An evidence of local structural disorder across spin-reorientation transition in DyFeO3: an extended x-ray absorption fine structure (EXAFS) study.

The present work is aimed at exploring the local atomic structure modifications related to the spin reorientation transition (SRT) in DyFeO3 orthoferrite exploiting x-ray absorption fine structure (XAFS) spectroscopy. For this purpose we studied by XAFS the evolution of the local atomic structure around Fe and Dy as function of temperature (10-300 K) in a DyFeO3 sample having the SRT around 50-100 K. For sake of comparison we studied a YFeO3 sample having no SRT. The analysis of the extended region has revealed an anomalous trend of Fe-O nearest neighbour distribution in DFO revealing (i) a weak but significant compression with increasing temperature above the SRT and (ii) a peculiar behavior of mean square relative displacement (MSRD) [[Formula: see text]] of Fe-O bonds showing an additional static contribution in the low temperature region, below the SRT. These effects are absent in the YFO sample supporting these anomalies related to the SRT. Interestingly the analysis of Dy L 3-edge data also reveal anomalies in the Dy-O neighbour distribution associated to the SRT, pointing out a role of magnetic Re ions across [Formula: see text]. These results point out micro-structural modification at both Fe and Dy sites associated to the magnetic transitions in DFO, it can be stated in general terms that such local distortions across [Formula: see text] and magnetic Re3+ may be present in other orthoferrites exhibiting multiferroic nature.

Gallium- and Iron-Pyoverdine Coordination Compounds Investigated by X-ray Photoelectron Spectroscopy and X-ray Absorption Spectroscopy.

Iron is an essential nutrient for nearly all forms of life, although scarcely available due to its poor solubility in nature and complex formation in higher eukaryotes. Microorganisms have evolved a vast array of strategies to acquire iron, the most common being the production of high-affinity iron chelators, termed siderophores. The opportunistic bacterial pathogen Pseudomonas aeruginosa synthesizes and secretes two siderophores, pyoverdine (PVD) and pyochelin (PCH), characterized by very different structural and functional properties. Due to its chemical similarity with Fe(III), Ga(III) interferes with several iron-dependent biological pathways. Both PVD and PCH bind Fe(III) and Ga(III). However, while the Ga-PCH complex is more effective than Ga(III) in inhibiting P. aeruginosa growth, PVD acts as a Ga(III) scavenger and protects bacteria from Ga(III) toxicity. To gain more insight into the different outcomes of the biological paths observed for the Fe(III) and Ga(III)-siderophore complexes, better knowledge is needed of their coordination geometries that directly influence the metal complexes chemical stability. The valence state and coordination geometry of the Ga-PCH and Fe-PCH complexes has recently been investigated in detail; as for PVD complexes, several NMR structural studies of Ga(III)-PVD are reported in the literature, using Ga(III) as a diamagnetic isosteric substitute for Fe(III). In this work, we applied up-to-date spectroscopic techniques as synchrotron-radiation-induced X-ray photoelectron spectroscopy (SR-XPS) and X-ray absorption fine structure (XAFS) spectroscopy coupled with molecular modeling to describe the electronic structure and coordination chemistry of Fe and Ga coordinative sites in PVD metal complexes. These techniques allowed us to unambiguously determine the oxidation state of the coordinative ions and to gather interesting information about the similarities and differences between the two coordination compounds as induced by the different metal.

The five-to-six-coordination transition of ferric human serum heme-albumin is allosterically-modulated by ibuprofen and warfarin: a combined XAS and MD study.

Human serum albumin (HSA) is involved physiologically in heme scavenging; in turn, heme-albumin (HSA-heme-Fe) displays globin-like properties. Here, the allosteric effect of ibuprofen and warfarin on the local atomic structure around the ferric heme-Fe (heme-Fe(III)) atom of HSA-heme-Fe (HSA-heme-Fe(III)) has been probed by Fe-K edge X-ray absorption spectroscopy (XAS). The quantitative analysis of the Fe-K edge extended X-ray absorption fine structure (EXAFS) signals and modeling of the near edge (XANES) spectral features demonstrated that warfarin and ibuprofen binding modify the local structure of the heme-Fe(III). Combined XAS data analysis and targeted molecular dynamics (MD) simulations provided atomic resolution insights of protein structural rearrangements required to accommodate the heme-Fe(III) upon ibuprofen and warfarin binding. In the absence of drugs, the heme-Fe(III) atom is penta-coordinated having distorted 4+1 configuration made by the nitrogen atoms of the porphyrin ring and the oxygen phenoxy atom of the Tyr161 residue. MD simulations show that ibuprofen and warfarin association to the secondary fatty acid (FA) binding site 2 (FA2) induces a reorientation of domain I of HSA-heme-Fe(III), this leads to the redirection of the His146 residue providing an additional bond to the heme-Fe(III) atom, providing the 5+1 configuration. The comparison of Fe-K edge XANES spectra calculated using MD structures with those obtained experimentally confirms the reliability of the proposed structural model. As a whole, combining XAS and MD simulations it has been possible to provide a reliable model of the heme-Fe(III) atom coordination state and to understand the complex allosteric transition occurring in HSA-heme-Fe(III) upon ibuprofen and warfarin binding.

XAS study of lead speciation in a central Italy calcareous soil.

PURPOSE: The Pb absorption processes on a heavy textured calcareous soil, typical of central Italy, were studied using synchrotron X-ray absorption spectroscopy (XAS) in order to probe, at molecular scale, the structure and chemical nature of Pb in contaminated soils and achieve precise description of Pb ions localization into these contaminated soils. MATERIALS AND METHODS: In order to distinguish the role of the different components of soils in Pb retention, samples were prepared from the original soils removing the carbonate fractions, the organic matter, the metal oxides, or selecting the clay fractions. Then these samples were fortified with Pb simulating the natural interactions processes of heavy metal solutions with soils. The quantitative analysis of near edge (XANES) as well extended (EXAFS) regions of Pb L(III) edge absorption spectra, in comparison with Pb XAS data of selected reference compounds, allowed the precise determination of local structure and chemical environment of Pb ions in these soil samples. RESULTS: Four components were individuated as the major responsible of Pb retention in calcareous soils: the carbonates, the metal oxide surfaces, the organic matter, and the colloidal inorganic surfaces containing clay components. The structural analysis suggests that, within these experimental conditions, the Pb adsorbed on the soil is generally present as Pb hydroxide with poor crystallization degree. However, the presence of carbonates (CaCO3) induces the co-precipitation of PbCO3-like phases with some degree of crystallinity.

High yield synthesis of pure alkanethiolate-capped silver nanoparticles.

One-phase, one-pot synthesis of Ag(0) nanoparticles capped with alkanethiolate molecules has been optimized to easily achieve a pure product in quantitative yield. We report the synthesis of dodecanethiolate-capped silver particles and the chemophysical, structural, and morphologic characterization performed by way of UV-vis, (1)H NMR, and X-ray photoelectron (XPS) spectroscopies, X-ray powder diffraction (XRD) and X-ray absorption fine structure analysis (XFAS), electron diffraction and high-resolution transmission electron microscopy (HR-TEM), and scanning and transmission electron microscopy (SEM and TEM). Depending on the molar ratio of the reagents (dodecylthiosulphate/Ag(+)), the mean Ag(0) particle size D(XRD) is tuned from 4 to 3 nm with a narrow size distribution. The particles are highly soluble, very stable in organic solvents (hexane, toluene, dichloromethane, etc.), and resistant to oxidation; the hexane solution after one year at room temperature does not show any precipitation or formation of oxidation byproducts.

Treatment of EXAFS data taken in the fluorescence mode in non-linear conditions.

The aim of this work is to investigate the possibility of extracting correct structural parameters from fluorescence EXAFS data taken at high count rates with an energy-resolving detector. This situation is often encountered on third-generation synchrotron radiation sources which provide a high flux on the sample. Errors caused by pulse pile-up in the extraction of structural information have been quantified in a real experiment, and different approaches to the problem of data correction have been elaborated. The different approaches are discussed in a comparison of the ability of each kind of correction to recover the correct structural parameters. The result of our analysis is that it is possible to work in non-linear conditions and correct the data, if the response of the acquisition system is known. Reliable structural information can be obtained with data acquired up to a count rate equal to approximately 60% of the inverse of the dead time.

The ReflEXAFS station at the GILDA beamline (BM08) of ESRF.

The experimental station for measuring X-ray absorption spectra in total reflection geometry operative at the GILDA CRG beamline of ESRF is described. The main features of the station are shown, namely: the possibility of detecting very small signals from thin (a few ML) samples, of depositing thin films under controlled conditions and thermal treating the samples in order to study dynamical processes. Case studies are reported in order to show the performances of the apparatus.

Rietveld refinement on x-ray diffraction patterns of bioapatite in human fetal bones.

Bioapatite, the main constituent of mineralized tissue in mammalian bones, is a calcium-phosphate-based mineral that is similar in structure and composition to hydroxyapatite. In this work, the crystallographic structure of bioapatite in human fetuses was investigated by synchrotron radiation x-ray diffraction (XRD) and microdiffraction ( micro -XRD) techniques. Rietveld refinement analyses of XRD and micro -XRD data allow for quantitative probing of the structural modifications of bioapatite as functions of the mineralization process and gestational age.