FDMX: extended X‐ray absorption fine structure calculations using the finite difference method

A new theoretical approach and computational package, FDMX, for general calculations of X‐ray absorption fine structure (XAFS) over an extended energy range within a full‐potential model is presented. The final‐state photoelectron wavefunction is calculated over an energy‐dependent spatial mesh, allowing for a complete representation of all scattering paths. The electronic potentials and corresponding wavefunctions are subject to constraints based on physicality and self‐consistency, allowing for accurate absorption cross sections in the near‐edge region, while higher‐energy results are enabled by the implementation of effective Debye–Waller damping and new implementations of second‐order lifetime broadening. These include inelastic photoelectron scattering and, for the first time, plasmon excitation coupling. This is the first full‐potential package available that can calculate accurate XAFS spectra across a complete energy range within a single framework and without fitted parameters. Example spectra are provided for elemental Sn, rutile TiO₂ and the FeO₆ octahedron.     

Development of a two‐dimensional imaging system of X‐ray absorption fine structure

A two‐dimensional imaging system of X‐ray absorption fine structure (XAFS) has been developed at beamline BL‐4 of the Synchrotron Radiation Center of Ritsumeikan University. The system mainly consists of an ionization chamber for I₀ measurement, a sample stage, and a two‐dimensional complementary metal oxide semiconductor (CMOS) image sensor for measuring the transmitted X‐ray intensity. The X‐ray energy shift in the vertical direction, which originates from the vertical divergence of the X‐ray beam on the monochromator surface, is corrected by considering the geometrical configuration of the monochromator. This energy correction improves the energy resolution of the XAFS spectrum because each pixel in the CMOS detector has a very small vertical acceptance of ～0.5 µrad. A data analysis system has also been developed to automatically determine the energy of the absorption edge. This allows the chemical species to be mapped based on the XANES feature over a wide area of 4.8 mm (H) × 3.6 mm (V) with a resolution of 10 µm × 10 µm. The system has been applied to the chemical state mapping of the Mn species in a LiMn₂O₄ cathode. The heterogeneous distribution of the Mn oxidation state is demonstrated and is considered to relate to the slow delocalization of Li⁺‐defect sites in the spinel crystal structure. The two‐dimensional‐imaging XAFS system is expected to be a powerful tool for analyzing the spatial distributions of chemical species in many heterogeneous materials such as battery electrodes.     

Local structure of NiAl compounds investigated by extended X‐ray absorption fine‐structure spectroscopy

The local structures of pure NiAl and Ti‐, Co‐doped NiAl compounds have been obtained utilizing extended X‐ray absorption fine‐structure (EXAFS) spectroscopy. The results provide experimental evidence that Ni antisite defects exist in the Ni‐rich NiAl compounds. The site preference of Ti and Co has been confirmed. Ti occupies the Al sublattice, while Co occupies the Ni sublattice. The structure parameters obtained by EXAFS were consistent with the X‐ray diffraction results. Owing to the precipitation of α‐Cr, the local structure of NiAl‐Cr has not been obtained, making the site preference of Cr unclear.     

miXAFS: a program for X‐ray absorption fine‐structure data analysis

A new program called miXAFS for the analysis of X‐ray absorption fine‐structure (XAFS) data is presented. miXAFS can analyze the XAFS functions simultaneously for all measured X‐ray absorption edges of the constituent elements in a sample under the constraints for the structural parameters over the edges. The program provides a surface plot of the R‐factor as a function of two structural parameters, which is useful to validate the optimized structural parameters. The structural parameters can be obtained from the XAFS data in a few steps using the setting file and batch process. The program, which is coded in MATLAB and freely available, runs on Macintosh and Windows operating systems. It has a graphical user interface and loads experimental data and XAFS functions in a variety of ASCII data formats.     

Effect of gamma irradiation on X‐ray absorption and photoelectron spectroscopy of Nd‐doped phosphate glass

X‐ray absorption near‐edge structure (XANES) and X‐ray photoelectron spectroscopy (XPS) of Nd‐doped phosphate glasses have been studied before and after gamma irradiation. The intensity and the location of the white line peak of the L₃‐edge XANES of Nd are found to be dependent on the ratio O/Nd in the glass matrix. Gamma irradiation changes the elemental concentration of atoms in the glass matrix, which affects the peak intensity of the white line due to changes in the covalence of the chemical bonds with Nd atoms in the glass (structural changes). Sharpening of the Nd 3d_5/2 peak profile in XPS spectra indicates a deficiency of oxygen in the glasses after gamma irradiation, which is supported by energy‐dispersive X‐ray spectroscopy measurements. The ratio of non‐bridging oxygen to total oxygen in the glass after gamma radiation has been found to be correlated to the concentration of defects in the glass samples, which are responsible for its radiation resistance as well as for its coloration.     

Biological X‐ray absorption spectroscopy and metalloproteomics

In the past seven years the size of the known protein sequence universe has been rapidly expanding. At present, more then five million entries are included in the UniProtKB/TrEMBL protein database. In this context, a retrospective evaluation of recent X‐ray absorption studies is undertaken to assess its potential role in metalloproteomics. Metalloproteomics is the structural and functional characterization of metal‐binding proteins. This is a new area of active research which has particular relevance to biology and for which X‐ray absorption spectroscopy is ideally suited. In the last three years, biological X‐ray absorption spectroscopy (BioXAS) has been included among the techniques used in post‐genomics initiatives for metalloprotein characterization. The emphasis of this review is on the progress in BioXAS that has emerged from recent meetings in 2007–2008. Developments required to enable BioXAS studies to better contribute to metalloproteomics throughput are also discussed. Overall, this paper suggests that X‐ray absorption spectroscopy could have a higher impact on metalloproteomics, contributing significantly to the understanding of metal site structures and of reaction mechanisms for metalloproteins.     

Investigation of short‐range structural order in Zr69.5Cu12Ni11Al7.5 and Zr41.5Ti41.5Ni17 glasses,using X‐ray absorption spectroscopy and ab initio molecular dynamics simulations

Short‐range order has been investigated in Zr_69.5Cu₁₂Ni₁₁Al_7.5 and Zr_41.5Ti_41.5Ni₁₇ metallic glasses using X‐ray absorption spectroscopy and ab initio molecular dynamics simulations. While both of these alloys are good glass formers, there is a difference in their glass‐forming abilities (Zr_41.5Ti_41.5Ni₁₇ > Zr_69.5Cu₁₂Ni₁₁Al_7.5). This difference is explained by inciting the relative importance of strong chemical order, icosahedral content, cluster symmetry and configuration diversity.     

High‐resolution spectroscopy on an X‐ray absorption beamline

A bent‐crystal spectrometer based on the Rowland circle geometry has been installed and tested on the BM30b/FAME beamline at the European Synchrotron Radiation Facility to improve its performances. The energy resolution of the spectrometer allows different kinds of measurements to be performed, including X‐ray absorption spectroscopy, resonant inelastic X‐ray scattering and X‐ray Raman scattering experiments. The simplicity of the experimental device makes it easily implemented on a classical X‐ray absorption beamline. This improvement in the fluorescence detection is of particular importance when the probed element is embedded in a complex and/or heavy matrix, for example in environmental sciences.     

Formation mechanism of Ge nanocrystals embedded in SiO2 studied by fluorescence x-ray absorption fine structure

This paper reports that the Ge nanocrystals embedded in SiO2 matrix are grown on Si（100） and quartz-glass substrates, and the formation mechanism is systematically studied by using fluorescence x-ray absorption fine structure （XAFS）. It is found that the formation of Ge nanocrystals strongly depends on the properties of substrate materials. In the as-prepared samples with Ge molar content of 60%, Ge atoms exist in amorphous Ge （about 36%） and GeO2 （about 24%） phases. At the annealing temperature of 1073 K, on the quartz-glass substrate Ge nanocrystals are generated from crystallization of amorphous Ge, rather than from the direct decomposition of GeO2 in the as-deposited sample. However, on the Si（100） substrate, the Ge nanocrystals are generated partly from crystallization of amorphous Ge, and partly from GeO2 phases through the permutation reaction with Si substrate. Quantitative analysis reveals that about 10% of GeO2 in the as-prepared sample are permuted with Si wafer to form Ge nanocrystals.     

Picosecond‐resolved X‐ray absorption spectroscopy at low signal contrast using a hard X‐ray streak camera

A picosecond‐resolving hard‐X‐ray streak camera has been in operation for several years at Sector 7 of the Advanced Photon Source (APS). Several upgrades have been implemented over the past few years to optimize integration into the beamline, reduce the timing jitter, and improve the signal‐to‐noise ratio. These include the development of X‐ray optics for focusing the X‐rays into the sample and the entrance slit of the streak camera, and measures to minimize the amount of laser light needed to generate the deflection‐voltage ramp. For the latter, the photoconductive switch generating the deflection ramp was replaced with microwave power electronics. With these, the streak camera operates routinely at 88 MHz repetition rate, thus making it compatible with all of the APS fill patterns including use of all the X‐rays in the 324‐bunch mode. Sample data are shown to demonstrate the performance.     

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.     

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.     

Image stack alignment in full‐field X‐ray absorption spectroscopy using SIFT_PyOCL

Full‐field X‐ray absorption spectroscopy experiments allow the acquisition of millions of spectra within minutes. However, the construction of the hyperspectral image requires an image alignment procedure with sub‐pixel precision. While the image correlation algorithm has originally been used for image re‐alignment using translations, the Scale Invariant Feature Transform (SIFT) algorithm (which is by design robust versus rotation, illumination change, translation and scaling) presents an additional advantage: the alignment can be limited to a region of interest of any arbitrary shape. In this context, a Python module, named SIFT_PyOCL, has been developed. It implements a parallel version of the SIFT algorithm in OpenCL, providing high‐speed image registration and alignment both on processors and graphics cards. The performance of the algorithm allows online processing of large datasets.     

Correction method for the self‐absorption effects in fluorescence extended X‐ray absorption fine structure on multilayer samples

A novel correction method for self‐absorption effects is proposed for extended X‐ray absorption fine structure (EXAFS) detected in the fluorescence mode on multilayer samples. The effects of refraction and multiple reflection at the interfaces are fully considered in this correction method. The correction is performed in k‐space before any further data analysis, and it can be applied to single‐layer or multilayer samples with flat surfaces and without thickness limit when the model parameters for the samples are known. The validity of this method is verified by the fluorescence EXAFS data collected for a Cr/C multilayer sample measured at different experimental geometries.     

X‐ray absorption study of the local structure at the NiO/oxide interfaces

This work reports an X‐ray absorption near‐edge structure (XANES) spectroscopy study at the Ni K‐edge in the early stages of growth of NiO on non‐ordered SiO₂, Al₂O₃ and MgO thin films substrates. Two different coverages of NiO on the substrates have been studied. The analysis of the XANES region shows that for high coverages (80 Eq‐ML) the spectra are similar to that of bulk NiO, being identical for all substrates. In contrast, for low coverages (1 Eq‐ML) the spectra differ from that of large coverages indicating that the local order around Ni is limited to the first two coordination shells. In addition, the results also suggest the formation of cross‐linking bonds Ni—O—M (M = Si, Al, Mg) at the interface.     

X‐ray absorption spectroscopy analysis of Ru in La2RuO5

The compound La₂RuO₅ was examined by the x‐ray absorption spectroscopy (XAS) methods, x‐ray absorption near edge structure (XANES) and extended x‐ray absorption fine structure (EXAFS). XANES technique was used to probe directly the average valence of Ru atoms in the compound. The energy shift of the Ru K‐edge in the XANES signal gave the average Ru valence state as 4.0 ± 0.1. EXAFS analysis provided, by yielding directly the interatomic distances and coordination numbers, the first information on the Ru atom neighborhood, on which the model for the Rietveld refinement of the unit cell of the new compound was devised. Finally, the local structure around the Ru atoms from the refinement was used in the FEFF6 code for a model EXAFS spectrum. The very good quantitative agreement with the measured spectrum proves that the refined crystal structure contains no systematic defects in the vicinity of Ru atoms. This result, together with the valence obtained from XANES, strongly confirms the proposed La₂RuO₅ stoichiometry. Copyright © 2007 John Wiley & Sons, Ltd.     

Combined measurement of X‐ray photon correlation spectroscopy and diffracted X‐ray tracking using pink beam X‐rays

Combined X‐ray photon correlation spectroscopy (XPCS) and diffracted X‐ray tracking (DXT) measurements of carbon‐black nanocrystals embedded in styrene–butadiene rubber were performed. From the intensity fluctuation of speckle patterns in a small‐angle scattering region (XPCS), dynamical information relating to the translational motion can be obtained, and the rotational motion is observed through the changes in the positions of DXT diffraction spots. Graphitized carbon‐black nanocrystals in unvulcanized styrene–butadiene rubber showed an apparent discrepancy between their translational and rotational motions; this result seems to support a stress‐relaxation model for the origin of super‐diffusive particle motion that is widely observed in nanocolloidal systems. Combined measurements using these two techniques will give new insights into nanoscopic dynamics, and will be useful as a microrheology technique.     

Pressure study of monoclinic ReO2 up to 1.2 GPa using X‐ray absorption spectroscopy and X‐ray diffraction

The crystal and local atomic structure of monoclinic ReO₂ (α‐ReO₂) under hydrostatic pressure up to 1.2 GPa was investigated for the first time using both X‐ray absorption spectroscopy and high‐resolution synchrotron X‐ray powder diffraction and a home‐built B₄C anvil pressure cell developed for this purpose. Extended X‐ray absorption fine‐structure (EXAFS) data analysis at pressures from ambient up to 1.2 GPa indicates that there are two distinct Re—Re distances and a distorted ReO₆ octahedron in the α‐ReO₂ structure. X‐ray diffraction analysis at ambient pressure revealed an unambiguous solution for the crystal structure of the α‐phase, demonstrating a modulation of the Re—Re distances. The relatively small portion of the diffraction pattern accessed in the pressure‐dependent measurements does not allow for a detailed study of the crystal structure of α‐ReO₂ under pressure. Nonetheless, a shift and reduction in the (011) Bragg peak intensity between 0.4 and 1.2 GPa is observed, with correlation to a decrease in Re—Re distance modulation, as confirmed by EXAFS analysis in the same pressure range. This behavior reveals that α‐ReO₂ is a possible inner pressure gauge for future experiments up to 1.2 GPa.     

Tris‐amidoximate uranyl complexes via η2 binding mode coordinated in aqueous solution shown by X‐ray absorption spectroscopy and density functional theory methods

The present study sheds some light on the long‐standing debate concerning the coordination properties between uranyl ions and the amidoxime ligand, which is a key ingredient for achieving efficient extraction of uranium. Using X‐ray absorption fine structure combined with theoretical simulation methods, the binding mode and bonding nature of a uranyl–amidoxime complex in aqueous solution were determined for the first time. The results show that in a highly concentrated amidoxime solution the preferred binding mode between UO₂²⁺ and the amidoxime ligand is η² coordination with tris‐amidoximate species. In such a uranyl–amidoximate complex with η² binding motif, strong covalent interaction and orbital hybridization between U 5f/6d and (N, O) 2p should be responsible for the excellent binding ability of the amidoximate ligand to uranyl. The study was performed directly in aqueous solution to avoid the possible binding mode differences caused by crystallization of a single‐crystal sample. This work also is an example of the simultaneous study of local structure and electronic structure in solution systems using combined diagnostic tools.     

X‐ray photon correlation spectroscopy under flow

X‐ray photon correlation spectroscopy was used to probe the diffusive dynamics of colloidal particles in a shear flow. Combining X‐ray techniques with microfluidics is an experimental strategy that reduces the risk of X‐ray‐induced beam damage and also allows time‐resolved studies of processes taking place in flow cells. The experimental results and theoretical predictions presented here show that in the low shear limit for a `transverse flow' scattering geometry (scattering wavevector q perpendicular to the direction of flow) the measured relaxation times are independent of the flow rate and determined only by the diffusive motion of the particles. This is not generally valid and, in particular, for a `longitudinal flow' ( q ∥ flow) scattering geometry the relaxation times are strongly affected by the flow‐induced motion of the particles. The results here show that the Brownian diffusion of colloidal particles can be measured in a flowing sample and that, up to flux limitations, the experimental conditions under which this is possible are easier to achieve at higher values of q.