The effect of self-consistent potentials on EXAFS analysis.

A theory program intended for use with extended X-ray-absorption fine structure (EXAFS) spectroscopy and based on the popular FEFF8 is presented. It provides an application programming interface designed to make it easy to integrate high-quality theory into EXAFS analysis software. This new code is then used to examine the impact of self-consistent scattering potentials on EXAFS data analysis by methodical testing of theoretical fitting standards against a curated suite of measured EXAFS data. For each data set, the results of a fit are compared using a well characterized structural model and theoretical fitting standards computed both with and without self-consistent potentials. It is demonstrated that the use of self-consistent potentials has scant impact on the results of the EXAFS analysis.

XAFS Data Interchange: A single spectrum XAFS data file format.

We propose a standard data format for the interchange of XAFS data. The XAFS Data Interchange (XDI) standard is meant to encapsulate a single spectrum of XAFS along with relevant metadata. XDI is a text-based format with a simple syntax which clearly delineates metadata from the data table in a way that is easily interpreted both by a computer and by a human. The metadata header is inspired by the format of an electronic mail header, representing metadata names and values as an associative array. The data table is represented as columns of numbers. This format can be imported as is into most existing XAFS data analysis, spreadsheet, or data visualization programs. Along with a specification and a dictionary of metadata types, we provide an application-programming interface written in C and bindings for programming dynamic languages.

Biogenic-to-lithogenic handoff of particulate Zn affects the Zn cycle in the Southern Ocean.

Zinc (Zn) is vital to marine organisms. Its active uptake by phytoplankton results in a substantial depletion of dissolved Zn, and Zn bound to particulate organic matter replenishes dissolved Zn in the ocean through remineralization. However, we found that particulate Zn changes from Zn bound to phosphoryls in cells to recalcitrant inorganic pools that include biogenic silica, clays, and iron, manganese, and aluminum oxides in the Southern Ocean water column. The abundances of inorganic pools increase with depth and are the only phases preserved in sediments. Changes in the particulate-Zn speciation influence Zn bioavailability and explain the decoupling of Zn and phosphorus and the correlation of Zn and silicon in the water column. These findings reveal a new dimension to the ocean Zn cycle, implicating an underappreciated role of inorganic Zn particles and their impact on biological productivity.

Towards data format standardization for X-ray absorption spectroscopy.

A working group on data format standardization for X-ray absorption spectroscopy (XAS) has recently formed under the auspices of the International X-ray Absorption Society and the XAFS Commission of the International Union of Crystallography. This group of beamline scientists and XAS practitioners has been tasked to propose data format standards to meet the needs of the world-wide XAS community. In this report, concepts for addressing three XAS data storage needs are presented: a single spectrum interchange format, a hierarchical format for multispectral X-ray experiment, and a relational database format for XAS data libraries.

Quantitative performance measurements of bent crystal Laue analyzers for X-ray fluorescence spectroscopy.

Third-generation synchrotron radiation sources pose difficult challenges for energy-dispersive detectors for XAFS because of their count rate limitations. One solution to this problem is the bent crystal Laue analyzer (BCLA), which removes most of the undesired scatter and fluorescence before it reaches the detector, effectively eliminating detector saturation due to background. In this paper experimental measurements of BCLA performance in conjunction with a 13-element germanium detector, and a quantitative analysis of the signal-to-noise improvement of BCLAs are presented. The performance of BCLAs are compared with filters and slits.

Ice-VII inclusions in diamonds: Evidence for aqueous fluid in Earth's deep mantle.

Water-rich regions in Earth's deeper mantle are suspected to play a key role in the global water budget and the mobility of heat-generating elements. We show that ice-VII occurs as inclusions in natural diamond and serves as an indicator for such water-rich regions. Ice-VII, the residue of aqueous fluid present during growth of diamond, crystallizes upon ascent of the host diamonds but remains at pressures as high as 24 gigapascals; it is now recognized as a mineral by the International Mineralogical Association. In particular, ice-VII in diamonds points toward fluid-rich locations in the upper transition zone and around the 660-kilometer boundary.

Shock-transformation of whitlockite to merrillite and the implications for meteoritic phosphate.

Meteorites represent the only samples available for study on Earth of a number of planetary bodies. The minerals within meteorites therefore hold the key to addressing numerous questions about our solar system. Of particular interest is the Ca-phosphate mineral merrillite, the anhydrous end-member of the merrillite-whitlockite solid solution series. For example, the anhydrous nature of merrillite in Martian meteorites has been interpreted as evidence of water-limited late-stage Martian melts. However, recent research on apatite in the same meteorites suggests higher water content in melts. One complication of using meteorites rather than direct samples is the shock compression all meteorites have experienced, which can alter meteorite mineralogy. Here we show whitlockite transformation into merrillite by shock-compression levels relevant to meteorites, including Martian meteorites. The results open the possibility that at least part of meteoritic merrillite may have originally been H+-bearing whitlockite with implications for interpreting meteorites and the need for future sample return.

micro-XANES and micro-XRF investigations of metal binding mechanisms in biosolids.

Micro-X-ray fluorescence (micro-XRF) microprobe analysis and micro-X-ray absorption near-edge structure (micro-XANES) spectroscopy were employed to identify Fe and Mn phases and their association with selected metals in two biosolids (limed composted [LC] and Nu-Earth) before and after treatment to remove organic carbon (OC). Spatial correlations derived from elemental mapping of XRF images showed strong correlations between Fe and Cd, Cr, Pb, or Zn (r2= 0.65-0.92) before and after removal of most of the OC. The strong correlation between Fe and Cu that was present in intact samples disappeared after OC removal, suggesting that Cu was associated with OC coatings that may have been present on Fe compounds. Except for Fe and Cr, the spatial correlations of metals with Mn were improved after treatment to remove OC, indicating that the treatment may have altered more than the OC in the system. The Fe micro-XANES spectra of the intact biosolids sample showed that every point had varying mixtures of Fe(II and III) species and no two points were identical. The lack of uniformity in Fe species in the biosolids sample illustrates the complexity of the materials and the difficulty of studying biosolids using conventional analytical tools or chemical extraction techniques. Still, these microscopic observations provide independent information supporting the previous laboratory and field hypothesis that Fe compounds play a major role in retention of environmentally important trace elements in biosolids. This could be due to co-precipitation of the metals with Fe, adsorption of metals by Fe compounds, or a combination of both mechanisms.

Spectroscopic properties of five-coordinated Co2+ in phosphates.

Co3(PO4)2, SrCo2(PO4)2, Co2P2O7, BaCoP2O7 and SrCoP2O7 present different geometries of five-coordinated Co(2+) (([5])Co(2+)) sites, coexisting with ([6])Co(2+) in Co3(PO4)2 and Co2P2O7, and ([4])Co(2+) in SrCo2(PO4)2. ([5])Co K-edge XANES spectra show that the intensity of the pre-edge and main-edge is intermediate between those of ([6])- and ([4])Co. Diffuse reflectance spectra show the contributions of Co(2+) in (D3h) symmetry for SrCo2(PO4)2, and (C4v) symmetry for BaCoP2O7 and SrCoP2O7. In Co3(PO4)2 and Co2P2O7 the multiple transitions observed arise from energy level splitting and may be labeled in (C2v) symmetry. Spectroscopic data confirm that (D3h) and (C4v) symmetries may be distinguished upon the intensity of the optical absorption bands and crystal field splitting values. We discuss the influence of the geometrical distortion and of the nature of the next nearest neighbors.

Evidence for nanoscale two-dimensional Co clusters in CoPt3 films with perpendicular magnetic anisotropy.

The length scale of the local chemical anisotropy responsible for the growth-temperature-induced perpendicular magnetic anisotropy of face-centered cubic CoPt(3) alloy films was investigated using polarized extended x-ray absorption fine structure (EXAFS). These x-ray measurements were performed on a series of four (111) CoPt(3) films epitaxially grown on (0001) sapphire substrates. The EXAFS data show a preference for Co-Co pairs parallel to the film plane when the film exhibits magnetic anisotropy, and random chemical order otherwise. Furthermore, atomic pair correlation anisotropy was evidenced only in the EXAFS signal from the next neighbors to the absorbing Co atoms and from multiple scattering paths focused through the next neighbors. This suggests that the Co clusters are no more than a few atoms in extent in the plane and one monolayer in extent out of the plane. Our EXAFS results confirm the correlation between perpendicular magnetic anisotropy and two-dimensional Co segregation in CoPt(3) alloy films, and establish a length scale on the order of 10 Å for the Co clusters.

The effect of CO2 on the speciation of bromine in low-temperature geological solutions: an XANES study.

CO(2)-rich solutions are common in geological environments. An XANES (X-ray absorption near-edge structure) study of Br in CO(2)-bearing synthetic fluid inclusions has revealed that Br exhibits a strong pre-edge feature at temperatures from 298 to 423 K. Br in CO(2)-free solutions does not show such a feature. The feature becomes smaller and disappears as temperature increases, but reappears when temperature is reduced. The size of the feature increases with increasing X(CO(2)) in the fluid inclusion, where X(CO(2)) is the mole fraction of CO(2) in the solution [n(CO(2))/(n(CO(2)) + n(H(2)(O)) + n(RbBr)); n indicates the number of moles]. The pre-edge feature is similar to that shown by covalently bonded Br, but observed and calculated concentrations of plausible Br-bearing covalent compounds (Br(2), CH(3)Br and HBr) are vanishingly small. An alternative possibility is that CO(2) affects the hydration of Br sufficiently that the charge density changes to favour the 1s-p level transitions that are thought to cause the pre-edge peak. The distance between the first two post-edge maxima in the XANES also decreases with increasing X(CO(2)). This is attributed to a CO(2)-related decrease in the polarity of the solvent. The proposed causes of the observed features are not integrated into existing geochemical models; thus CO(2)-bearing solutions could be predicted poorly by such models, with significant consequences for models of geological processes such as ore-formation and metamorphism.

ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectroscopy using IFEFFIT.

A software package for the analysis of X-ray absorption spectroscopy (XAS) data is presented. This package is based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl programming language using the Perl/Tk graphics toolkit. The programs described here are: (i) ATHENA, a program for XAS data processing, (ii) ARTEMIS, a program for EXAFS data analysis using theoretical standards from FEFF and (iii) HEPHAESTUS, a collection of beamline utilities based on tables of atomic absorption data. These programs enable high-quality data analysis that is accessible to novices while still powerful enough to meet the demands of an expert practitioner. The programs run on all major computer platforms and are freely available under the terms of a free software license.

IFEFFIT: interactive XAFS analysis and FEFF fitting.

IFEFFIT, an interactive program and scriptable library of XAFS algorithms is presented. The core algorithms of AUTOBK and FEFFIT have been combined with general data manipulation and interactive graphics into a single package. IFEFFIT comes with a command-line program that can be run either interactively or in batch-mode. It also provides a library of functions that can be used easily from C or Fortran, as well as high level scripting languages such as Tcl, Perl and Python. Using this library, a Graphical User Interface for rapid 'online' data analysis is demonstrated. IFEFFIT is freely available with an Open Source license. Outside use, development, and contributions are encouraged.