Predicting XAFS scattering path cumulants and XAFS spectra for metals (Cu,Ni, Fe,Ti, Au) using molecular dynamics simulations

The ability of molecular dynamics (MD) simulations to support the analysis of X‐ray absorption fine‐structure (XAFS) data for metals is evaluated. The low‐order cumulants (ΔR, σ², C₃) for XAFS scattering paths are calculated for the metals Cu, Ni, Fe, Ti and Au at 300 K using 28 interatomic potentials of the embedded‐atom method type. The MD cumulant predictions were evaluated within a cumulant expansion XAFS fitting model, using global (path‐independent) scaling factors. Direct simulations of the corresponding XAFS spectra, χ(R), are also performed using MD configurational data in combination with the FEFFab initio code. The cumulant scaling parameters compensate for differences between the real and effective scattering path distributions, and for any errors that might exist in the MD predictions and in the experimental data. The fitted value of ΔR is susceptible to experimental errors and inadvertent lattice thermal expansion in the simulation crystallites. The unadjusted predictions of σ² vary in accuracy, but do not show a consistent bias for any metal except Au, for which all potentials overestimate σ². The unadjusted C₃ predictions produced by different potentials display only order‐of‐magnitude consistency. The accuracy of direct simulations of χ(R) for a given metal varies among the different potentials. For each of the metals Cu, Ni, Fe and Ti, one or more of the tested potentials was found to provide a reasonable simulation of χ(R). However, none of the potentials tested for Au was sufficiently accurate for this purpose.     

XAFS spectra from X-ray fluorescence Kβ line using conventional energy-discriminating detector

X-ray fluorescence spectra of copper (Cu) metal, copper monoxide (CuO), and potassium chromate (K₂CrO₄) were recorded as a function of incident X-ray energy near the Cu K-edge and chromium (Cr) K-edge, respectively, using a conventional silicon drift detector. The spectra contained components due to elastic, inelastic, and multiple scattering, in addition to the Kα and Kβ lines. Cu and Cr K-edge X-ray absorption fine structure (XAFS) spectra of Cu, CuO, and K₂CrO₄ were obtained by an intensity analysis of the Kα and Kβ lines. The intensity of the Kβ line for the different incident photon energies was obtained by numerically removing the additional scattering components using the MUSCAT program. These spectra exhibited a jump near the K absorption edges, which reproduced the spectral features obtained in transmission mode for both Cu, CuO, and K₂CrO₄. A chemical shift was also clearly identified in the X-ray absorption near edges structure using the X-ray fluorescence Kβ line. In addition, the Cr K-edge extended XAFS spectrum of K₂CrO₄ was clearly observed using the Cr Kβ fluorescent line. The XAFS measurements on the Kα and Kβ lines are possible, and they carry equally valuable information.     

Finite difference method calculations of X-ray absorption fine structure for copper

The finite difference method is extended to calculate X-ray absorption fine structure (XAFS) for solid state copper. These extensions include the incorporation of a Monte Carlo frozen phonon technique to simulate the effect of thermal vibrations under a correlated Debye–Waller model, and the inclusion of broadening effects from inelastic processes. Spectra are obtained over an energy range in excess of 300 eV above the K absorption edge—more than twice the greatest energy range previously reported for a solid state calculation using this method. We find this method is highly sensitive to values of the photoelectron inelastic mean free path, allowing us to probe the accuracy of current models of this parameter, particularly at low energies. We therefore find that experimental data for the photoelectron inelastic mean free path can be obtained by this method. Our results compare favourably with high precision measurements of the X-ray mass attenuation coefficient for copper, reaching agreement to within 3%, and improving previous results using the finite difference method by an order of magnitude.     

Spontaneous Raman scattering: a useful tool for investigating the afterglow of nanosecond scale discharges in air

Nanosecond scale discharges are considered an interesting way for assisting combustion by enhancing either flame stabilization or ignition. Better understanding of energy deposit and radical species production processes is still required under pressure conditions normally encountered in combustion. The purpose of the present paper is to show that spontaneous Raman scattering, seldom used to investigate nanosecond pulsed discharges, is a useful measurement method for investigating the energy deposit of these discharges. The advantage of spontaneous Raman scattering is described by analyzing N₂ and O₂ spectra during the post-discharge of a filamentary nanosecond air discharge under atmospheric pressure, using phase-locked average spectra. The main advantages of spontaneous Raman scattering measurements are that they allow line-wise probing of different species with the same experimental setup and the determination of vibrational distribution by comparison with theoretical modeling over a wide range of vibrational levels (from v=0 to v=20 for N₂). The model proposed takes into account the high level of vibrational excitation and the strong non-equilibrium observed, allowing the characterization of the vibrational relaxation over the complete post-discharge duration. Although the rotational structure is not resolved, the rotational temperature and thus translational temperature are determined with a moderate uncertainty for T above 500 K.     

Measurement of the X‐ray mass attenuation coefficients of silver in the 5–20 keV range

The X‐ray mass attenuation coefficients of silver were measured in the energy range 5–20 keV with an accuracy of 0.01–0.2% on a relative scale down to 5.3 keV, and of 0.09–1.22% on an absolute scale to 5.0 keV. This analysis confirms that with careful choice of foil thickness and careful correction for systematics, especially including harmonic contents at lower energies, the X‐ray attenuation of high‐Z elements can be measured with high accuracy even at low X‐ray energies (<6 keV). This is the first high‐accuracy measurement of X‐ray mass attenuation coefficients of silver in the low energy range, indicating the possibility of obtaining high‐accuracy X‐ray absorption fine structure down to the L₁ edge (3.8 keV) of silver. Comparison of results reported here with an earlier data set optimized for higher energies confirms accuracy to within one standard error of each data set collected and analysed using the principles of the X‐ray extended‐range technique (XERT). Comparison with theory shows a slow divergence towards lower energies in this region away from absorption edges. The methodology developed can be used for the XAFS analysis of compounds and solutions to investigate structural features, bonding and coordination chemistry.     

Three particle correlation function of metal ions in tetrahedral coordination determined by XANES

The three particle correlation function of local atomic distribution at metal ion sites in solutions has been extracted from XANES (X-ray absorption near edge structure) spectra of [CrO₄]²⁻ and [MnO₄]⁻ ions measured by using synchrotron radiation. The absorption cross section for 1s core level excitation is calculated in the real space multiple scattering approach using the Hedin and Lundqvist energy dependent potential. We show that in these systems the expansion of the total absorption cross section in terms of contributions of higher order scattering processes is possible over a large energy range. This gives a unified theory of XANES and EXAFS and allows the third order correlation function to be extracted from experimental data.     

Development of dispersive XAFS system for analysis of time‐resolved spatial distribution of electrode reaction

Apparatus for a technique based on the dispersive optics of X‐ray absorption fine structure (XAFS) has been developed at beamline BL‐5 of the Synchrotron Radiation Center of Ritsumeikan University. The vertical axis of the cross section of the synchrotron light is used to disperse the X‐ray energy using a cylindrical polychromator and the horizontal axis is used for the spatially resolved analysis with a pixel array detector. The vertically dispersive XAFS (VDXAFS) instrument was designed to analyze the dynamic changeover of the inhomogeneous electrode reaction of secondary batteries. The line‐shaped X‐ray beam is transmitted through the electrode sample, and then the dispersed transmitted X‐rays are detected by a two‐dimensional detector. An array of XAFS spectra in the linear footprint of the transmitted X‐ray on the sample is obtained with the time resolution of the repetition frequency of the detector. Sequential measurements of the space‐resolved XAFS data are possible with the VDXAFS instrument. The time and spatial resolutions of the VDXAFS instrument depend on the flux density of the available X‐ray beam and the size of the light source, and they were estimated as 1 s and 100 µm, respectively. The electrode reaction of the LiFePO₄ lithium ion battery was analyzed during the constant current charging process and during the charging process after potential jumping.     

In situ XAFS experiments using a microfluidic cell: application to initial growth of CdSe nanocrystals

The design and performance of a compact fluorescense XAFS apparatus equipped with a microfluidic cell for in situ studies of nanoparticles are described. CdSe nanoparticles were prepared by solution reaction starting from trioctylphosphine‐Se. Time‐resolved experiments were performed by precisely controlling the reactor coordinates (x,y), allowing the synchrotron X‐ray beam to travel along a reactor channel, covering nucleation and initial growth of nanoparticles. Detailed analysis of EXAFS data combined with UV–vis spectra allow reliable estimation of particle size and density in the initial growth that cannot be accessible by conventional optical techniques based on a long‐range order. The Se K‐XANES spectra are interpreted by multi‐scattering calculations providing bond formation kinetics consistent with the EXAFS data.     

Small copper clusters: Study of the local atomic and electronic structure by the XANES and DFT methods

The Cu L ₃ edge X-ray absorption spectra of free Cu _n clusters containing 5–15 atoms were obtained for the first time. It is shown that the geometry of small clusters, including the bond length and bond angle, can be studied by analyzing the X-ray absorption spectra. The experimental X-ray absorption spectra of Cu₁₃ clusters were theoretically interpreted using the self-consistent method of full multiple scattering, the finite difference method in the muffin-tin potential approximation, and the full potential method for the icosahedral cluster structure. Good agreement between the theoretical and experimental spectra is achieved for the calculation in the full potential approximation.     

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.     

Characteristics of a tapered undulator for the X‐ray absorption fine‐structure technique at PLS‐II

An in‐vacuum undulator (IVU) with a tapered configuration was installed in the 8C nanoprobe/XAFS beamlime (BL8C) of the Pohang Light Source in Korea for hard X‐ray nanoprobe and X‐ray absorption fine‐structure (XAFS) experiments. It has been operated in planar mode for the nanoprobe experiments, while gap‐scan and tapered modes have been used alternatively for XAFS experiments. To examine the features of the BL8C IVU for XAFS experiments, spectral distributions were obtained theoretically and experimentally as functions of the gap and gap taper. Beam profiles at a cross section of the X‐ray beam were acquired using a slit to visualize the intensity distributions which depend on the gap, degree of tapering and harmonic energies. To demonstrate the effect of tapering around the lower limit of the third‐harmonic energy, V K‐edge XAFS spectra were obtained in each mode. Owing to the large X‐ray intensity variation around this energy, XAFS spectra of the planar and gap‐scan modes show considerable spectral distortions in comparison with the tapered mode. This indicates that the tapered mode, owing to the smooth X‐ray intensity profile at the expense of the highest and most stable intensity, can be an alternative for XAFS experiments where the gap‐scan mode gives a considerable intensity variation; it is also suitable for quick‐XAFS scanning.     

Structural investigation of mM Ni(II) complex isomers using transmission XAFS: the significance of model development

High‐accuracy transmission XAFS determined using the hybrid technique has been used to refine the geometries of bis(N‐n‐propyl‐salicylaldiminato) nickel(II) (n‐pr Ni) and bis(N‐i‐propyl‐salicylaldiminato) nickel(II) (i‐pr Ni) complexes which have approximately square planar and tetrahedral metal coordination. Multiple‐scattering formalisms embedded in FEFF were used for XAFS modelling of the complexes. Here it is shown that an IFEFFIT‐like package using weighting from experimental uncertainty converges to a well defined XAFS model. Structural refinement of (i‐pr Ni) was found to yield a distorted tetrahedral geometry providing an excellent fit, χ_r² = 2.94. The structure of (n‐pr Ni) is best modelled with a distorted square planar geometry, χ_r² = 3.27. This study demonstrates the insight that can be obtained from the propagation of uncertainty in XAFS analysis and the consequent confidence which can be obtained in hypothesis testing and in analysis of alternate structures ab initio. It also demonstrates the limitations of this (or any other) data set by defining the point at which signal becomes embedded in noise or amplified uncertainty, and hence can justify the use of a particular k‐range for one data set or a different range for another. It is demonstrated that, with careful attention to data collection, including the correction of systematic errors with statistical analysis of uncertainty (the hybrid method), it is possible to obtain reliable structural information from dilute solutions using transmission XAFS data.     

Experimental and theoretical X-ray K-spectra of sulfur of zincblende-based compounds AgGaS2-CdGa2S4-InPS4

The K-edge X-ray absorption spectrum of sulfur in AgGaS₂, CdGa₂S₄, and InPS₄ was investigated both experimentally and theoretically. The lattices of these compounds can be represented as chalcopyrite with various amounts of defectiveness. The spectra were obtained with an experimental resolution about 0.2 eV. To obtain the theoretical absorption spectrum, the FEFF7 high order multiple scattering code was used. The clusters considered contained 80-87 atoms; up to 624 multiple-scattering paths of the photoelectron were taken into account, with the highest order scattering equal to 6. A very good correspondence between the theoretical and experimental spectra was achieved when the energy dependent exchange energy was calculated according to the Dirac-Hara approximation.     

Optical properties of BiSBr and BiSeBr crystals

Optical properties of BiSBr and BiSeBr crystals were investigated by the full potential linearized augmented plane wave (FP-LAPW) method with density-functional theory (DFT). The complex dielectric function and optical constants, such as optical absorption coefficient, refractive index, extinction coefficient, energy-loss spectrum and reflectivity, were calculated and compared in the energy range of 0–30 eV. Origin of anisotropic behavior of optical spectra was also discussed. The plasmon energy ?ω_p was estimated to be 18 eV for BiSeBr and 20 eV for BiSBr crystal.     

Application of glancing‐emergent‐angle fluorescence for polarized XAFS studies of single crystals

X‐ray absorption fine‐structure (XAFS) data were obtained for the V K‐edge for a series of anisotropic single crystals of (Cr_xV_1–x)₂O₃. The data and the results were compared for the as‐prepared bulk single crystals (measured in fluorescence in two different orientations) and those ground to powder (measured in transmission). For the bulk single crystals, the glancing‐emergent‐angle (GEA) method was used to minimize fluorescence distortion. The reliability of the GEA technique was tested by comparing the polarization‐weighted single‐crystal XAFS data with the experimental powder data. These data were found to be in excellent agreement throughout the entire energy range. Thus, it was possible to reliably measure individual V–V contributions parallel and perpendicular to the c axis of the single crystals, i.e. those unavailable by powder data XAFS analysis. These experiments demonstrate that GEA is a premiere method for non‐destructive high‐photon‐count in situ studies of local structure in bulk single crystals.     

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.     

Simultaneous XAFS measurements of multiple samples

A four‐channel ionization chamber has been designed, constructed and tested. This ionization chamber allows X‐ray absorption spectra to be collected in transmission from up to four samples simultaneously. This results in spectra that are free of systematic uncertainty in relative energy alignment introduced by scan‐to‐scan stability of the monochromator or of numerical uncertainty associated with a post‐processing alignment algorithm, allowing, in a single shot, an absolute measure of edge shift between four samples of different valence. As four samples can be measured in parallel, the time expended over the course of an experiment to cycle the measurement environment between its rest state and the measurement condition is substantially reduced. The ionization chamber is simple in design and could be implemented at virtually any XAFS beamline with a horizontal fan of radiation such as that provided by a bend magnet or wiggler.     

Synergic approach to XAFS analysis for the identification of most probable binding motifs for mononuclear zinc sites in metalloproteins

In the present work a data analysis approach, based on XAFS data, is proposed for the identification of most probable binding motifs of unknown mononuclear zinc sites in metalloproteins. This approach combines multiple‐scattering EXAFS analysis performed within the rigid‐body refinement scheme, non‐muffin‐tin ab initio XANES simulations, average structural information on amino acids and metal binding clusters provided by the Protein Data Bank, and Debye–Waller factor calculations based on density functional theory. The efficiency of the method is tested by using three reference zinc proteins for which the local structure around the metal is already known from protein crystallography. To show the applicability of the present analysis to structures not deposited in the Protein Data Bank, the XAFS spectra of six mononuclear zinc binding sites present in diverse membrane proteins, for which we have previously proposed the coordinating amino acids by applying a similar approach, is also reported. By comparing the Zn K‐edge XAFS features exhibited by these proteins with those pertaining to the reference structures, key spectral characteristics, related to specific binding motifs, are observed. These case studies exemplify the combined data analysis proposed and further support its validity.     

Optical, X-ray absorption and photoelectron spectroscopy investigation of the Co site configuration in Zn1−xCoxO films prepared by pulsed laser deposition

In this paper, we investigate the Co site configuration in Zn_1−xCo_xO thin films by means of different spectroscopic techniques. Thin films were prepared by pulsed laser deposition with Co proportion from 1% to 30%. The Co 2p doublet observed in the X-ray photoelectron spectra exhibits the spin–orbit splitting and shake-up satellites typical of Co⁺² ionization states. X-ray absorption spectra at the Co K-edge, taken in fluorescence mode, unambiguously show that Co atoms are in tetrahedral configuration substituting for Zn over the whole composition range. Optical absorption spectra provide further evidence of the tetrahedral coordination of Co cations, both through the internal transitions in the Co 3d shell and through the shift to higher energies of the band-to-band absorption edge with the increase of the Co proportion.     

Suppression of Bragg reflection glitches of a single‐crystal diamond anvil cell by a polycapillary half‐lens in high‐pressure XAFS spectroscopy

In combination with a single‐crystal diamond anvil cell (DAC), a polycapillary half‐lens (PHL) re‐focusing optics has been used to perform high‐pressure extended X‐ray absorption fine‐structure measurements. It is found that a large divergent X‐ray beam induced by the PHL leads the Bragg glitches from single‐crystal diamond to be broadened significantly and the intensity of the glitches to be reduced strongly so that most of the DAC glitches are efficiently suppressed. The remaining glitches can be easily removed by rotating the DAC by a few degrees with respect to the X‐ray beam. Accurate X‐ray absorption fine‐structure (XAFS) spectra of polycrystalline Ge powder with a glitch‐free energy range from ?200 to 800 eV relative to the Ge absorption edge are obtained using this method at high pressures up to 23.7 GPa, demonstrating the capability of PHL optics in eliminating the DAC glitches for high‐pressure XAFS experiments. This approach brings new possibilities to perform XAFS measurements using a DAC up to ultrahigh pressures.