Showing papers on "Extended X-ray absorption fine structure published in 2008"
TL;DR: In this article, two 2p → 5d transitions were observed in the second derivative of the W L 3-edge X-ray absorption near-edge structure (XANES) spectra of all samples containing W (WO3, Na2WO4, Cr2WOWO6, Ba2NiWO6 and Ba2NOWO2), and these two transitions can be assigned to 5d orbitals split by the ligand field.
Abstract: We analyzed the X-ray absorption fine structure (XAFS) spectra of W L1- and L3-edges in order to determine the structure of various W species on TiO2. Two 2p → 5d transitions were observed in the second derivative of the W L3-edge X-ray absorption near-edge structure (XANES) spectra of all samples containing W (WO3, Na2WO4, Cr2WO6, Ba2NiWO6, (NH4)10W12O41·5H2O, Sc2W3O12, H3PW12O40·13H2O, and TiO2-loaded WO3 samples). These two transitions can be assigned to 5d orbitals split by the ligand field. The split in the 5d orbital has a linear relationship with the area of pre-edge peak of the W L1-edge XANES spectrum. This linear relationship is supported by density functional theory (DFT) calculations of the octahedral and tetrahedral W models. On the basis of this linear relationship, we estimated the structure of various W species on TiO2. The obtained structure is in accordance with the curve fitting analysis of W L3-edge extended X-ray absorption fine structure (EXAFS). Additionally, we found that the octah...
159 citations
TL;DR: Density functional theory (DFT) calculations indicated that alkylamine will strongly stabilize Pd to the surface, resulting in diffusion of Au atoms into the core region to form a non-random alloy, and this paper reports a synthesis of a Au/Pd alloy nanostructure through the galvanic replacement reaction.
Abstract: Bimetallic nanostructures with non-random metal atoms distribution are very important for various applications. To synthesize such structures via benign wet chemistry approach remains challenging. This paper reports a synthesis of a Au/Pd alloy nanostructure through the galvanic replacement reaction between Pd ultrathin nanowires (2.4 ± 0.2 nm in width, over 30 nm in length) and AuCl3 in toluene. Both morphological and structural changes were monitored during the reaction up to 10 h. Continuous changes of chemical composition and crystalline structure from Pd nanowires to Pd68Au32 and Pd45Au55 alloys, and to Au nanoparticles were observed. More interestingly, by using combined techniques such as high-resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), energy dispersive X-ray spectrometry (EDS), UV−vis absorption, and extended X−ray absorption fine structure (EXAFS) spectroscopy, we found the formation of Pd68Au32 non-random alloy with Au-rich core and Pd-rich shell, and random Pd...
150 citations
TL;DR: In this paper, advanced spectroscopic and microscopic methods were used to elucidate the Cu speciation in a calcareous soil contaminated since the 1940s, which indicated that most of the Cu was not associated with metal oxides, silicates, phosphates, or carbonates.
Abstract: Contamination of agricultural soils with Cu as a result of fungicide application and spills threatens environmental quality and reduces soil quality for crop growth. In this paper advanced spectroscopic and microscopic methods were used to elucidate the Cu speciation in a calcareous soil contaminated since the 1940s. Microscopically focused synchrotron-based XRF (μ-SXRF) was used to map the elemental distribution in the soils. Results indicated that most of the Cu was not associated with metal oxides, silicates, phosphates, or carbonates. Bulk and microscopically focused X-absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) spectra indicated that the Cu in the soil was predominantly Cu adsorbed on soil organic matter (SOM). Interpretation of the fitting results suggests that the Cu is complexed to SOM via bidentate inner-sphere coordination with carboxyl or amine ligands. Results presented in this paper provide detailed information on the molecular coordination of C...
147 citations
TL;DR: In this article, the structural evolution from structural disorder to order was monitored by X-ray diffraction and near-edge spectroscopy using high-level quantum mechanical calculations within the density functional theory framework.
134 citations
TL;DR: In this paper, in situ X-ray absorption near-edge structure (XANES) and extended Xray absorption fine structure (EXAFS) studies have been conducted to follow gold structural changes of low-content (<1%Au) gold-ceria catalysts in water-gas shift (WGS) reaction tests at 100 and 200 °C.
Abstract: Combined in situ X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) studies have been conducted to follow gold structural changes of low-content (<1%Au) gold-ceria catalysts in water-gas shift (WGS) reaction tests at 100 and 200 °C; and after heating the used catalysts in oxygen gas at 150 °C. Gold in the fresh (400 °C-calcined) material was atomically dispersed in cerium oxide. Under WGS reaction conditions, reduction of the oxidized gold species was observed, accompanied by gradual gold aggregation. The Au−Au coordination number is zero for the fresh material, but increases with the reaction temperature, to 6.5 ± 2.4 (after use at 100 °C) and to 8.7 ± 1.5 (after 200 °C) in a gas mixture containing 5% CO- 3% H2O in helium. The second important parameter is the reaction gas composition which determines the extent of Au−O reduction. The lower the reduction potential of the reaction gas mixture, the more oxidized the gold is in the used catalyst, and the higher...
132 citations
Journal Article•
TL;DR: In this paper, the structure of the Mn4Ca catalytic center has been studied using resonant inelastic X-ray scattering spectroscopy (RIXS), in addition to the earlier Xray absorption and emission spectrographic methods.
Abstract: Light-driven oxidation of water to dioxygen in plants, algae and cyanobacteria is catalyzed within photosystem II (PS II) by a Mn4Ca cluster. Although the cluster has been studied by many different methods, the structure and the mechanism have remained elusive. X-ray absorption and emission spectroscopy and EXAFS studies have been particularly useful in probing the electronic and geometric structure, and the mechanism of the water oxidation reaction. Recent progress, reviewed here, includes polarized X-ray absorption spectroscopy measurements of PS II single crystals. Analysis of those results has constrained the Mn4Ca cluster geometry to a set of three similar high-resolution structures. The structure of the cluster from the present study is unlike either the 3.0 or 3.5 Angstrom-resolution X-ray structures or other previously proposed models. The differences between the models derived from X-ray spectroscopy and crystallography are predominantly because of damage to the Mn4Ca cluster by X-rays under the conditions used for structure determination by X-ray crystallography. X-ray spectroscopy studies are also used for studying the changes in the structure of the Mn4Ca catalytic center as it cycles through the five intermediate states known as the Si-states (i=0-4). The electronic structure of the Mn4Ca cluster has been studied more recently using resonant inelastic X-ray scattering spectroscopy (RIXS), in addition to the earlier X-ray absorption and emission spectroscopy methods. These studies are revealing that the assignment of formal oxidation states is overly simplistic. A more accurate description should consider the charge density on the Mn atoms that includes the covalency of the bonds and delocalization of the charge over the cluster. The geometric and electronic structure of the Mn4Ca cluster in the S-states derived from X-ray spectroscopy are leading to a detailed understanding of the mechanism of the O-O bond formation during the photosynthetic water splitting process.
131 citations
TL;DR: In this article, a mesoporous V-SBA-15 catalysts were synthesized using a controlled grafting process, which showed structural properties similar to those of vanadium-incorporated MCM-41 catalyst.
124 citations
TL;DR: In this paper, the photocatalytic properties in correlation with the structural and optical peculiarities of the hydrothermal samples are discussed, in both UV and visible light regions.
94 citations
TL;DR: It was found that the nature of the sulfide mineral dictates the final speciation since respectively Se(0) and FeSe(x) were formed, meaning that the reaction mechanism is different and that these phases cannot be regarded as geochemically similar.
Abstract: The solid-phase Se speciation after short-term (3 weeks) contact of selenite [Se(IV)] oxyanions with pyrite (FeS2) and troilite (FeS) was investigated using X-ray absorption spectroscopy (XAS; X-ray absorption near-edge spectroscopy−extended X-ray absorption fine structure (XANES-EXAFS)). It was found that the nature of the sulfide mineral dictates the final speciation since respectively Se0 and FeSex were formed, meaning that the reaction mechanism is different and that these phases cannot be regarded as geochemically similar. The experimental results support the previously proposed sorption/reduction mechanism for the reaction of selenite with pyrite (8). In the presence of troilite the reduction proceeds through the intermediate formation of Se0 by reduction of selenite with dissolved sulfide. XAS data recorded for the FeS2 and FeS were compared with different Se reference phases, ranging in oxidation state from —II to +IV, used for validation of the XAS analysis methodology. This methodology can in pr...
87 citations
TL;DR: In this paper, the structure of TiO2-derived nanotubes with about 10 nm outer diameter and 5 nm inner diameter and a few hundred nanometers in length prepared by the hydrothermal process in an aqueous NaOH solution was investigated.
Abstract: The structure of TiO2-derived nanotubes with about 10 nm outer diameter and 5 nm inner diameter and a few hundred nanometers in length prepared by the hydrothermal process in an aqueous NaOH solution was investigated. Especially, the local structure of TiO2-derived nanotubes was analyzed in detail on short-range order by extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) measurements. It was found that TiO2-derived nanotubes were mainly composed of layered titanate and the anatase-like structure was partly present in the titanate-based nanotubes. The formation of the anatase-like structure was thought to be caused from the consolidation of nanotubes.
86 citations
TL;DR: The different distribution of iron and manganese cations in the octahedral and tetrahedral sites in pure jacobsite and in the aerogels can be ascribed to partial oxidation of Mn(2+) to Mn(3+) in pureJACobsite, confirmed by XANES analysis.
Abstract: Extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) techniques at both Fe and Mn K-edges were used to investigate the formation of MnFe2O4nanoparticles embedded in a silica aerogel matrix as a function of calcination temperature (at 450, 750 and 900 °C). Up to 450 °C, two separated highly-disordered phases of iron and manganese are present. With increasing the temperature (to 750 and 900 °C), the structure of aerogel nanoparticles becomes progressively similar to that of the spinel structure MnFe2O4 (jacobsite). Quantitative determination of cations distribution in the spinel structure shows that aerogels calcined at 750 and 900 °C have a degree of inversion i = 0.20. A pure jacobsite sample synthesised by co-precipitation and used as a reference compound shows a much higher degree of inversion (i = 0.70). The different distribution of iron and manganese cations in the octahedral and tetrahedral sites in pure jacobsite and in the aerogels can be ascribed to partial oxidation of Mn2+ to Mn3+ in pure jacobsite, confirmed by XANES analysis, probably due to the synthesis conditions.
TL;DR: In this article, the location, structure and protein environment of the Mn 4 Ca 2+ cluster which catalyses the light driven, water splitting reaction of photosystem II is investigated.
TL;DR: In this paper, a simple combustion method using urea−nitrate precursors was successfully prepared by a simple XRD pattern, and the samples were sintered at different temperatures, namely 600, 800, 1000, and 1100 °C.
Abstract: CuFe2O4−xNiO (x = 1, 5, 10, and 20 wt %) nanocomposites have been successfully prepared by a simple combustion method using urea−nitrate precursors. The samples were sintered at different temperatures, namely 600, 800, 1000, and 1100 °C, for 5 h to enhance the compound formation and phase purity, studied by means of XRD patterns. Then the 1100 °C sintered sample was further characterized for its structural (EXAFS, XANES, FT-IR, UV–vis), morphological (SEM, TEM, HRTEM, SAED), electrical (ac conductivity, dielectric constant, dielectric loss tangent), and magnetic (Mossbauer) properties. The EXAFS and XANES studies reveal the formation of NiFe2O4 and CuO, in addition to the existence of CuFe2O4 and NiO phases. A partial substitution of metal cations by nickel ions could also be evidenced. The stretching and bending vibration of the tetrahedral and octahedral complexes have been established from FT-IR spectra. The UV–vis spectra elucidate that the prepared materials are semiconductors and also show the quant...
TL;DR: A robust data analysis method suitable for chemical speciation and structure determination of reaction intermediates is presented and can be directly adapted to many time-resolved x-ray spectroscopy experiments where new rapid throughput data collection and analysis methods are needed.
Abstract: We present a robust data analysis method of time-resolved x-ray absorption spectroscopy experiments suitable for chemical speciation and structure determination of reaction intermediates. Chemical speciation is done by principal component analysis (PCA) of the time-resolved x-ray absorption near-edge structure data. Structural analysis of intermediate phases is done by theoretical modeling of their extended x-ray absorption fine-structure data isolated by PCA. The method is demonstrated using reduction and reoxidation of Cu-doped ceria catalysts where we detected reaction intermediates and measured fine details of the reaction kinetics. This approach can be directly adapted to many time-resolved x-ray spectroscopy experiments where new rapid throughput data collection and analysis methods are needed.
TL;DR: In this article, a series of nickel oxide intercalated layered niobates was used to improve the photocatalytic hydrogen production for water splitting under visible light irradiation.
TL;DR: In this paper, the local molecular structure of Cd sorbed to kaolinite was examined with X-ray absorption fine structure spectroscopy (XAFS) over a range of pH and initial Cd solution concentrations, ([Cd{sub aq}]{sub in}).
TL;DR: In this paper, the extended X-ray absorption fine structure (EXAFS) technique is used to study the local atomic structure around the solute atoms in a number of binary nickel alloys.
TL;DR: Extended X-ray absorption fine structure (EXAFS) spectroscopy measurements revealed that Co particles have poor crystallinity and are finely dispersed in the sample, which could lead to a high catalytic efficiency.
Abstract: A doping of 5 wt% CoCl2 considerably decreases the dehydrogenation temperature of a mixture of LiNH2 and LiBH4. More that 8 wt% of hydrogen can be released at ca. 155 °C. X-Ray absorption near edge structure (XANES) spectroscopy indicated the formation of metallic Co after ball milling CoCl2 with LiNH2 and LiBH4. Extended X-ray absorption fine structure (EXAFS) spectroscopy measurements revealed that Co particles have poor crystallinity and are finely dispersed in the sample, which could lead to a high catalytic efficiency.
TL;DR: The structure and speciation of the complexes formed between mercury(II) ions and glutathione (GSH) have been studied by means of extended X-ray absorption fine structure (EXAFS) and 199Hg NMR spectroscopy at ambient temperature and the effect of temperature was studied.
Abstract: The structure and speciation of the complexes formed between mercury(II) ions and glutathione (GSH = L-glutamyl-L-cysteinyl-glycine) have been studied for a series of alkaline aqueous solutions (
$$ C_{{{\text{Hg}}^{{2 + }}}}\,{\sim18\,{\rm{mmol}}\,{\rm{{dm^{-3}}}}}$$
and C
GSH = 40–200 mmol dm−3 at pH ∼10.5) by means of extended X-ray absorption fine structure (EXAFS) and 199Hg NMR spectroscopy at ambient temperature. The dominant complexes are [Hg(GS)2]4− and [Hg(GS)3]7−, with mean Hg–S bond distances of 2.32(1) and 2.42(2) A observed in digonal and trigonal Hg–S coordination, respectively. The proportions of the Hg2+–glutathione complexes were evaluated by fitting linear combinations of model EXAFS oscillations representing each species to the experimental EXAFS spectra. The [Hg(GS)4]10− complex, with four sulfur atoms coordinated at a mean Hg–S bond distance of 2.52(2) A, is present in minor amounts (<30%) in solutions containing a large excess of glutathione (C
GSH ≥ 160 mmol dm−3). Comparable alkaline mercury(II) cysteine (H2Cys) solutions were also investigated and a reduced tendency to form higher complexes was observed, because the deprotonated amino group of Cys2− allows the stable [Hg(S,N-Cys)2]2− chelate to form. The effect of temperature on the distribution of the Hg2+–glutathione complexes was studied by comparing the EXAFS spectra at ambient temperature and at 25 K of a series of glycerol/water (33/67, v/v) frozen glasses with $$ C_{{{\text{Hg}}^{{2 + }} }} \,{\sim7\,{\rm{mmol}}\,{\rm{{dm^{-3}}}}} $$
and C
GSH = 16–81 mmol dm−3. Complexes with high Hg–S coordination numbers, [Hg(GS)3]7− and [Hg(GS)4]10−, became strongly favored when just a moderate excess of glutathione (C
GSH ≥28 mmol dm−3) was used in the glassy samples, as expected for a stepwise exothermic bond formation. Addition of glycerol had no effect on the Hg(II)–glutathione speciation, as shown by the similarity of the EXAFS spectra obtained at room temperature for two parallel series of Hg(II)-glutathione solutions with $$ C_{{{\text{Hg}}^{{2 + }} }} \,{\sim7\,{\rm{mmol}}\,{\rm{{dm^{-3}}}}},$$
with and without 33% glycerol. Also, the 199Hg NMR chemical shifts of a series of ∼18 mmol dm−3 mercury(II) glutathione solutions with 33% glycerol were not significantly different from those of the corresponding series in aqueous solution.
Journal Article•
TL;DR: In situ X-ray absorption spectroscopy (XAS) using both EXAFS and the {Delta}{mu}-XANES analysis procedures, is utilized to examine Ru deposition onto Pt/C cathodes at millimolar concentration of Ru in a 1 M HClO{sub 4} electrolyte as mentioned in this paper.
Abstract: In situ X-ray absorption spectroscopy (XAS), using both EXAFS and the {Delta}{mu}-XANES analysis procedures, is utilized to examine Ru deposition onto Pt/C cathodes at millimolar concentration of Ru in a 1 M HClO{sub 4} electrolyte. Also, electron spin resonance (ESR) spectroscopy is utilized to examine the effects of Ru{sup 3+} ion exchanged Nafion membranes. The {Delta}{mu}-XANES analysis of the data allows a determination of the coverage of Ru with time (minutes to hours) and also to identify the binding site of the deposited Ru species (atop/bridged at low coverage and 3-fold at higher coverage) apparently onto the corners and edges initially and at higher coverage onto the faces of the cubooctahedral clusters when exposed to Ru{sup n+} at OCP. The deposition of Ru appears to be inhibited at potentials where adsorbates (such as H and O(H)) usually adsorb, and Coulomb enhanced at OCP when substantial O exists on the surface. The ESR analysis of Ru{sup 3+} in the Nafion membrane indicates significant detrimental changes to the membrane in the presence of Ru ions; a decrease in the water uptake and an increase in the microviscosity of the fluid regions were noticed. Together these data indicate the critical nature of keepingmore » the fuel cell under potential control and avoiding an uncontrolled shut down under direct methanol operating conditions.« less
TL;DR: In this paper, an investigation of Fe-doped TiO2 anatase nanoparticles (2.8 and 5.4 at.% Fe) where Fe substitutes Ti atoms without the presence of other phases is presented.
Abstract: We present an investigation of Fe-doped TiO2 anatase nanoparticles (2.8 and 5.4 at.% Fe) where Fe substitutes Ti atoms without the presence of other phases. In order to characterize these samples we used x-ray absorption experiments, 57Fe Mossbauer spectroscopy, ab initio calculations and magnetometry. Results from iron K-edge near-edge and extended x-ray absorption fine structure confirm that Fe3+ replaces Ti4+ in the TiO2 anatase structure increasing the metal-anion bond length. Mossbauer spectra recorded at room temperature show asymmetric Fe3+ broad doublets. These results agree with structural, hyperfine and magnetic properties calculated using density-functional theory, if oxygen vacancies are present in the iron–oxygen octahedra. Mossbauer and magnetic measurements indicate that samples are paramagnetic at room temperature. At low temperatures, two kind of magnetic species can be distinguished: (i) isolated paramagnetic Fe3+ ions and (ii) antiferromagnetically coupled Fe3+ ions. These results also show that substitutional Fe in nanosized anatase TiO2 does not induce ferromagnetic ordering.
TL;DR: In this paper, the first shell distance of Au nanoparticles was determined by x-ray absorption fine structure spectroscopy in the temperature range of $20 -300\phantom{\rule{0.3em}{0ex}}\text{to}
Abstract: The ${L}_{3}$ edge of Au nanoparticles, having sizes ranging from $2.4\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}5.0\phantom{\rule{0.3em}{0ex}}\mathrm{nm}$, have been investigated by x-ray absorption fine structure spectroscopy in the temperature range of $20--300\phantom{\rule{0.3em}{0ex}}\mathrm{K}$. Data were recorded at the European Synchrotron Radiation Facility with a very good signal to noise ratio. To achieve a very high accuracy in the determination of the first shell distance, a very careful data analysis was performed also taking into account the presence of asymmetry effects. In all samples, the temperature dependence of the first neighbor distance results is different from that of the macrocrystalline counterpart. In the largest size samples, a reduction of the thermal expansion was found, whereas in the smallest ones, the presence of a crossover from an initial thermal expansion to a thermal contraction was observed. Calculations based on a simple model show that localization effects that increase as the nanoparticle size decreases can explain the reported thermal effects.
01 Jun 2008-Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms
TL;DR: In this article, the effects of high energy fission products on high-burnup UO 2 nuclear fuel pellets were simulated by using Extended X-ray Absorption Fine Structure (EXAFS) measurement and Xray photoelectron spectroscopy (XPS) at synchrotron radiation facilities.
Abstract: In order to simulate the effects of high energy fission products on high-burnup UO 2 nuclear fuel pellets, CeO 2 thin films and bulk specimens were irradiated with 200 MeV Xe ions. Effects of the irradiation were studied by using Extended X-ray Absorption Fine Structure (EXAFS) measurement and X-ray photoelectron spectroscopy (XPS) at synchrotron radiation facilities. The EXAFS spectra for the irradiated thin films near the Ce K-edge show the formation of the oxygen deficiency around Ce ions. XPS Spectra show that the valence state of Ce atoms is changed from intrinsic Ce 4+ to Ce 3+ state by the irradiation. As such irradiation effects appear even for low fluence irradiation, the experimental result suggests that the oxygen deficiency and the change in Ce valence state are due to high-density electronic excitation induced by the 200 MeV Xe ions.
TL;DR: A comparative K- and L(3)-edge EXAFS data analysis of nonahydrated crystalline neodymium(III) trifluoromethanesulfonate demonstrates the clear advantages of K-edge analysis over conventionally performed studies at the L( 3)-absorption edge for structural investigations of lanthanoid and third-row transition metal compounds.
Abstract: This is the first systematic study exploring the potential of high-energy EXAFS as a structural tool for lanthanoids and third-row transition elements. The K-edge X-ray absorption spectra of the hydrated lanthanoid(III) ions both in aqueous solution and in solid trifluoromethanesulfonate salts have been studied. The K-edges of lanthanoids cover the energy range from 38 (La) to 65 keV (Lu), while the corresponding energy range for the L 3 -edges is 5.5 (La) to 9.2 keV (Lu). We show that the large widths of the corehole states do not appreciably reduce the potential structural information in the high-energy K-edge EXAFS data. Moreover, for lanthanoid compounds, more accurate structural parameters are obtained from analysis of K-edge than from L 3 -edge EXAFS data. The main reasons are the much wider k range available and the absence of double-electron transitions, especially for the lighter lanthanoids. A comparative K- and L 3 -edge EXAFS data analysis of nonahydrated crystalline neodymium(III) trifluoromethanesulfonate demonstrates the clear advantages of K-edge analysis over conventionally performed studies at the L 3 -absorption edge for structural investigations of lanthanoid and third-row transition metal compounds. The coordination chemistry of the hydrated lanthanoid-(III) ions in aqueous solution and solid trifluoromethanesulfonate salts, based on the results of both the K- and L 3 -edge EXAFS data, is thoroughly discussed in the next paper in this series (I. Persson, P. D'Angelo, S. De Panfilis, M. Sandstrom, L. Eriksson, Chem. Eur. J. 2008, 14, DOI: 10.1002/ chem.200701281).
TL;DR: The Fe-heme structure has been obtained by analyzing independently the Extended X-ray Absorption Fine Structure (EXAFS) region and the X-rays Near Edge Structure (XANES) region, and states the actual state-of-the-art of XANES analysis when used to extract heme-normal parameters in a solution spectrum dominated by he me-plane scattering.
Abstract: A full quantitative analysis of Fe K-edge X-ray absorption spectra has been performed for hemes in two porphynato complexes, that is, iron(III) tetraphenylporphyrin chloride (Fe(III)TPPCl) and iron(III) tetraphenylporphyrin bis(imidazole) (Fe(III)TPP(Imid)2), in two protein complexes whose X-ray structure is known at atomic resolution (1.0 A), that is, ferrous deoxy-myoglobin (Fe(II)Mb) and ferric aquo-myoglobin (Fe(III)MbH2O), and in ferric cyano-myoglobin (Fe(III)MbCN), whose X-ray structure is known at lower resolution (1.4 A). The analysis has been performed via the multiple scattering approach, starting from a muffin tin approximation of the molecular potential. The Fe-heme structure has been obtained by analyzing independently the Extended X-ray Absorption Fine Structure (EXAFS) region and the X-ray Absorption Near Edge Structure (XANES) region. The EXAFS structural results are in full agreement with the crystallographic values of the models, with an accuracy of +/- 0.02 A for Fe-ligand distances, and +/-6 degrees for angular parameters. All the XANES features above the theoretical zero energy (in the lower rising edge) are well accounted for by single-channel calculations, for both Fe(II) and Fe(III) hemes, and the Fe-N p distance is determined with the same accuracy as EXAFS. XANES evaluations of Fe-5th and Fe-6th ligand distances are determined with 0.04-0.07 A accuracy; a small discrepancy with EXAFS (0.01 to 0.05 A beyond the statistical error), is found for protein compounds. Concerns from statistical correlation among parameters and multiple minima in the parameter space are discussed. As expected, the XANES accuracy is slightly lower than what was found for polarized XANES on Fe(III)MbCN single crystal (0.03-0.04 A), and states the actual state-of-the-art of XANES analysis when used to extract heme-normal parameters in a solution spectrum dominated by heme-plane scattering.
TL;DR: The results are consistent with the conclusion that the interstitial light atom is already present at an early stage in FeMo-co biosynthesis prior to the incorporation of Mo and R-homocitrate.
Abstract: NifB-co, an Fe-S cluster produced by the enzyme NifB, is an intermediate on the biosynthetic pathway to the iron molybdenum cofactor (FeMo-co) of nitrogenase. We have used Fe K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy together with (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to probe the structure of NifB-co while bound to the NifX protein from Azotobacter vinelandii. The spectra have been interpreted in part by comparison with data for the completed FeMo-co attached to the NafY carrier protein: the NafY:FeMo-co complex. EXAFS analysis of the NifX:NifB-co complex yields an average Fe-S distance of 2.26 A and average Fe-Fe distances of 2.66 and 3.74 A. Search profile analyses reveal the presence of a single Fe-X (X = C, N, or O) interaction at 2.04 A, compared to a 2.00 A Fe-X interaction found in the NafY:FeMo-co EXAFS. This suggests that the interstitial light atom (X) proposed to be present in FeMo-co has already inserted at the NifB-co stage of biosynthesis. The NRVS exhibits strong bands from Fe-S stretching modes peaking around 270, 315, 385, and 408 cm(-1). Additional intensity at approximately 185-200 cm(-1) is interpreted as a set of cluster "breathing" modes similar to those seen for the FeMo-cofactor. The strength and location of these modes also suggest that the FeMo-co interstitial light atom seen in the crystal structure is already in place in NifB-co. Both the EXAFS and NRVS data for NifX:NifB-co are best simulated using a Fe 6S 9X trigonal prism structure analogous to the 6Fe core of FeMo-co, although a 7Fe structure made by capping one trigonal 3S terminus with Fe cannot be ruled out. The results are consistent with the conclusion that the interstitial light atom is already present at an early stage in FeMo-co biosynthesis prior to the incorporation of Mo and R-homocitrate.
TL;DR: The cytochrome P450 enzyme CYP119, its compound II derivative, and its nitrosyl complex were studied by iron K-edge x-ray absorption spectroscopy and showed shifts in edge and pre-edge energies consistent with increasing effective positive charge on iron.
Abstract: The cytochrome P450 enzyme CYP119, its compound II derivative, and its nitrosyl complex were studied by iron K-edge x-ray absorption spectroscopy. The compound II derivative was prepared by reaction of the resting enzyme with peroxynitrite and had a lifetime of ≈10 s at 23°C. The CYP119 nitrosyl complex was prepared by reaction of the enzyme with nitrogen monoxide gas or with a nitrosyl donor and was stable at 23°C for hours. Samples of CYP119 and its derivatives were studied by x-ray absorption spectroscopy at temperatures below 140 (K) at the Advanced Photon Source of Argonne National Laboratory. The x-ray absorption near-edge structure spectra displayed shifts in edge and pre-edge energies consistent with increasing effective positive charge on iron in the series native CYP119 < CYP119 nitrosyl complex < CYP119 compound II derivative. Extended x-ray absorption fine structure spectra were simulated with good fits for k = 12 Å−1 for native CYP119 and k = 13 Å−1 for both the nitrosyl complex and the compound II derivative. The important structural features for the compound II derivative were an iron-oxygen bond length of 1.82 Å and an iron-sulfur bond length of 2.24 Å, both of which indicate an iron-oxygen single bond in a ferryl-hydroxide, FeIVOH, moiety.
TL;DR: X-ray photoelectron spectroscopy measurements of kaolinite particles that had been exposed to HA suspensions showed that significant parts of theKaolinite surface are not covered by HA, and despite the presence of HA, U(VI) prefers to sorb directly onto Kaolinite and not to HA that is bound to the clay surface.
TL;DR: The theoretical and experimental studies showed that the indium s orbitals in AgGa(1-x)In(x)S(2) tailored the band gap energy, thereby modified the photocatalytic activity of the AgGa
Abstract: Indium was substituted at gallium site in chalcopyrite AgGaS2 structure by using a simple solid solution method. The spectroscopic analysis using extended x-ray absorption fine structure and x-ray photoelectron spectroscopy confirmed the indium substitution in AgGaS2 lattice. The band gap energy of AgGa1−xInxS2 (x=0–1) estimated from the onset of absorption edge was found to be reduced from 2.67eV (x=0) to 1.9eV (x=1) by indium substitution. The theoretical and experimental studies showed that the indium s orbitals in AgGa1−xInxS2 tailored the band gap energy, thereby modified the photocatalytic activity of the AgGa1−xInxS2.
TL;DR: Extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional theory (DFT) calculations are used to postulate a structure for this cofactor, which uses a stable Mn(IV)/Fe(III) cofactor to initiate nucleotide reduction by a free-radical mechanism.
Abstract: The class Ic ribonucleotide reductase from Chlamydia trachomatis ( Ct) uses a stable Mn(IV)/Fe(III) cofactor to initiate nucleotide reduction by a free-radical mechanism. Extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional theory (DFT) calculations are used to postulate a structure for this cofactor. Fe and Mn K-edge EXAFS data yield an intermetallic distance of approximately 2.92 A. The Mn data also suggest the presence of a short 1.74 A Mn-O bond. These metrics are compared to the results of DFT calculations on 12 cofactor models derived from the crystal structure of the inactive Fe 2(III/III) form of the protein. Models are differentiated by the protonation states of their bridging and terminal OH X ligands as well as the location of the Mn(IV) ion (site 1 or 2). The models that agree best with experimental observation feature a mu-1,3-carboxylate bridge (E120), terminal solvent (H 2O/OH) to site 1, one mu-O bridge, and one mu-OH bridge. The site-placement of the metal ions cannot be discerned from the available data.