A compact-rigid multi-analyser for energy and angle filtering of high-resolution X-ray experiments. Part 2. Efficiency of a single-crystal-comb.

Diffraction instruments using filtering by one or several analyser crystals exist since the 1980s and 1990s at synchrotron radiation sources, but, due to its low efficiency, this filtering is little used on laboratory sources. In order to overcome this limitation, the efficiency of a small diffraction filtering multi-analyzer block (MAD block) realized with a `single-crystal-comb' curved on a rigid support is demonstrated here. The geometry of this curved surface is logarithmic spiral and is optimized to allow multi-filtering over a relatively important diffraction angular range and to be also applicable over an X-ray spectral range. The efficiency of such a small rigid-compact MAD block consisting of this single-crystal-comb generating 20-50 Si(111) single-crystal blades, associated with a block of Soller collimators, is demonstrated. The angle between each crystal is 0.1°, so the measurement range of the comb is 2-5°. The geometry of this system has been optimized for operation with a synchrotron X-ray source over an energy range of 22 keV to 46 keV and could be used with laboratory X-ray sources (Ag Kα1, 22.1 keV). This MAD block complements and exploits the qualities of the `photon-counting' detectors which have very low intrinsic noise. Their joint efficacy is supported by powder pattern measurements of a LaB6 reference sample and of several heterogeneous samples of cultural heritage materials, carried out at 22 keV on the D2AM beamline at the ESRF. Their signal-to-noise ratio is excellent (1000/1) and allows the detection thresholds of the measurements (from 3-1% to 0.1%) to detect minor phases in the studies of `real' heterogeneous materials to be drastically improved.

Sub-ppm level high energy resolution fluorescence detected X-ray absorption spectroscopy of selenium in articular cartilage.

The speciation of highly-diluted elements by X-ray absorption spectroscopy in a diverse range of materials is extremely challenging, especially in biological matrices such as articular cartilage. Here we show that using a high energy resolution fluorescence detected X-ray absorption spectroscopy (HERFD-XAS) technique coupled to an array of crystal analyzers, selenium speciation down to 400 ppb (µg kg-1) within articular cartilage can be demonstrated. This is a major advance in the speciation of highly-diluted elements through X-ray absorption spectroscopy and opens new possibilities to study the metabolic role of selenium and other elements in biological samples.

In situ X-ray absorption spectroscopy study of Si(1-x)Ge(x)O2 dissolution and germanium aqueous speciation under hydrothermal conditions.

The dissolution of Si(1-x)Ge(x)O(2) solid solutions under hydrothermal conditions was studied by in situ X-ray absorption spectroscopy. Experiments were performed at the Ge K-edge using a high-pressure cell mounted on the FAME beamline of the European Synchrotron Radiation Facility. Spectra in both transmission and fluorescence mode were collected in isobaric conditions (100 and 150 MPa) up to 475 °C. The local atomic structure around the Ge atom was investigated as a function of the temperature and in pure water and sodium hydroxide solutions. In pure water, the solubility of the cristobalite-type Si(0.8)Ge(0.2)O(2) increases with the temperature and the Ge atom is in 4-fold coordination. In a sodium hydroxide aqueous solution, a complex between Ge and Na atoms forms and gives rise to precipitation of sodium germanates. Under these conditions, the Ge content in the solution decreases with increasing temperature. These results show that a sodium hydroxide aqueous solution, usually used for quartz crystal growth, is not suitable for Ge-containing crystals. The dissolution kinetics and phase transformation of the solid solution were studied as a function of the atomic fraction of Ge. Ge-rich solid solutions dissolve and transform to stable phases faster than Ge-poorer composition, giving rise to important variations of the Ge content in solution.

Random alloy-like local structure of Fe(Se, S)(1-x)Te(x) superconductors revealed by extended x-ray absorption fine structure.

The local structure of Fe(Se, S)(1-x)Te(x) ternary (11-type) chalcogenides has been studied by temperature dependent Fe K-edge extended x-ray absorption fine structure measurements. We find that the Fe-Se and Fe-Te distances in ternary FeSe(1-x)Te(x) are closer to the respective distances in the binary systems, revealing significant divergence of the local structure from the average one. The mean square relative displacements show a systematic change with Te content, consistent with bond relaxation in the inhomogeneous ternary phases. Also, the Fe-Te and Fe-S distances in the FeS(0.2)Te(0.8) ternary system are found to be different in the crystallographically homogeneous structure. The observed features are characteristic of ternary random alloys, suggesting that a proper consideration should be given to the atomic distribution for describing the complex electronic structure of these multi-band Fe-based chalcogenides.

Combining size fractionation, scanning electron microscopy, and X-ray absorption spectroscopy to probe zinc speciation in pig slurry.

Zinc occurs in high quantity in pig slurry since it is used as an essential micronutrient at high concentrations in animal feeds despite the low Zn assimilation by pigs. Zinc accumulation was measured in soil surface layers that had been amended with pig slurry, while also determining the phytotoxicity as well as the extent of groundwater quality degradation. To accurately predict the mobility and bioavailability of Zn derived from pig slurry spreading, the speciation of this element has to be assessed since the total concentration is not sufficient. This study involved a combination of techniques to investigate Zn speciation in pig slurry. Size fractionation was first performed to account for the complexity of pig slurry, and 75% of total Zn was detected in the 0.45- to 20-mum particle-size range. Then X-ray diffraction, scanning electron microscopy, coupled with energy dispersive spectrometer, and extended X-ray absorption fine structure analyses were combined to assess Zn speciation. The findings highlighted the presence of 49% Zn bound to organic matter, 37% amorphous Zn hydroxides [Zn(OH)(2)], and 14% sphalerite (ZnS).

Speciation of Cd and Pb in dust emitted from sinter plant.

Many studies have provided evidence of the impact of heavy metals in atmospheric emission. Sinter plants represent the first step in steel production, and are important emitters of Cd and Pb. The toxicity of these two metals depends above all on their speciation. Particles collected before and after the filtration system were analysed to determine the Cd- and Pb-bearing phases, using analytical tools such as XRF, EXAFS or ICP-AES and chemical leaching (sequential extractions adapted to steel dusts). Results show that Pb is associated with carbonate and Cd with chloride. These two types of speciation lead to high solubility under common environmental conditions, which may produce impacts on the environment and health.

Structural characterization of the active form of PerR: insights into the metal-induced activation of PerR and Fur proteins for DNA binding.

In Bacillus subtilis, the transcription factor PerR is an iron dependant sensor of H(2)O(2). The sensing mechanism relies on a selective metal catalysed oxidation of two histidine residues of the regulatory site. Here we present the first crystal structure of the active PerR protein in complex with a Mn(2+) ion. In addition, X-ray absorption spectroscopy experiments were performed to characterize the corresponding iron form of the protein. Both studies reveal a penta-coordinate arrangement of the regulatory site that involves three histidines and two aspartates. One of the histidine ligand belongs to the N-terminal domain. Binding of this residue to the regulatory metal allows the protein to adopt a caliper-like conformation suited to DNA binding. Since this histidine is conserved in all PerR and a vast majority of Fur proteins, it is likely that the allosteric switch induced by the regulatory metal is general for this family of metalloregulators.

Changes in arsenic speciation through a contaminated soil profile: a XAS based study.

An impacted soil located near an industrial waste site in the Massif Central near Auzon, France, where arsenical pesticides were manufactured, has been studied in order to determine the speciation (chemical forms) of arsenic as a function of soil depth. Bulk As concentrations range from 8780 mg kg(-1) in the topsoil horizon to 150 mg kg(-1) at 60 cm depth. As ores (orpiment As2S3, realgar AsS, arsenopyrite FeAsS) and former Pb- and Al-arsenate pesticides have been identified by XRD at the site and are suspected to be the sources of As contamination for this soil. As speciation was found to vary with depth, based on XRD, SEM-EDS, EPMA measurements and selective chemical extractions. Based on oxalate extraction, As is mainly associated with amorphous Fe oxides through the soil profile, except in the topsoil horizons where As is hosted by another phase. SEM-EDS and EPMA analyses led to the identification of arseniosiderite (Ca2Fe3+3(AsVO4)3O2.3H2O), a secondary mineral that forms upon oxidation of primary As-bearing minerals like arsenopyrite, in these topsoil horizons. These mineralogical and chemical results were confirmed by synchrotron-based X-ray absorption spectroscopy. XANES spectra of soil samples indicate that As occurs exclusively as As(V), and EXAFS results yield direct evidence of changes in As speciation with depth. Linear combination fits of EXAFS spectra of soil samples with those of various model compounds indicate that As occurs mainly As-bearing Fe(III)-(hydr)oxides (65%) and arseniosiderite (35%) in the topsoil horizon (0-5 cm depth). Similar analyses also revealed that there is very little arseniosiderite below 15 cm depth and that As(V) is associated primarily with amorphous Fe oxides below this depth. This vertical change of As speciation likely reflects a series of chemical reactions downward in the soil profile. Arseniosiderite, formed most likely by oxidation of arsenopyrite, is progressively dissolved and replaced by less soluble As-bearing poorly ordered Fe oxides, which are the main hosts for As in well aerated soils.

Determination of zinc speciation in basic oxygen furnace flying dust by chemical extractions and X-ray spectroscopy.

There is a growing concern regarding the environmental and public health risks associated with airborne particulate matter (PM). The basic oxygen furnace is one of the most important atmospheric dust sources of the steel manufacturing process. It emits dust enriched in heavy metal such as Zn, which is assumed to contribute to the toxic potential of atmospheric PM. Dust collected before and after the filtration system was analyzed to determine Zn speciation. To this end, a variety of analytical tools were used and a sequential extraction protocol has been specifically developed for iron and steel dust. The Zn speciation results obtained by EXAFS and sequential extraction were in excellent agreement. Before filtration, the speciation of Zn in BOF was 43% ZnFe(2)O(4), 23% ZnCO(3) and 16% ZnO. The same species were detected after filtration with different proportions. BOF dust after filtration contains more soluble Zn phases which may play a role in the toxic effects of the emissions.

Spectroscopic characterization of microscopic hydrogen-bonding disparities in supercritical water.

The local hydrogen-bonding environment in supercritical water (380 degrees C, 300 bars, density 0.54 gcm3) was studied by x-ray Raman scattering at the oxygen K edge. The spectra are compared to those of the gas phase, liquid surface, bulk liquid, and bulk ice, as well as to calculated spectra. The experimental model systems are used to assign spectral features and to quantify specific local hydrogen-bonding situations in supercritical water. The first coordination shell of the molecules is characterized in more detail with the aid of the calculations. Our analysis suggests that approximately 65% of the molecules in supercritical water are hydrogen bonded in configurations that are distinctly different from those in liquid water and ice. In contrast to liquid water the bonded molecules in supercritical water have four intact hydrogen bonds and in contrast to ice large variations of bond angles and distances are observed. The remaining approximately 35% of the molecules exhibit two free O-H bonds and are thus either not involved in hydrogen bonding at all or have one or two hydrogen bonds on the oxygen side. We determine an average O-O distance of 3.1+/-0.1 A in supercritical water for the H bonded molecules at the conditions studied here. This and the corresponding hydrogen bond lengths are shown to agree with neutron- and x-ray-diffraction data at similar conditions. Our results on the local hydrogen-bonding environment with mainly two disparate hydrogen-bonding configurations are consistent with an extended structural model of supercritical water as a heterogeneous system with small patches of bonded molecules in various tetrahedral configurations and surrounding nonbonded gas-phase-like molecules.

Light-induced relaxation of photolyzed carbonmonoxy myoglobin: a temperature-dependent x-ray absorption near-edge structure (XANES) study.

X-ray absorption near-edge structure (XANES) spectra at the Fe K-edge have been measured and compared on solution samples of horse carbonmonoxy-myoglobin and its photoproducts, prepared by two different photolysis protocols: 1), extended illumination at low temperature (15 K) by white light; and 2), slow-cool from 140 to 10 K at a rate of 0.5 K/min while illuminating the sample with a 532-nm continuous-wave laser source. CO recombination has been followed while increasing the temperature at a rate of 1.2 K/min. After extended illumination at 15 K, a single process is observed, corresponding to CO recombination from a completely photolyzed species with CO bound to the primary docking site (formally B-state, in agreement with previous x-ray diffraction studies). The temperature peak for this single process is approximately 50 K. Using slow-cool illumination, data show a two-state recombination curve, the two temperature peaks being roughly assigned to 50 K and 110 K. These results are in good agreement with previous FTIR studies using temperature-derivative spectroscopy. The XANES spectroscopic markers probe structural differences between the photoproduct induced by extended illumination at 15 K and the photoproduct induced by slow-cool illumination. These differences in the XANES data have been interpreted as due to light-induced Fe-heme relaxation that does not involve CO migration from the B-state. A quantitative description of the unrelaxed and relaxed B-states, including the measurements of the Fe-N(p), Fe-N(His), and Fe-CO distances, and the out-of-plane Fe displacement, has been obtained via a procedure (MXAN) recently developed by us. This work shows that XANES, being able to extract both kinetic and structural parameters in a single experiment, is a powerful tool for structural dynamic studies of proteins.

XAS evidence of As(V) association with iron oxyhydroxides in a contaminated soil at a former arsenical pesticide processing plant.

The molecular-level speciation of arsenic has been determined in a soil profile in the Massif Central near Auzon, France that was impacted by As-based pesticides by combining conventional techniques (XRD, selective chemical extractions) with X-ray absorption spectroscopy (XAS). The arsenic concentration is very high at the top (>7000 mg kg(-1)) and decreases rapidly downward to a few hundreds of milligrams per kilogram. A thin layer of schultenite (PbHAsO4), a lead arsenate commonly used as an insecticide until the middle of the 20th century, was found at 10 cm depth. Despite the occurrence of this As-bearing mineral, oxalate extraction indicated that more than 65% of the arsenic was released upon dissolution of amorphous iron oxides, suggesting a major association of arsenic with these phases within the soil profile. Since oxalate extraction cannot unambiguously distinguish among the various chemical forms of arsenic, these results were confirmed by a direct in situ determination of arsenic speciation using XAS analysis. XANES data indicate that arsenic occurs mainly as As(V) along the soil profile except for the topsoil sample where a minor amount (7%) of As(III) was detected. EXAFS spectra of soil samples were fit by linear combinations of model compounds spectra and by a shell-by-shell method. These procedures clearly confirmed that As(V) is mainly (at least 80 wt %) associated with amorphous Fe(III) oxides as coprecipitates within the soil profile. If any, the proportion of schultenite, which was evidenced by XRD in a separate thin white layer, does not account for more than 10 wt % of arsenic in soil samples. This study emphasizes the importance of iron oxides in restricting arsenic dispersal within soils following dissolution of primary As-bearing solids manufactured for use as pesticides and released into the soils.

Redox-induced structural dynamics of Fe-heme ligand in myoglobin by X-ray absorption spectroscopy.

The Fe(III) --> Fe(II) reduction of the heme iron in aquomet-myoglobin, induced by x-rays at cryogenics temperatures, produces a thermally trapped nonequilibrium state in which a water molecule is still bound to the iron. Water dissociates at T > 160 K, when the protein can relax toward its new equilibrium, deoxy form. Synchrotron radiation x-ray absorption spectroscopy provides information on both the redox state and the Fe-heme structure. Owing to the development of a novel method to analyze the low-energy region of x-ray absorption spectroscopy, we obtain structural pictures of this photo-inducible, irreversible process, with 0.02-0.06-A accuracy, on the protein in solution as well as in crystal. After photo-reduction, the iron-proximal histidine bond is shortened by 0.15 A, a reinforcement that should destabilize the iron in-plane position favoring water dissociation. Moreover, we are able to get the distance of the water molecule even after dissociation from the iron, with a 0.16-A statistical error.

Quantitative analysis of x-ray absorption near edge structure data by a full multiple scattering procedure: the Fe-CO geometry in photolyzed carbonmonoxy-myoglobin single crystal.

We report the first quantitative analysis of the Fe K-edge polarized x-ray absorption near edge structure of the iron protein carbonmonoxy-myoglobin (MbCO) single crystal and of its cryogenic photoproduct Mb(*)CO. The CO-Fe-heme local structure has been determined using a novel fitting procedure based on the full multiple scattering approach. The extracted local structure of Mb(*)CO includes a Fe-CO distance of (3.08+/-0.07) A, with a tilting angle between the heme normal and the Fe-C vector of (37+/-7) degrees, and a bending angle between the Fe-C vector and the C-O bond of (31+/-5) degrees.

An X-ray absorption spectroscopy study of the pressure and temperature dependence of ZnBr2 aqueous supercritical solutions.

X-ray absorption spectroscopy (XAS) experiments have been performed on 1.0 and 1.6 M ZnBr2 aqueous solutions under ambient to supercritical conditions. Both the X-ray absorption near-edge structure (XANES) and the extended X-ray absorption fine structure (EXAFS) show striking evolutions, which indicate major structural changes, with a strong reduction in hydration and the increasing formation of ZnBr pairs. A quantitative analysis of the evolution of the Zn environment is presented that supports the existence of a transition from an octahedral to a tetrahedral environment.

Accumulation forms of Zn and Pb in Phaseolus vulgaris in the presence and absence of EDTA.

The internalized speciation of Zn and Pb in roots and leaves of Phaseolus vulgaris grown in zinc sulfate, zinc EDTA, lead nitrate, and lead EDTA solutions were studied by electron microscopy (Zn) and extended X-ray absorption fine structure (EXAFS) spectroscopy (Zn and Pb). Zn was predominantly present as Zn phosphate dihydrate in the roots and leaves of the plant regardless of its form in solution. Pb was predominantly found in the leaves as cerussite (lead carbonate) when the plant was grown in Pb nitrate solution and as a mixture of PbEDTA and an undetermined species in contact with PbEDTA solution. Therefore, Phaseolus vulgaris is able to dissociate totally (Zn) or partly (Pb) the two metal-EDTA complexes from the nutrient solution and to bind these metals in other forms.

Ferromagnetic hcp chromium in Cr/Ru(0001) superlattices.

We report the first observation of a weak ferromagnetic state of Cr in Cr/Ru(0001) superlattices, based on magnetic hysteresis and corroborated by x-ray magnetic circular dichroism at the CrL(2,3) edges. In situ reflection high-energy electron diffraction, x-ray diffraction, and Cr K-edge polarized x-ray absorption investigations have shown that the Cr layers thinner than 8 angstroms adopt a slightly distorted hcp structure, accompanied by a large atomic volume expansion of up to 14% compared to the bcc packing volume. The expanded hcp structure clearly induces the observed ferromagnetism, in agreement with theory.

Spectroscopic and saturation magnetization properties of the manganese- and cobalt-substituted Fur (ferric uptake regulation) protein from Escherichia coli.

The Fur apoprotein has been purified and reconstituted with Co2+ and Mn2+ ions. These samples have been analyzed by UV-visible, EPR, and 1H NMR spectroscopies, by XAS, and by magnetization measurements. The apo-Fur protein is able to bind one metal dication (Co2+ or Mn2+) per monomer. A saturation magnetization study confirms the presence of a high-spin metal dication [Mn(II) S = 5/2 and Co(II) S = 3/2]. The two metal ions per Fur dimer are not in magnetic interaction (|J| < 0.1 cm-1 ). The UV-visible spectrum of the cobalt-substituted form (Co-Fur) presents two main bands at 660 nm and 540(br) nm with epsilon540 nm = 65 M-1 cm-1. The EPR spectrum gives the following g values: gx = 5.0(5), gy = 4.0(2), and gz = 2. 3(1), which are in accordance with a nearly axial (E/D < 0.11) site. The value of 55 cm-1 for the splitting (Delta) between the ground and the first excited state has been derived from an EPR saturation study and is in agreement with magnetization data. The EXAFS data of Co-Fur indicate a metal environment comprising five nitrogen/oxygen atoms at 2.11 A, the absence of sulfur, and the presence of histidines as ligands. 1H NMR of Co-Fur in H2O and D2O shows at least two exchangeable signals coming from histidine NH protons and shows the signature of carboxylate group(s). The combined spectroscopic data allow us to propose that the main metal site of Fur in Co-Fur contains at least two histidines, at least one aspartate or glutamate, and no cysteine as ligands and is in an axially distorted octahedral environment.

X-ray absorption spectroscopy of a new zinc site in the fur protein from Escherichia coli.

The zinc K-edge X-ray absorption spectra of the Fur (ferric uptake regulation) protein isolated from Escherichia coli have been analyzed in frozen solution to determine details of the zinc coordination. The spectra of apoFur and of the cobalt-substituted protein have been analyzed and compared in order to see the influence of the cobalt incorporation on the geometry of the zinc site. EXAFS analysis gave for both samples (apoFur and CoFur) a tetrahedral environment for the zinc atom with two sulfur donor ligands at a distance of 2.3 A from the zinc and two N/O donor ligands at 2.0 A. The two sulfur donor ligands are probably two of the four cysteines present in each Fur monomer and could be Cys92 and Cys95, which are known from mutagenesis studies to be essential for Fur activity [Coy, M., Doyle, C., Besser, J., and Neilands, J. B. (1994) BioMetals 7, 292-298]. The distances obtained from our fits were always too short to be compatible with penta or hexa coordination. The typical pattern observed for the Fourier transform of the EXAFS oscillations suggests the presence of at least one imidazole ligand. The XANES of these two forms of the protein are similar but significantly different. This suggests a change of the conformation of the zinc site upon cobalt incorporation. The present study provides the first unambiguous evidence for the presence of a structural zinc site in the Fur protein from Escherichia coli.