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.     

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.     

Performance of a fuel cell optimized for in situ X‐ray absorption experiments

A commercial fuel cell has been successfully modified to carry out X‐ray absorption spectroscopy (XAS) measurements under optimized in operando conditions. The design is conceived for the performance of XAS experiments in transmission mode over a wide range of X‐ray energies above 6 keV, owing to the reduced absorption of the cell. The wide angular aperture allows the collection of XAS in fluorescence mode and of X‐ray diffraction patterns when needed. Details of the design of the cell and its performances are given. The quality of the extended X‐ray absorption fine‐structure spectra under working conditions has been verified at the ESRF and ELETTRA synchrotron radiation facilities, showing that relatively fast and low‐noise transmission measurements on electrodes over a wide range of catalyst concentrations and energies are feasible.     

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.     

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.     

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.     

Augmentation of the step‐by‐step Energy‐Scanning EXAFS beamline BL‐09 to continuous‐scan EXAFS mode at INDUS‐2 SRS

An innovative scheme to carry out continuous‐scan X‐ray absorption spectroscopy (XAS) measurements similar to quick‐EXAFS mode at the Energy‐Scanning EXAFS beamline BL‐09 at INDUS‐2 synchrotron source (Indore, India), which is generally operated in step‐by‐step scanning mode, is presented. The continuous XAS mode has been implemented by adopting a continuous‐scan scheme of the double‐crystal monochromator and on‐the‐fly measurement of incident and transmitted intensities. This enabled a high signal‐to‐noise ratio to be maintained and the acquisition time was reduced to a few seconds from tens of minutes or hours. The quality of the spectra (signal‐to‐noise level, resolution and energy calibration) was checked by measuring and analysing XAS spectra of standard metal foils. To demonstrate the energy range covered in a single scan, a continuous‐mode XAS spectrum of copper nickel alloy covering both Cu and Ni K‐edges was recorded. The implementation of continuous‐scan XAS mode at BL‐09 would expand the use of this beamline in in situ time‐resolved XAS studies of various important systems of current technological importance. The feasibility of employing this mode of measurement for time‐resolved probing of reaction kinetics has been demonstrated by in situ XAS measurement on the growth of Ag nanoparticles from a solution phase.     

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.     

Monitoring synchrotron X‐ray‐induced radiolysis effects on metal (Fe,W) ions in high‐temperature aqueous fluids

Radiolysis‐induced effects on aqueous tungsten ions are observed to form a precipitate within seconds upon exposure to a synchrotron X‐ray micro‐beam in a WO₃ + H₂O system at 873 K and 200 MPa. In situ Fe K‐edge energy‐dispersive X‐ray absorption spectroscopy (ED‐XAS) measurements were made on Fe(II)Cl₂ aqueous solutions to 773 K in order to study the kinetics of high‐temperature reactions of Fe²⁺ and Fe³⁺ ions with transient radiolysis species. The radiolytic reactions in a fluid sample within a hydrothermal diamond anvil cell result in oxidation of the Fe²⁺ ion at 573 K and reduction of Fe³⁺ at temperatures between 673 and 773 K and of the Fe²⁺ ion at 773 K. The edge‐energy drift evident in the ED‐XAS data directly reflects the kinetics of reactions resulting in oxidation and/or reduction of the Fe²⁺ and Fe³⁺ ions in the aqueous solutions at high temperatures. The oxidation and reduction trends are found to be highly consistent, making reliable determinations of reaction kinetics possible.     

On‐line optical and X‐ray spectroscopies with crystallography: an integrated approach for determining metalloprotein structures in functionally well defined states

X‐ray‐induced redox changes can lead to incorrect assignments of the functional states of metals in metalloprotein crystals. The need for on‐line monitoring of the status of metal ions (and other chromophores) during protein crystallography experiments is of growing importance with the use of intense synchrotron X‐ray beams. Significant efforts are therefore being made worldwide to combine different spectroscopies in parallel with X‐ray crystallographic data collection. Here the implementation and utilization of optical and X‐ray absorption spectroscopies on the modern macromolecular crystallography (MX) beamline 10, at the SRS, Daresbury Laboratory, is described. This beamline is equipped with a dedicated monolithic energy‐dispersive X‐ray fluorescence detector, allowing X‐ray absorption spectroscopy (XAS) measurements to be made in situ on the same crystal used to record the diffraction data. In addition, an optical microspectrophotometer has been incorporated on the beamline, thus facilitating combined MX, XAS and optical spectroscopic measurements. By uniting these techniques it is also possible to monitor the status of optically active and optically silent metal centres present in a crystal at the same time. This unique capability has been applied to observe the results of crystallographic data collection on crystals of nitrite reductase from Alcaligenes xylosoxidans, which contains both type‐1 and type‐2 Cu centres. It is found that the type‐1 Cu centre photoreduces quickly, resulting in the loss of the 595 nm peak in the optical spectrum, while the type‐2 Cu centre remains in the oxidized state over a much longer time period, for which independent confirmation is provided by XAS data as this centre has an optical spectrum which is barely detectable using microspectrophotometry. This example clearly demonstrates the importance of using two on‐line methods, spectroscopy and XAS, for identifying well defined redox states of metalloproteins during crystallographic data collection.     

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.     

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.     

K‐edge XANES analysis of sulfur compounds: an investigation of the relative intensities using internal calibration

Sulfur K‐edge XANES (X‐ray absorption near‐edge structure) spectroscopy is an excellent tool for determining the speciation of sulfur compounds in complex matrices. This paper presents a method to quantitatively determine the kinds of sulfur species in natural samples using internally calibrated reference spectra of model compounds. Owing to significant self‐absorption of formed fluorescence radiation in the sample itself the fluorescence signal displays a non‐linear correlation with the sulfur content over a wide concentration range. Self‐absorption is also a problem at low total absorption of the sample when the sulfur compounds are present as particles. The post‐edge intensity patterns of the sulfur K‐edge XANES spectra vary with the type of sulfur compound, with reducing sulfur compounds often having a higher post‐edge intensity than the oxidized forms. In dilute solutions (less than 0.3–0.5%) it is possible to use sulfur K‐edge XANES reference data for quantitative analysis of the contribution from different species. The results show that it is essential to use an internal calibration system when performing quantitative XANES analysis. Preparation of unknown samples must take both the total absorption and possible presence of self‐absorbing particles into consideration.     

Complexation of bis‐crown stilbene with alkali and alkaline‐earth metal cations. Ultrafast excited state dynamics of the stilbene‐viologen analogue charge transfer complex

The complex formation of bis(18‐crown‐6)stilbene ( 1 ) and its supramolecular donor‐acceptor complex with N,N′‐bis(ammonioethyl) 1,2‐di(4‐pyridyl)ethylene derivative ( 2 ) with alkali and alkaline‐earth metal perchlorates has been studied using absorption, steady‐state fluorescence, and femtosecond transient absorption spectroscopy. The formation of 1 ?Mⁿ⁺ and 1 ?(Mⁿ⁺)₂ complexes in acetonitrile was demonstrated. The weak long‐wavelength charge‐transfer absorption band of 1 · 2 completely vanishes upon complexation with metal cations because of disruption of the pseudocyclic structure. The spectroscopic and luminescence parameters, stability constants, and 2‐stage dissociation constants were calculated. The initial stage of a recoordination process was found in the excited complexes 1 ?M⁺ and 1 ?(M⁺)₂ (M = Li, Na). The pronounced fluorescence quenching of 1 · 2 is explained by very fast back electron transfer (τ_et = 0.397 ps). The structure of complex 1 · 2 was studied by X‐ray diffraction; stacked ( 1 · 2 )_m polymer in which the components were connected by hydrogen bonding and stacking was found in the crystal. These compounds can be considered as novel optical molecular sensors for alkali and alkaline‐earth metal cations.     

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.     

Polycapillary‐optics‐based micro‐XANES and micro‐EXAFS at a third‐generation bending‐magnet beamline

A focusing system based on a polycapillary half‐lens optic has been successfully tested for transmission and fluorescence µ‐X‐ray absorption spectroscopy at a third‐generation bending‐magnet beamline equipped with a non‐fixed‐exit Si(111) monochromator. The vertical positional variations of the X‐ray beam owing to the use of a non‐fixed‐exit monochromator were shown to pose only a limited problem by using the polycapillary optic. The expected height variation for an EXAFS scan around the Fe K‐edge is approximately 200 µm on the lens input side and this was reduced to ～1 µm for the focused beam. Beam sizes (FWHM) of 12–16 µm, transmission efficiencies of 25–45% and intensity gain factors, compared with the non‐focused beam, of about 2000 were obtained in the 7–14 keV energy range for an incoming beam of 0.5 × 2 mm (vertical × horizontal). As a practical application, an As K‐edge µ‐XANES study of cucumber root and hypocotyl was performed to determine the As oxidation state in the different plant parts and to identify a possible metabolic conversion by the plant.     

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.     

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.     

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.     

Confocal depth‐resolved fluorescence micro‐X‐ray absorption spectroscopy for the study of cultural heritage materials: a new mobile endstation at the Beijing Synchrotron Radiation Facility

A confocal fluorescence endstation for depth‐resolved micro‐X‐ray absorption spectroscopy is described. A polycapillary half‐lens defines the incident beam path and a second polycapillary half‐lens at 90° defines the probe sample volume. An automatic alignment program based on an evolutionary algorithm is employed to make the alignment procedure efficient. This depth‐resolved system was examined on a general X‐ray absorption spectroscopy (XAS) beamline at the Beijing Synchrotron Radiation Facility. Sacrificial red glaze (AD 1368–1644) china was studied to show the capability of the instrument. As a mobile endstation to be applied on multiple beamlines, the confocal system can improve the function and flexibility of general XAS beamlines, and extend their capabilities to a wider user community.