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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Characterization of Fe plaque and associated metals on the roots of mine-waste impacted aquatic plants.

Iron plaque on aquatic plant roots are ubiquitous and sequester metals in wetland soils; however, the mechanisms of metal sequestration are unresolved. Thus, characterizing the Fe plaque and associated metals will aid in understanding and predicting metal cycling in wetland ecosystems. Accordingly, microscopic and spectroscopic techniques were utilized to identify the spatial distributions, associations, and chemical environments of Fe, Mn, Pb, and Zn on the roots of a common, indigenous wetland plant (Phalaris arundinacea). Iron forms a continuous precipitate on the root surface, which is composed dominantly of ferrihydrite (ca. 63%) with lesser amounts of goethite (32%) and minor levels of siderite (5%). Although Pb is juxtaposed with Fe on the root surface, it is complexed to organic functional groups, consistent with those of bacterial biofilms. In contrast, Mn and Zn exist as discrete, isolated mixed-metal carbonate (rhodochrosite/hydrozincite) nodules on the root surface. Accordingly, the soil-root interface appears to be a complex biochemical environment, containing both reduced and oxidized mineral species, as well as bacterial-induced organic-metal complexes. As such, hydrated iron oxides, bacterial biofilms, and metal carbonates will influence the availability and mobility of metals within the rhizosphere of aquatic plants.

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.

A study of the coordination environment in aqueous cadmium-thiol complexes by EXAFS spectroscopy: experimental vs. theoretical standards.

Using EXAFS, we investigated the changes in the local structure of Cd(II) complexes formed with a series of low-molecular-weight thiols at different thiol/cadmium stoichiometries. For dilute solutions, a comparison of theoretical and experimental standards proved the latter approach superior. The number of bound oxygen atoms decreased while the number of sulfur atoms increased as the thiol/cadmium ratios increased, indicating that up to four thiol compounds can bind to cadmium in aqueous solutions. The computer code FEFFIT was modified to employ experimental and theoretical standards with equal facility.

Growth induced magnetic and chemical anisotropy in CoPt3 alloy films.

We report the results of polarized Co EXAFS experiments on a series of CoPt3 films grown by molecular beam epitaxy on (100) MgO singe crystal substrates over a range of temperatures from 473 K to 1073 K. These samples exhibit substantial perpendicular magnetic anisotropy that is strongly dependent on the substrate growth temperature Tg. We measure a preference for in-plane Co-Co pairs that is correlated with the magnetic properties.

EXAFS analysis using FEFF and FEFFIT.

Some of the advanced EXAFS analysis features of FEFF and FEFFIT are described. The scattering path formalism from FEFF and cumulant expansion are used as the basic building blocks of EXAFS analysis, giving a flexible and robust parameterization of most EXAFS problems. The ability to model EXAFS data in terms of generalized physical variables is shown, including the simultaneous refinement of two different polarizations for Co K EXAFS data of CoPt3.

Chromium diffusion and reduction in soil aggregates.

The distribution of metal contaminants such as chromium in soils can be strongly localized by transport limitations and redox gradients within soil aggregates. Measurements of Cr(VI) diffusion and reduction to Cr(III) were obtained in soil columns representing transects into soil aggregates in order to quantify influences of organic carbon (OC) and redox potentials on Cr transport distances and microbial community composition. Shifts in characteristic redox potentials, and the extent of Cr(VI) reduction to Cr(III) were related to OC availability. Depth profiles of Cr(VI, III) obtained with micro X-ray absorption near edge structure (micro-XANES) spectroscopy reflected interdependent effects of diffusion and spatially dependent redox potentials on reduction kinetics and microbial community composition. Shallow diffusion depths (2-10 mm) and very sharply terminated diffusion fronts in columns amended with OC (80 and 800 ppm) reflected rapid increases in Cr reduction kinetics over very short (mm) distances. These results suggest that Cr contamination in soils can be restricted to the outsides of soil aggregates due to localized transport and rapid reduction and that bulk sample characterization is inadequate for understanding the controlling biogeochemical processes.

Structure of the hydrated alpha-Al(2)O(3) (0001) surface

The physical and chemical properties of the hydrated alpha-Al(2)O(3) (0001) surface are important for understanding the reactivity of natural and synthetic aluminum-containing oxides. The structure of this surface was determined in the presence of water vapor at 300 kelvin by crystal truncation rod diffraction at a third-generation synchrotron x-ray source. The fully hydrated surface is oxygen terminated, with a 53% contracted double Al layer directly below. The structure is an intermediate between alpha-Al(2)O(3) and gamma-Al(OH)(3), a fully hydroxylated form of alumina. A semiordered oxygen layer about 2.3 angstroms above the terminal oxygen layer is interpreted as adsorbed water. The clean alpha-Al(2)O(3) (0001) surface, in contrast, is Al terminated and significantly relaxed relative to the bulk structure. These differences explain the different reactivities of the clean and hydroxylated surfaces.

X-Ray Absorption Spectroscopy of Strontium(II) Coordination.

Detailed analyses of crystalline, hydrated, and precipitated strontium compounds and an aqueous strontium solution by synchrotron extended X-ray absorption fine structure (EXAFS) were used to quantify local thermal and static disorder and to characterize strontium coordination in a variety of oxygen-ligated bonding environments. Analysis of anharmonic vibrational disorder (i.e., significant contribution from a third cumulant term (C(3)) in the EXAFS phase-shift function) in compounds with low and high static disorder around strontium showed that first-shell anharmonic contributions were generally not significant above experimental error in the EXAFS fits (R+/-0.02 Å with and without C(3)). The only case in which a significant apparent decrease in Sr-O distance was observed with increasing temperature, and for which a third cumulant term was significant, was for dilute strontium in aqueous solution. Empirical parameterization of Debye-Waller factor (sigma(2)) for strontium compounds as a function of backscatterer atomic number (Z), interatomic Sr-Z distance, and temperature of spectral data collection showed systematic increases in sigma(2) as a function of increasing temperature and Sr-Z bond length. At values of sigma(2) greater than approximately 0.025 Å(2) (for N<12 and R(Sr)-Z>3 Å), backscattering was generally not significant above noise levels in spectra of compounds of known crystal structure. Comparison of the EXAFS spectra of freshly precipitated SrCO(3) (spectra collected wet) to that of dry, powdered strontianite (SrCO(3)(s)) indicated no significant differences in the local atomic structure around strontium. Analysis of partially hydrated strontium in natural Ca-zeolite (heulandite) showed that strontium is substituted only in the calcium (Ca2) site. Backscattering from aluminum and silicon atoms in the zeolite framework were apparent in the EXAFS spectra at low and room temperature at distances from central strontium of <4.2 Å. Comparison of strontium structural coordination determined in this and previous studies suggests that previous EXAFS determinations of hydrated strontium may have underestimated first-shell interatomic distances and coordination numbers because minor contributions to the EXAFS phase-shift and amplitude functions were not accounted for, either theoretically or empirically. Copyright 2000 Academic Press.