, Al₂O₃, S₈, FeS, FeSO₄, Cu, Cu₂O and CuO, and EXAFS spectra of Cu and CuO are presented.     

An attempt at kidney stone analysis with the application of synchrotron radiation

X‐ray absorption near‐edge spectroscopy (XANES) is a spectroscopic technique using synchrotron light to determine the valence state of excited atoms as well as the electronegativity of their neighbouring atoms. XANES spectra can provide information about the chemical bond in the second coordination shell of the excited atom. In this study, XANES spectra of unknown compounds from human kidney stones were recorded around the K‐edges of sulfur, phosphorus and calcium. The XANES results agree well with the diffractogram data of the same stones obtained through an X‐ray powder diffraction (XRPD) technique. By comparing the measurement techniques presented here, it is shown that XANES requires a smaller amount of each sample than XRPD for analysis.     

X‐ray spectroscopic approaches to the investigation and characterization of photochemical processes

Despite a wealth of studies exemplifying the utility of the 2–5 keV X‐ray range in speciation and electronic structure elucidation, the exploitation of this energy regime for the study of photochemical processes has not been forthcoming. Herein, a new endstation set‐up for in situ photochemical soft X‐ray spectroscopy in the 2–5 keV energy region at the Stanford Synchrotron Radiation Lightsource is described for continuous photolysis under anaerobic conditions at both cryogenic and ambient temperatures. Representative examples of this approach are used to demonstrate the potential information content in several fields of study, including organometallic chemistry, biochemistry and materials chemistry.     

Ratio-contrast imaging of dual-energy absorption for element mapping with a scanning transmission X-ray microscope

The detection of chemical mapping with a spatial resolution of 30 nm has been achieved with a scanning transmission X‐ray microscope at the Shanghai Synchrotron Radiation Facility. For each specimen, two absorption images were scanned separately with energies E₁ and E₂: E₁ was focused on the absorption edge of the chosen element and E₂ was focused below the edge. A K‐edge division method is proposed and applied to obtain the element mapping. Compared with the frequently used K‐edge subtraction method, this ratio‐contrast method is shown to be more accurate and sensitive in identifying the elements of interest, where the definition of the contrast threshold is simple and clear in physics. Several examples are presented to illustrate the effectiveness of the method.     

Assessment of sulfur and iron speciation in a soil aggregate by combined S and Fe micro‐XANES: microspatial patterns and relationships

To test whether synchrotron‐based spectromicroscopy can be used to identify spatial patterns of sulfur (S) and iron (Fe) speciation as well as relationships between the speciation of S and Fe in soil colloids or aggregates at the micrometre and sub‐micrometre level, an anoxically prepared dissected soil aggregate (size ～1 mm³) was analyzed by µ‐XANES at the K‐edges of S (2472 eV) and Fe (7112 eV). The experiment included (i) elemental mapping at the S K‐edge (S, Si, Al) and the Fe K‐edge (Fe, Si), (ii) acquisition of 300 µm × 300 µm images of the region of interest with X‐ray energies of 2474 eV (addressing reduced organic and inorganic S), 2483 eV (total S), 7121 eV (divalent Fe) and 7200 eV (total Fe), as well as (iii) acquisition of S and Fe µ‐XANES spectra at two different positions, where image analysis suggested the dominance of reduced and oxidized S and Fe, respectively. Image analysis revealed a heterogeneous distribution of total Si, S and Fe as well as of different S and Fe species in the aggregate. Microregions which were either enriched in reduced or in oxidized S and Fe could be identified. A microregion with a large contribution of oxidized S (sulfate, sulfonate) to total S contained exclusively Fe(III) oxyhydroxides (probably ferrihydrite) as S‐bearing phase, whereas another microregion with a large contribution of reduced organic S (thiol, organic disulfide) to total S contained a small amount of Fe(II)‐bearing silicate in addition to the dominating Fe(III) oxyhydroxides. Our results show that combined S and Fe µ‐XANES is a powerful tool for studying microscale spatial patterns of S and Fe speciation as well as microscale relationships between the speciation of S and Fe in soil aggregates.     

Soft X‐ray absorption spectroscopy and resonant inelastic X‐ray scattering spectroscopy below 100 eV: probing first‐row transition‐metal M‐edges in chemical complexes

X‐ray absorption and scattering spectroscopies involving the 3d transition‐metal K‐ and L‐edges have a long history in studying inorganic and bioinorganic molecules. However, there have been very few studies using the M‐edges, which are below 100 eV. Synchrotron‐based X‐ray sources can have higher energy resolution at M‐edges. M‐edge X‐ray absorption spectroscopy (XAS) and resonant inelastic X‐ray scattering (RIXS) could therefore provide complementary information to K‐ and L‐edge spectroscopies. In this study, M_2,3‐edge XAS on several Co, Ni and Cu complexes are measured and their spectral information, such as chemical shifts and covalency effects, are analyzed and discussed. In addition, M_2,3‐edge RIXS on NiO, NiF₂ and two other covalent complexes have been performed and different d–d transition patterns have been observed. Although still preliminary, this work on 3d metal complexes demonstrates the potential to use M‐edge XAS and RIXS on more complicated 3d metal complexes in the future. The potential for using high‐sensitivity and high‐resolution superconducting tunnel junction X‐ray detectors below 100 eV is also illustrated and discussed.     

Performance of a four‐element Si drift detector for X‐ray absorption fine‐structure spectroscopy: resolution, maximum count rate,and dead‐time correction with incorporation into the ATHENA data analysis software

The performance of a four‐element Si drift detector for energy‐dispersive fluorescence‐yield X‐ray absorption fine‐structure measurements is reported, operating at the National Institute of Standards and Technology beamline X23A2 at the National Synchrotron Light Source. The detector can acquire X‐ray absorption fine‐structure spectra with a throughput exceeding 4 × 10⁵ counts per second per detector element (>1.6 × 10⁶ total counts per second summed over all four channels). At this count rate the resolution at 6 keV is approximately 220 eV, which adequately resolves the Mn Kα and Kβ fluorescence lines. Accurate dead‐time correction is demonstrated, and it has been incorporated into the ATHENA data analysis program. To maintain counting efficiency and high signal to background, it is suggested that the incoming count rate should not exceed ～70% of the maximum throughput.     

Solid energy calibration standards for P K‐edge XANES: electronic structure analysis of PPh4Br

P K‐edge X‐ray absorption near‐edge structure (XANES) spectroscopy is a powerful method for analyzing the electronic structure of organic and inorganic phosphorus compounds. Like all XANES experiments, P K‐edge XANES requires well defined and readily accessible calibration standards for energy referencing so that spectra collected at different beamlines or under different conditions can be compared. This is especially true for ligand K‐edge X‐ray absorption spectroscopy, which has well established energy calibration standards for Cl (Cs₂CuCl₄) and S (Na₂S₂O₃·5H₂O), but not neighboring P. This paper presents a review of common P K‐edge XANES energy calibration standards and analysis of PPh₄Br as a potential alternative. The P K‐edge XANES region of commercially available PPh₄Br revealed a single, highly resolved pre‐edge feature with a maximum at 2146.96 eV. PPh₄Br also showed no evidence of photodecomposition when repeatedly scanned over the course of several days. In contrast, we found that PPh₃ rapidly decomposes under identical conditions. Density functional theory calculations performed on PPh₃ and PPh₄⁺ revealed large differences in the molecular orbital energies that were ascribed to differences in the phosphorus oxidation state (III versus V) and molecular charge (neutral versus +1). Time‐dependent density functional theory calculations corroborated the experimental data and allowed the spectral features to be assigned. The first pre‐edge feature in the P K‐edge XANES spectrum of PPh₄Br was assigned to P 1s → P‐C π* transitions, whereas those at higher energy were P 1s → P‐C σ*. Overall, the analysis suggests that PPh₄Br is an excellent alternative to other solid energy calibration standards commonly used in P K‐edge XANES experiments.     

Characterizing arsenic in preserved hair for assessing exposure potential and discriminating poisoning

Advanced analytical techniques have been used to characterize arsenic in taxidermy specimens. Arsenic was examined to aid in discriminating its use as a preservative from that incorporated by ingestion and hence indicate poisoning (in the case of historical figures). The results are relevant to museum curators, occupational and environmental exposure concerns, toxicological and anthropological investigations. Hair samples were obtained from six taxidermy specimens preserved with arsenic in the late 1800s and early 1900s to investigate the arsenic incorporation. The presence of arsenic poses a potential hazard in museum and private collections. For one sample, arsenic was confirmed to be present on the hair with time‐of‐flight secondary ion mass spectrometry and then measured with neutron activation analysis to comprise 176 µg g^?1. The hair cross section was analysed with synchrotron micro‐X‐ray fluorescence to investigate the transverse distribution of topically applied arsenic. It was found that the arsenic had significantly penetrated all hair samples. Association with melanin clusters and the medulla was observed. Lead and mercury were also identified in one sample. X‐ray absorption near‐edge spectroscopy of the As K‐edge indicated that an arsenate species predominantly existed in all samples; however, analysis was hindered by very rapid photoreduction of the arsenic. It would be difficult to discriminate arsenic consumption from topically applied arsenic based on the physical transverse distribution. Longitudinal distributions and chemical speciation may still allow differentiation.     

XAS analysis of iron and palladium bonded to a polysaccharide produced anaerobically by a strain of Klebsiella oxytoca

Klebsiella oxytoca BAS‐10 ferments citrate to acetic acid and CO₂, and secretes a specific exopolysaccharide (EPS), which is able to bind different metallic species. These biomaterials may be used for different biotechnological purposes, including applications as innovative green biogenerated catalysts. In production of biogenerated Pd species, the Fe(III) as ferric citrate is added to anaerobic culture of K. oxytoca BAS‐10, in the presence of palladium species, to increase the EPS secretion and improve Pd‐EPS yield. In this process, bi‐metallic (FePd‐EPS) biomaterials were produced for the first time. The morphology of bi‐metallic EPS, and the chemical state of the two metals in the FePd‐EPS, are investigated by transmission electron microscopy, Fourier transform infra‐red spectroscopy, micro‐X‐ray fluorescence, and X‐ray absorption spectroscopy methods (XANES and EXAFS), and compared with mono‐metallic Pd‐EPS and Fe‐EPS complexes. Iron in FePd‐EPS is in the mineralized form of iron oxides/hydroxides, predominantly in the form of Fe³⁺, with a small amount of Fe²⁺ in the structure, most probably a mixture of different nano‐crystalline iron oxides and hydroxides, as in mono‐metallic Fe‐EPS. Palladium is found as Pd(0) in the form of metallic nanoparticles with face‐centred cubic structure in both bi‐metallic (FePd‐EPS) and mono‐metallic (Pd‐EPS) species. In bi‐metallic species, Pd and Fe nanoparticles agglomerate in larger clusters, but they remain spatially separated. The catalytic ability of bi‐metallic species (FePd‐EPS) in a hydrodechlorination reaction is improved in comparison with mono‐metallic Pd‐EPS.     

Software for the data analysis of the arrival‐timing monitor at SACLA

X‐ray free‐electron laser (XFEL) pulses from SPring‐8 Ångstrom Compact free‐electron LAser (SACLA) with a temporal duration of <10 fs have provided a variety of benefits in scientific research. In a previous study, an arrival‐timing monitor was developed to improve the temporal resolution in pump–probe experiments at beamline 3 by rearranging data in the order of the arrival‐timing jitter between the XFEL and the synchronized optical laser pulses. This paper presents Timing Monitor Analyzer (TMA), a software package by which users can conveniently obtain arrival‐timing data in the analysis environment at SACLA. The package is composed of offline tools that pull stored data from cache storage, and online tools that pull data from a data‐handling server in semi‐real time during beam time. Users can select the most suitable tool for their purpose, and share the results through a network connection between the offline and online analysis environments.     

XDS: a flexible beamline for X‐ray diffraction and spectroscopy at the Brazilian synchrotron

The majority of the beamlines at the Brazilian Synchrotron Light Source Laboratory (LNLS) use radiation produced in the storage‐ring bending magnets and are therefore currently limited in the flux that can be used in the harder part of the X‐ray spectrum (above ～10 keV). A 4 T superconducting multipolar wiggler (SCW) was recently installed at LNLS in order to improve the photon flux above 10 keV and fulfill the demands set by the materials science community. A new multi‐purpose beamline was then installed at the LNLS using the SCW as a photon source. The XDS is a flexible beamline operating in the energy range between 5 and 30 keV, designed to perform experiments using absorption, diffraction and scattering techniques. Most of the work performed at the XDS beamline concentrates on X‐ray absorption spectroscopy at energies above 18 keV and high‐resolution diffraction experiments. More recently, new setups and photon‐hungry experiments such as total X‐ray scattering, X‐ray diffraction under high pressures, resonant X‐ray emission spectroscopy, among others, have started to become routine at XDS. Here, the XDS beamline characteristics, performance and a few new experimental possibilities are described.     

Stereochemical analysis of ferrocene and the uncertainty of fluorescence XAFS data

Methods for the quantification of statistically valid measures of the uncertainties associated with X‐ray absorption fine structure (XAFS) data obtained from dilute solutions using fluorescence measurements are developed. Experimental data obtained from 10 mM solutions of the organometallic compound ferrocene, Fe(C₅H₅)₂, are analysed within this framework and, following correction for various electronic and geometrical factors, give robust estimates of the standard errors of the individual measurements. The reliability of the refinement statistics of standard current XAFS structure approaches that do not include propagation of experimental uncertainties to assess subtle structural distortions is assessed in terms of refinements obtained for the staggered and eclipsed conformations of the C₅H₅ rings of ferrocene. Standard approaches (XFIT, IFEFFIT) give refinement statistics that appear to show strong, but opposite, preferences for the different conformations. Incorporation of experimental uncertainties into an IFEFFIT‐like analysis yield refinement statistics for the staggered and eclipsed forms of ferrocene which show a far more realistic preference for the eclipsed form which accurately reflects the reliability of the analysis. Moreover, the more strongly founded estimates of the refined parameter uncertainties allow more direct comparison with those obtained by other techniques. These XAFS‐based estimates of the bond distances have accuracies comparable with those obtained using single‐crystal diffraction techniques and are superior in terms of their use in comparisons of experimental and computed structures.     

Beam‐induced redox transformation of arsenic during As K‐edge XAS measurements: availability of reducing or oxidizing agents and As speciation

During X‐ray absorption spectroscopy (XAS) measurements of arsenic (As), beam‐induced redox transformation is often observed. In this study, the As species immobilized by poorly crystallized mackinawite (FeS) was assessed for the susceptibility to beam‐induced redox reactions as a function of sample properties including the redox state of FeS and the solid‐phase As speciation. The beam‐induced oxidation of reduced As species was found to be mediated by the atmospheric O₂ and the oxidation products of FeS [e.g. Fe(III) (oxyhydr)oxides and intermediate sulfurs]. Regardless of the redox state of FeS, both arsenic sulfide and surface‐complexed As(III) readily underwent the photo‐oxidation upon exposure to the atmospheric O₂ during XAS measurements. With strict O₂ exclusion, however, both As(0) and arsenic sulfide were less prone to the photo‐oxidation by Fe(III) (oxyhydr)oxides than NaAsO₂ and/or surface‐complexed As(III). In case of unaerated As(V)‐reacted FeS samples, surface‐complexed As(V) was photocatalytically reduced during XAS measurements, but arsenic sulfide did not undergo the photo‐reduction.     

European research platform IPANEMA at the SOLEIL synchrotron for ancient and historical materials

IPANEMA, a research platform devoted to ancient and historical materials (archaeology, cultural heritage, palaeontology and past environments), is currently being set up at the synchrotron facility SOLEIL (Saint‐Aubin, France; SOLEIL opened to users in January 2008). The new platform is open to French, European and international users. The activities of the platform are centred on two main fields: increased support to synchrotron projects on ancient materials and methodological research. The IPANEMA team currently occupies temporary premises at SOLEIL, but the platform comprises construction of a new building that will comply with conservation and environmental standards and of a hard X‐ray imaging beamline today in its conceptual design phase, named PUMA. Since 2008, the team has supported synchrotron works at SOLEIL and at European synchrotron facilities on a range of topics including pigment degradation in paintings, composition of musical instrument varnishes, and provenancing of medieval archaeological ferrous artefacts. Once the platform is fully operational, user support will primarily take place within medium‐term research projects for `hosted' scientists, PhDs and post‐docs. IPANEMA methodological research is focused on advanced two‐dimensional/three‐dimensional imaging and spectroscopy and statistical image analysis, both optimized for ancient materials.     

Versatile variable temperature insert at the DEIMOS beamline for in situ electrical transport measurements

The design and the first experiments are described of a versatile cryogenic insert used for its electrical transport capabilities. The insert is designed for the cryomagnet installed on the DEIMOS beamline at the SOLEIL synchrotron dedicated to magnetic characterizations through X‐ray absorption spectroscopy (XAS) measurements. This development was spurred by the multifunctional properties of novel materials such as multiferroics, in which, for example, the magnetic and electrical orders are intertwined and may be probed using XAS. The insert thus enables XAS to in situ probe this interplay. The implementation of redundant wiring and careful shielding also enables studies on operating electronic devices. Measurements on magnetic tunnel junctions illustrate the potential of the equipment toward XAS studies of in operando electronic devices.     

X‐ray spectroscopy for chemistry in the 2‐4 keV energy regime at the XMaS beamline: ionic liquids,Rh and Pd catalysts in gas and liquid environments,and Cl contamination in γ‐Al2O3

The 2–4 keV energy range provides a rich window into many facets of materials science and chemistry. Within this window, P, S, Cl, K and Ca K‐edges may be found along with the L‐edges of industrially important elements from Y through to Sn. Yet, compared with those that cater for energies above ca. 4–5 keV, there are relatively few resources available for X‐ray spectroscopy below these energies. In addition, in situ or operando studies become to varying degrees more challenging than at higher X‐ray energies due to restrictions imposed by the lower energies of the X‐rays upon the design and construction of appropriate sample environments. The XMaS beamline at the ESRF has recently made efforts to extend its operational energy range to include this softer end of the X‐ray spectrum. In this report the resulting performance of this resource for X‐ray spectroscopy is detailed with specific attention drawn to: understanding electrostatic and charge transfer effects at the S K‐edge in ionic liquids; quantification of dilution limits at the Cl K‐ and Rh L₃‐edges and structural equilibria in solution; in vacuum deposition and reduction of [Rh^I(CO)₂Cl]₂ to γ‐Al₂O₃; contamination of γ‐Al₂O₃ by Cl and its potential role in determining the chemical character of supported Rh catalysts; and the development of chlorinated Pd catalysts in `green' solvent systems. Sample environments thus far developed are also presented, characterized and their overall performance evaluated.     

Relationship between the structural distortion and the Mn electronic state in La1−xCaxMnO3: a Mn K‐edge XANES study

A theoretical study of the X‐ray absorption near‐edge structure (XANES) spectra at the Mn K‐edge in the La_1?xCa_xMnO₃ series is reported. The relationship between the edge shift, the Ca–La substitution and the distortion of the MnO₆ octahedra in these systems has been studied. It is shown that, by correctly considering these effects simultaneously, the experimental XANES data are consistent with the presence of two different Mn local environments in the intermediate La_1?xCa_xMnO₃ compounds. By taking into account the energy shift associated with the modification of the MnO₆ distortion as Ca substitutes for La, it is possible to reproduce the XANES spectra of the intermediate‐doped compounds starting from the experimental spectra of the end‐members LaMnO₃ and CaMnO₃. These results point out the need to re‐examine the conclusions derived in the past from the simple analysis of the Mn K‐edge XANES edge‐shift in these materials. In particular, it is shown that the modification of the Mn K‐edge absorption through the La_1?xCa_xMnO₃ series is well reproduced by considering the simultaneous presence of both distorted and undistorted octahedra and, consequently, that the existence of charge‐ordering phenomena cannot be ruled out from the XANES data.