Development and exploration of a new methodology for the fitting and analysis of XAS data

A new data analysis methodology for X‐ray absorption near‐edge spectroscopy (XANES) is introduced and tested using several examples. The methodology has been implemented within the context of a new Matlab‐based program discussed in a companion related article [Delgado‐Jaime et al. (2010), J. Synchrotron Rad. 17 , 132–137]. The approach makes use of a Monte Carlo search method to seek appropriate starting points for a fit model, allowing for the generation of a large number of independent fits with minimal user‐induced bias. The applicability of this methodology is tested using various data sets on the Cl K‐edge XAS data for tetragonal CuCl₄^2?, a common reference compound used for calibration and covalency estimation in M—Cl bonds. A new background model function that effectively blends together background profiles with spectral features is an important component of the discussed methodology. The development of a robust evaluation function to fit multiple‐edge data is discussed and the implications regarding standard approaches to data analysis are discussed and explored within these examples.     

High‐accuracy X‐ray absorption spectra from mM solutions of nickel (II) complexes with multiple solutions using transmission XAS

A new approach is introduced for determining X‐ray absorption spectroscopy (XAS) spectra on absolute and relative scales using multiple solutions with different concentrations by the characterization and correction of experimental systematics. This hybrid technique is a development of standard X‐ray absorption fine structure (XAFS) along the lines of the high‐accuracy X‐ray extended range technique (XERT) but with applicability to solutions, dilute systems and cold cell environments. This methodology has been applied to determining absolute XAS of bis(N‐n‐propyl‐salicylaldiminato) nickel(II) and bis(N‐i‐propyl‐salicylaldiminato) nickel(II) complexes with square planar and tetrahedral structures in 15 mM and 1.5 mM dilute solutions. It is demonstrated that transmission XAS from dilute systems can provide excellent X‐ray absorption near‐edge structure (XANES) and XAFS spectra, and that transmission measurements can provide accurate measurement of subtle differences including coordination geometries. For the first time, (transmission) XAS of the isomers have been determined from low‐concentration solutions on an absolute scale with a 1–5% accuracy, and with relative precision of 0.1% to 0.2% in the active XANES and XAFS regions after inclusion of systematic corrections.     

Insight into growth of Au–Pt bimetallic nanoparticles: an in situ XAS study

Au–Pt bimetallic nanoparticles have been synthesized through a one‐pot synthesis route from their respective chloride precursors using block copolymer as a stabilizer. Growth of the nanoparticles has been studied by simultaneous in situ measurement of X‐ray absorption spectroscopy (XAS) and UV–Vis spectroscopy at the energy‐dispersive EXAFS beamline (BL‐08) at Indus‐2 SRS at RRCAT, Indore, India. In situ XAS spectra, comprising both X‐ray near‐edge structure (XANES) and extended X‐ray absorption fine‐structure (EXAFS) parts, have been measured simultaneously at the Au and Pt L₃‐edges. While the XANES spectra of the precursors provide real‐time information on the reduction process, the EXAFS spectra reveal the structure of the clusters formed in the intermediate stages of growth. This insight into the formation process throws light on how the difference in the reduction potential of the two precursors could be used to obtain the core–shell‐type configuration of a bimetallic alloy in a one‐pot synthesis method. The core–shell‐type structure of the nanoparticles has also been confirmed by ex situ energy‐dispersive spectroscopy line‐scan and X‐ray photoelectron spectroscopy measurements with in situ ion etching on fully formed nanoparticles.     

The CTM4XAS program for EELS and XAS spectral shape analysis of transition metal L edges

The CTM4XAS program for the analysis of transition metal L edge Electron Energy Loss Spectroscopy (EELS) or X-ray Absorption Spectra (XAS) is explained. The physical background of the calculations is briefly discussed. The program consists of three theoretical components, based on, respectively, atomic multiplet theory, crystal field theory and charge transfer theory. The theoretical concepts are explained and a number of examples are presented. The calculation of the 2p EELS and XAS spectra of transition metal ions, is given in detail, including their Magnetic Circular Dichroism (MCD). In addition, examples of 1s, 2s, 3s, 2p and 3p X-ray Photoemission Spectroscopy (XPS) are given.     

Alternative difference analysis scheme combining R‐space EXAFS fit with global optimization XANES fit for X‐ray transient absorption spectroscopy

Time‐resolved X‐ray absorption spectroscopy (TR‐XAS), based on the laser‐pump/X‐ray‐probe method, is powerful in capturing the change of the geometrical and electronic structure of the absorbing atom upon excitation. TR‐XAS data analysis is generally performed on the laser‐on minus laser‐off difference spectrum. Here, a new analysis scheme is presented for the TR‐XAS difference fitting in both the extended X‐ray absorption fine‐structure (EXAFS) and the X‐ray absorption near‐edge structure (XANES) regions. R‐space EXAFS difference fitting could quickly provide the main quantitative structure change of the first shell. The XANES fitting part introduces a global non‐derivative optimization algorithm and optimizes the local structure change in a flexible way where both the core XAS calculation package and the search method in the fitting shell are changeable. The scheme was applied to the TR‐XAS difference analysis of Fe(phen)₃ spin crossover complex and yielded reliable distance change and excitation population.     

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

ABSTRACT

Nano-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.     

Iron speciation in ancient Attic pottery pigments: a non‐destructive SR‐XAS investigation

The present work reports a detailed investigation on the speciation of iron in the pigments of decorated pottery fragments of cultural heritage relevance. The fragments come from the Gioiosa Guardia archaeological site in the area of the `Strait of Messina' (Sicily, Southern Italy), and date back to VI–V century BC. The purpose of this study is to characterize the main pigmenting agents responsible for the dark‐red coloration of the specimens using non‐destructive analytical techniques such as synchrotron radiation X‐ray absorption spectroscopy (SR‐XAS), a well established technique for cultural heritage and environmental subjects. Absorption spectra were collected at the Fe K‐edge on the Italian beamline for absorption and diffraction (BM8‐GILDA) at the European Synchrotron Radiation Facility in Grenoble (France). In order to determine the speciation of Fe in the samples, principal component analysis and least‐squares fitting procedures were applied to the near‐edge part of the absorption spectra (XANES). Details on the local structure around the Fe sites were obtained by analyzing the extended part of the spectra (EXAFS). Furthermore, an accurate determination of the average Fe oxidation state was carried out through analysis of the pre‐edge peaks of the absorption spectra. Samples resulted composed of an admixture of Fe₂O₃ (hematite or maghemite) and magnetite (Fe₃O₄), occurring in different relative abundance in the dark‐ and light‐colored areas of the specimens. The results obtained are complementary to information previously obtained by means of instrumental neutron activation analysis, Fourier transform infrared absorbance and time‐of‐flight neutron diffraction.     

Influence of crystallographic orientation of biogenic calcite on in situ Mg XANES analyses

Micro X‐ray absorption near‐edge spectroscopy at the Mg K‐edge is a useful technique for acquiring information about the environment of Mg²⁺ in biogenic calcite. These analyses can be applied to shell powders or intact shell structures. The advantage of the latter is that the XANES analyses can be applied to specific areas, at high (e.g. micrometre) spatial resolution, to determine the environment of Mg²⁺ in a biomineral context. Such in situ synchrotron analysis has to take into account the potential effect of crystallographic orientation given the anisotropy of calcite crystals and the polarized nature of X‐rays. Brachiopod shells of species with different crystallographic orientations are used to assess this crystallographic effect on in situ synchrotron measurements at the Mg K‐edge. Results show that, owing to the anisotropy of calcite, in situ X‐ray absorption spectra (XAS) are influenced by the crystallographic orientation of calcite crystals with a subsequent potentially erroneous interpretation of Mg²⁺ data. Thus, this study demonstrates the importance of crystallography for XAS analyses and, therefore, the necessity to obtain crystallographic information at high spatial resolution prior to spectroscopic analysis.     

Influence of crystal structure,ligand environment and morphology on Co L‐edge XAS spectral characteristics in cobalt compounds

The electronic structure of a material plays an important role in its functionality for different applications which can be probed using synchrotron‐based spectroscopy techniques. Here, various cobalt‐based compounds, differing in crystal structure, ligands surrounding the central metal ion and morphology, have been studied by soft X‐ray absorption spectroscopy (XAS) at the Co L‐edge in order to measure the effect of these parameters on the electronic structure. A careful qualitative analysis of the spectral branching ratio and relative intensities of the L₃ and L₂ peaks provide useful insight into the electronic properties of compounds such as CoO/Co(OH)₂, CoCl₂.6H₂O/CoF₂.4H₂O, CoCl₂/CoF₂, Co₃O₄ (bulk/nano/micro). For further detailed analysis of the XAS spectra, quantitative analysis has been performed by fitting the spectral profile with simulated spectra for a number of cobalt compounds using crystal field atomic multiplet calculations.     

XAS spectroelectrochemistry: reliable measurement of X‐ray absorption spectra from redox manipulated solutions at room temperature

The design and operation of a low‐volume spectroelectrochemical cell for X‐ray absorption spectroscopy (XAS) of solutions at room temperature is described. Fluorescence XAS measurements are obtained from samples contained in the void space of a 50 µL reticulated vitreous carbon (sponge) working electrode. Both rapid electrosynthesis and control of the effects of photoreduction are achieved by control over the flow properties of the solution through the working electrode, where a good balance between the rate of consumption of sample and the minimization of decomposition was obtained by pulsing the flow of the solution by 1–2 µL with duty cycle of ～3 s while maintaining a small net flow rate (26–100 µL h^?1). The performance of the cell in terms of control of the redox state of the sample and minimization of the effects of photoreduction was demonstrated by XAS measurements of aqueous solutions of the photosensitive Fe^III species, [Fe(C₂O₄)₃]^3?, together with that of the electrogenerated [Fe(C₂O₄)₃]^4? product. The current response from the cell during the collection of XAS spectra provides an independent measure of the stability of the sample of the measurement. The suitability of the approach for the study of small volumes of mM concentrations of protein samples was demonstrated by the measurement of the oxidized and electrochemically reduced forms of cytochrome c.     

Novel high‐temperature reactors for in situ studies of three‐way catalysts using turbo‐XAS

Two novel high‐temperature reactors for in situ X‐ray absorption spectroscopy (XAS) measurements in fluorescence are presented, each of them being optimized for a particular purpose. The powerful combination of these reactors with the turbo‐XAS technique used in a dispersive‐XAS beamline permits the study of commercial three‐way catalysts under realistic gas composition and temporal conditions.     

X‐ray absorption spectroscopy at the Ni?K edge in Stackhousia tryonii Bailey hyperaccumulator

Young plants of Stackhousia tryonii Bailey were exposed to 34 mM Ni kg^?1 in the form of NiSO₄· 6H₂O solution and grown under controlled glasshouse conditions for a period of 20 days. Fresh leaf, stem and root samples were analysed in vivo by micro x‐ray absorption spectroscopy (XAS) at the Ni? K edge. Both x‐ray absorption near edge structure and extended x‐ray absorption fine structure spectra were analysed, and the resulting spectra were compared with spectra obtained from nine biologically important Ni‐containing model compounds. The results revealed that the majority of leaf, stem and root Ni in the hyperaccumulator was chelated by citrate. Our results also suggest that in leaves Ni is complexed by phosphate and histidine, and in stems and roots, phytate and histidine. The XAS results provide an important physiological insight into transport, detoxification and storage of Ni in S. tryonii plants. Copyright © 2008 John Wiley & Sons, Ltd.     

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.     

Combined XAS/SAXS/Electrochemical studies on the conformation of poly(vinylferrocene) under redox conditions

Metal-organic ligand complexes are important to many processes, ranging from the formation of supramolecular assemblies to electrochemical processes. Poly(vinylferrocene), PVF, is an example of a metal-organic polymer that contains localised sites which may be oxidised and reduced. Combined XAS (X-ray Absorption Spectroscopy)/SAXS (Small Angle X-ray Scattering) and electrochemical studies on PVF films in aqueous solution of 0.10 M LiClO₄ and in non-aqueous solution of propylene carbonate/0.25 M TBABF₄ have been carried out. The change in the oxidation Fe²⁺/Fe³⁺state of the PVF film was observed by analysing the near edge region of the XAS spectrum. The local environment around the Fe-centres of the oxidised/reduced films (from the extended region of the XAS spectrum) indicates an increase/reduction of ligand distances during the oxidation and reduction of the film. The SAXS results correlate well with the findings from XAS. The scattering profiles at very low angles are consistent with an expansion/contraction of the overall size of polymer chains upon oxidation/reduction. Paper presented at the 8th EuroConference on Ionics, Carvoeiro, Algarve, Portugal, Sept. 16–22, 2001.     

Vanadium K‐edge XANES in vanadium‐bearing model compounds: a full multiple scattering study

A systematic study is presented on a set of vanadium‐bearing model compounds, representative of the most common V coordination geometries and oxidation states, analysed by means of vanadium K‐edge X‐ray absorption near‐edge spectroscopy calculations in the full multiple scattering (FMS) framework. Analysis and calibration of the free parameters of the theory under the muffin‐tin approximation (muffin‐tin overlap and interstitial potential) have been carried out by fitting the experimental spectra using the MXAN program. The analysis shows a correlation of the fit parameters with the V coordination geometry and oxidation state. By making use of this correlation it is possible to approach the study of unknown V‐bearing compounds with useful preliminary information.     

Upgrade of beamline BL08B at Taiwan Light Source from a photon‐BPM to a double‐grating SGM beamline

During the last 20 years, beamline BL08B has been upgraded step by step from a photon beam‐position monitor (BPM) to a testing beamline and a single‐grating beamline that enables experiments to record X‐ray photo‐emission spectra (XPS) and X‐ray absorption spectra (XAS) for research in solar physics, organic semiconductor materials and spinel oxides, with soft X‐ray photon energies in the range 300–1000 eV. Demands for photon energy to extend to the extreme ultraviolet region for applications in nano‐fabrication and topological thin films are increasing. The basic spherical‐grating monochromator beamline was again upgraded by adding a second grating that delivers photons of energy from 80 to 420 eV. Four end‐stations were designed for experiments with XPS, XAS, interstellar photoprocess systems (IPS) and extreme‐ultraviolet lithography (EUVL) in the scheduled beam time. The data from these experiments show a large count rate in core levels probed and excellent statistics on background normalization in the L‐edge adsorption spectrum.     

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.     

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.     

Cation site environment in ultrathin TiOx films grown on Pt(1 1 1) probed by X-ray absorption spectroscopy at the Ti 2p edge

We present the results of a XAS experiment carried out at the Ti 2p edge on well-ordered TiO_x ultrathin films grown on the Pt(1 1 1) surface. XAS at the Ti 2p edge has been extensively applied to the study of Ti bulk compounds, particularly to the study of titania. According to the literature, the corresponding Ti 2p edge spectral shape is related to the stoichiometry and crystal field symmetry at the Ti sites. In the present study we aim at extending the potential of the XAS technique by discussing Ti 2p spectra obtained on several, dimensionally confined, TiO_x phases in the form of ultrathin films. One of the main features of these films is their high degree of structural order. Furthermore, the results of previous studies provide valuable information about the chemistry and structure of the films, so that we are able to analyse the current XAS data in detail and to compare them with the appropriate Ti 2p XAS data of bulk oxides. We find that in the case of ultrathin film with a fully oxidised Ti⁴⁺ stoichiometry, the Ti 2p XAS data display features that are very similar to the ones observed in related bulk systems. The XAS data of the reduced TiO_x films (with x < 2) show a rather different and specific shape. By comparing the experimental spectra with an atomic type of model calculation we show that the Ti 2p XAS profiles can be attributed mainly to stoichiometry-symmetry effects.     

A robust method for automated background subtraction of tissue fluorescence

This paper introduces a new robust method for the removal of background tissue fluorescence from Raman spectra. Raman spectra consist of noise, fluorescence and Raman scattering. In order to extract the Raman scattering, both noise and background fluorescence must be removed, ideally without human intervention and preserving the original data. We describe the rationale behind our robust background subtraction method, determine the parameters of the method and validate it using a Raman phantom against other methods currently used. We also statistically compare the methods using the residual mean square (RMS) with a fluorescence‐to‐signal (F/S) ratio ranging from 0.1 to 1000. The method, ‘adaptive minmax’, chooses the subtraction method based on the F/S ratio. It uses multiple fits of different orders to maximize each polynomial fit. The results show that the adaptive minmax method was significantly better than any single polynomial fit across all F/S ratios. This method can be implemented as part of a modular automated real‐time diagnostic in vivo Raman system. Copyright © 2007 John Wiley & Sons, Ltd.