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.     

A fast energy‐dispersive multi‐element detector for X‐ray absorption spectroscopy

In this paper results are presented from fluorescence‐yield X‐ray absorption fine‐structure spectroscopy measurements with a new seven‐cell silicon drift detector (SDD) module. The complete module, including an integrated circuit for the detector readout, was developed and realised at DESY utilizing a monolithic seven‐cell SDD. The new detector module is optimized for applications like XAFS which require an energy resolution of ～250–300 eV (FWHM Mn Kα) at high count rates. Measurements during the commissioning phase proved the excellent performance for this type of application.     

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.     

Investigation of cadmium accumulation mechanism in hepatopancreas of Patinopecten yessoensis by synchrotron radiation X‐ray absorption fine structure and synchrotron radiation X‐ray fluorescence analyses

Chemical state of cadmium in a hepatopancreas of a scallop (Patinopecten yessoensis) was studied by means of synchrotron radiation‐based X‐ray analytical techniques. X‐ray absorption fine structure (XAFS) and X‐ray fluorescence (XRF) imaging were used to identify the chemical state and the distribution of cadmium in the hepatopancreas, respectively. The results of in vivo Cd K‐edge XAFS suggested that the neighboring atoms of the cadmium in the hepatopancreas are of sulfur. Therefore, we propose that cadmium was accumulated by a metalloprotein with sulfur. Micro XRF imaging of thin sections of the hepatopancreas showed that cadmium is distributed on the surface of intestinal epithelia and concentrated in the internal tissue of the hepatopancreas. These results indicated that scallops accumulate cadmium inside the hepatopancreas through the intestinal epithelium.     

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.     

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.     

同步辐射XAFS研究高比能LiMn2O4材料的局域结构

用EXAFS和XANES技术研究了高温固相反应法合成尖晶石结构的LiMn2O4中Mn原子的局域结构受到焙烧温度的影响.XANES结果表明,B1峰和B2峰强度分别与Mn3+,Mn4+的含量高低相关,焙烧温度愈高,B1峰的强度愈大.EXAFS给出的结构参数结果进一步表明,LiMn2O4(673K)的Mn-O第一配位和MnMn第二配位的无序度σ1(0.0059nm)和σ2(0.0092nm)分别小于及大于LiMn2O4(973K)的σ1(0.0066nm)和σ2(0.0081nm),LiMn2O4(1073K) 关键词： XAFS 局域结构 尖晶石LiMn2O4     

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.     

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.     

Analysis of engine motor oils by X‐ray absorption and X‐ray fluorescence spectroscopies

The molecular structure of lubricating motor oils is investigated by X‐ray absorption fine structure spectroscopy measurements. Both fresh and used oils are studied. Although the Zn K‐edge spectra gave information about the degradation of the antiwear/antioxidant zinc dialkyl dithiophosphate (ZDDP) additives within the oil, Fe K‐edge spectra are representatives for iron species dispersed in the oil during operation at elevated temperatures and pressures in the engine. The detailed analysis of the measured data shows that substantial differences are detectable in the spectra of the fresh and used oil. Our results show that the Zn–S bonds of the ZDDP are decomposed during the operation, resulting in Zn–O bonds instead. Furthermore, sixfold Fe–O bonds similar to those in Fe₂O₃ are found within the used oil, suggesting the presence of debris from the antiwear film of lubricated motor parts in the used oil. Copyright © 2014 John Wiley & Sons, Ltd.     

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.     

A three‐crystal spectrometer for high‐energy resolution fluorescence‐detected X‐ray absorption spectroscopy and X‐ray emission spectroscopy at SSRF

A Johann‐type spectrometer for the study of high‐energy resolution fluorescence‐detected X‐ray absorption spectroscopy, X‐ray emission spectroscopy and resonant inelastic X‐ray scattering has been developed at BL14W1 X‐ray absorption fine structure spectroscopy beamline of Shanghai Synchrotron Radiation Facility. The spectrometer consists of three crystal analyzers mounted on a vertical motion stage. The instrument is scanned vertically and covers the Bragg angle range of 71.5–88°. The energy resolution of the spectrometer ranges from sub‐eV to a few eV. The spectrometer has a solid angle of about 1.87 × 0^?3 of 4π sr, and the overall photons acquired by the detector could be 10⁵ counts per second for the standard sample. The performances of the spectrometer are illustrated by the three experiments that are difficult to perform with the conventional absorption or emission spectroscopy. Copyright © 2016 John Wiley & Sons, Ltd.     

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.