First X-ray spectral ptychography and resonant ptychographic computed tomography experiments at the SWING beamline from Synchrotron SOLEIL

X-ray ptychography and ptychographic computed tomography have seen a rapid rise since the advent of fourth-generation synchrotrons with a high degree of coherent radiation. In addition to quantitative multiscale structural analysis, ptychography with spectral capabilities has been developed, allowing for spatial-localized multiscale structural and spectral information of samples. The SWING beamline of Synchrotron SOLEIL has recently developed a nanoprobe setup where the endstation's first spectral and resonant ptychographic measurements have been successfully conducted. A metallic nickel wire sample was measured using 2D spectral ptychography in XANES mode and resonant ptychographic tomography. From the 2D spectral ptychography measurements, the spectra of the components of the sample's complex-valued refractive index, δ and β, were extracted, integrated along the sample thickness. By performing resonance ptychographic tomography at two photon energies, 3D maps of the refractive index decrement, δ, were obtained at the Ni K-edge energy and another energy above the edge. These maps allowed the detection of impurities in the Ni wire. The significance of accounting for the atomic scattering factor is demonstrated in the calculation of electron density near a resonance through the use of the δ values. These results indicate that at the SWING beamline it is possible to conduct state-of-the-art spectral and resonant ptychography experiments using the nanoprobe setup.

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.

High-resolution spectroscopy on an X-ray absorption beamline

A bent-crystal spectrometer based on the Rowland circle geometry has been installed and tested on the BM30b/FAME beamline at the European Synchrotron Radiation Facility to improve its performances. The energy resolution of the spectrometer allows different kinds of measurements to be performed, including X-ray absorption spectroscopy, resonant inelastic X-ray scattering and X-ray Raman scattering experiments. The simplicity of the experimental device makes it easily implemented on a classical X-ray absorption beamline. This improvement in the fluorescence detection is of particular importance when the probed element is embedded in a complex and/or heavy matrix, for example in environmental sciences.

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.

Feedback system of a liquid-nitrogen-cooled double-crystal monochromator: design and performances

A new set-up is reported of an indirect cryogenic cooling system for a double-crystal monochromator which runs on the BM30b/FAME beamline at the ESRF (Grenoble, France). This device has been conceived to limit the vibrations on the first diffracting crystal and to maintain it at a constant temperature. These points are crucial for maximizing the beamline stability. Moreover, the relative angular position of the second crystal can be dynamically adjusted by a piezoelectric transducer coupled with a feedback system in order to always be at the maximum of the rocking curve during an X-ray absorption spectroscopy scan. The temperature is stabilized to an accuracy of 0.01 degrees , with two principal consequences. The energy resolution is close to the theoretical value [DeltaE/E = 5.6 x 10(-6) for Si(220)] and the precision of the energy positioning is extremely good even if the power load changes. A feedback mechanism allows a permanent and automatic optimization of the angle between the two crystals of the monochromator. The intensity of the monochromatic beam remains optimized (i) when the intensity of the electron beam decreases in the storage ring and (ii) during an energy scan.

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.

X-ray Absorption Investigation of a Unique Protein Domain Able To Bind both Copper(I) and Copper(II) at Adjacent Sites of the N-Terminus of Haemophilus ducreyi Cu,Zn Superoxide Dismutase

The N-terminal metal binding extension of the Cu,Zn superoxide dismutase from Haemophilus ducreyi is constituted by a histidine-rich region followed by a methione-rich sequence which shows high similarity with protein motifs involved in the binding of Cu(I). X-ray absorption spectroscopy experiments selectively carried out with peptides corresponding to the two metal binding regions indicate that both sequences can bind either Cu(II) or Cu(I). However, competition experiments demonstrate that Cu(II) is preferred by histidine residues belonging to the first half of the motif, while the methionine-rich region preferentially binds Cu(I) via the interaction with three methionine sulfur atoms. Moreover, we have observed that the rate of copper transfer from the peptides to the active site of a copper-free form of the Cu,Zn superoxide dismutase mutant lacking the N-terminal extension depends on the copper oxidation state and on the residues involved in metal binding, histidine residues being critically important for the efficient transfer. Differences in the enzyme reactivation rates in the presence of mixtures of the two peptides when compared to those obtained with the single peptides suggest that the two halves of the N-terminal domain functionally interact during the process of copper transfer, possibly through subtle modifications of the copper coordination environment.

Small angle x-ray scattering of a supercritical electrolyte solution: The effect of density fluctuations on the hydration of ions

Synchrotron small angle x-ray scattering measurements on water and zinc bromide ZnBr2 aqueous solutions were carried out from ambient to supercritical conditions. For both systems several isobars (between 285 and 600 bars) were followed beyond the critical isochore. The data were analyzed through an Ornstein-Zernike formalism in terms of correlation length and null angle structure factor. The results for pure water are in agreement with previously published values. Solutions of different electrolyte concentrations were studied. In each case, the values of the correlation length and null angle structure factor are larger than those of pure water. This effect is more pronounced for higher concentrations and/or for pressure closer to the critical point of pure water. This is in agreement with the shift of the critical point determined in the literature for NaCl solutions. Comparing these results to previous x-ray absorption measurements carried out on identical samples we propose the following two step sequence for ionic hydration up to supercritical conditions: (1) from ambient to about 300 degrees C, an increase of ion pairing and formation of multi-ionic complexes which can be correlated to the decrease of the dielectric constant; (2) an enhancement of the local solvation shell of ions due to the onset of the thermal density fluctuations at high temperature, leading to a screening effect between ions and inhibiting the ion pairing processes.

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.

Unusual heme iron-lipid acyl chain coordination in Escherichia coli flavohemoglobin

Escherichia coli flavohemoglobin is endowed with the notable property of binding specifically unsaturated and/or cyclopropanated fatty acids both as free acids or incorporated into a phospholipid molecule. Unsaturated or cyclopropanated fatty acid binding to the ferric heme results in a spectral change observed in the visible absorption, resonance Raman, extended x-ray absorption fine spectroscopy (EXAFS), and x-ray absorption near edge spectroscopy (XANES) spectra. Resonance Raman spectra, measured on the flavohemoglobin heme domain, demonstrate that the lipid (linoleic acid or total lipid extracts)-induced spectral signals correspond to a transition from a five-coordinated (typical of the ligand-free protein) to a hexacoordinated, high spin heme iron. EXAFS and XANES measurements have been carried out both on the lipid-free and on the lipid-bound protein to assign the nature of ligand in the sixth coordination position of the ferric heme iron. EXAFS data analysis is consistent with the presence of a couple of atoms in the sixth coordination position at 2.7 A in the lipid-bound derivative (bonding interaction), whereas a contribution at 3.54 A (nonbonding interaction) can be singled out in the lipid-free protein. This last contribution is assigned to the CD1 carbon atoms of the distal LeuE11, in full agreement with crystallographic data on the lipid-free protein at 1.6 A resolution obtained in the present work. Thus, the contributions at 2.7 A distance from the heme iron are assigned to a couple of carbon atoms of the lipid acyl chain, possibly corresponding to the unsaturated carbons of the linoleic acid.

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.

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.

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.

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.

Pi-conjugated ligand polymers entwined around copper centres

We describe conjugated polymers entwined around Cu1 with alternating alpha-quaterthienyl (poly[Cu(T2)2]) or 3',4',3'''',4''''-tetrahexyl-alpha-sexythienyl (poly[Cu(T3)2]) moieties and 1,10-phenanthroline complexing sites. Our strategy is to synthesise the 2,9-bis(oligothienyl)-1,10-phenanthroline precursors, then to assemble these ligands by means of Cu1 templating followed by electropolymerisation. Poly[Cu(T2)2] shows separate electroactivities for Cu redox centres and conjugated backbones, whereas the electroactivities overlap in the case of poly[Cu(T3)2]. An X-ray absorption study on these polymers in their reduced state at the Cu-K edge identifies, in both cases, four nitrogen atoms as the closest copper(I) neighbours. For poly[Cu(T2)2], the Cu1 environment is a distorted tetrahedron similar to a monomer model compound, but with a slightly higher number of steric constraints. The Cu1 environment for poly[Cu(T3)2] is a less distorted tetrahedron with an unusually short Cu1-N average bond length. Cu1 removal in poly[Cu(T2)2] induces an irreversible collapse of the structure, whereas the reversibility of Cu1 binding is almost perfect for poly[Cu(T3)2], as the hexyl chains prevent irreversible gliding of the wires after copper removal. Combined electrochemical and resistance measurements reveal that the Cu centres in poly[Cu(T2)2] play the role of mechanical support for the structure with no significant electronic interactions with the conjugated backbone, whereas in the case of poly[Cu(T3)2] copper centres contribute to the conductivity of the structure.

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.