Extended X-ray Absorption Fine Structure Data Research Articles

Structural Features of the Extraordinary Low Glass Transition Temperature for Au65Cu18Si17 Bulk Metallic Glass

Au65Cu18Si17 bulk metallic glass (BMG) exhibits an extraordinary low glass transition temperature (<100°C) and a wide supercooled liquid region. In order to elucidate the structural features of the extraordinary low glass transition temperature and high glass forming ability of the Au65Cu18Si17 BMG, high-energy X-ray diffraction (HEXRD) and Extended X-ray Absorption Fine Structure (EXAFS) measurements were carried out using synchrotron radiation. A sharp first peak and oscillation of the structure factor S(Q) up to the high wave number Q can be attributed to the dominant weighting factor of the Au­Au correlation over others. A reverse Monte Carlo (RMC) simulation was applied simultaneously to the HEXRD and EXAFS data. The obtained RMC model shows a quite highly dense packed structure with large amount of icosahedral type clusters around Au atoms while small ones around Si atoms. The partial Cu­Cu pair distribution function gCu,Cu(r) shows a sharp peak at a short interatomic distance, i.e., 2.38 i. The Cu­Cu pairs with short interatomic distances and the large thermal fluctuation around Cu atoms are considered to be one of the structural characteristics of the low glass transition temperature of the Au65Cu18Si17 BMG.

Structural analysis of colloidal MnO x composites

We report on the detailed structure of MnOx nanoparticles (MnOxNP) which are either stabilized by cationic spherical polyelectrolyte brushes or by star-shaped cationic polyelectrolyte chains. In both cases, the polycation is composed of 2-(trimethylammonium)ethyl methacrylate chloride (TMAEMC). The analysis by transmission electron microscopy (TEM), cryogenic transmission electron microscopy (cryoTEM), and powder X-ray diffraction leads to the conclusion that the MnOx nanoparticles in aqueous dispersed state are composed of only a few or even single lamellae of c-disordered potassium birnessite (birnessite). Using star-shaped pTMAEMC homopolymer for the synthesis of composite particles, we obtain MnOxNP with an average diameter of about 5 nm. MnOxNP immobilized on cationic spherical polyelectrolyte brush have a length of about 20 nm and a width of 1.6 nm. Comparison of the extended X-ray absorption fine structure (EXAFS) spectra of the MnOx composites with reference spectra leads to the conclusion that all materials include c-disordered birnessite-type nanoparticles. A comparison of the energy shift of the Mn K-edge absorption peak of the X-ray absorption near-edge structure spectra of different manganese oxide reference materials with the different MnOxNP revealed an average oxidation state of about 3.5–3.7 for synthesized compounds. No distinct structural difference is found when comparing the dried samples to samples dispersed in water. A comparison of the EXAFS data of the birnessite nanoparticles with the crystal structure of macroscopic systems showed a compression along the c direction accompanied by a slight elongation within the ab plane of the layered material.

Dual-Copper Catalytic Site Formed in CuMFI Zeolite Makes Effective Activation of Ethane Possible Even at Room Temperature

The role of dual-cation sites in zeolites has received a renaissance in chemistry and industry directed toward fixation and activation of various gases; such sites may be expected to be more efficient than a single-cation site. We aimed to clarify the real active centers in the copper-ion-exchanged MFI-type zeolite (CuMFI) for ethane (C2H6). A peculiar feature was found in the appearance of the characteristic IR bands at 2644 and 2582 cm–1 when C2H6 was adsorbed on Cu+ formed in CuMFI. The existence of dual species composed of two Cu+ ions bridging C2H6 was clearly indicated by extended X-ray absorption fine structure (EXAFS) data. Density functional theory calculations gave clear evidence that the two IR bands are distinctly due to C2H6 adsorbed on the dual-Cu+ site and not on a single site; this agrees with the EXAFS data. These data lead us to conclude that the dual-Cu+ site in the CuMFI sample is indispensable for efficient activation of C2H6 through the simultaneous interaction of C2H6 with two Cu+ ions.

X-ray absorption spectroscopy of doped ZrO2 systems

ZrO2 samples with 11% Nd and La doping and with 7, 9, 11, and 13% Gd doping have been prepared by co-precipitation route followed by sintering at 700 °C and 1100 °C, for potential application as high conductivity electrolytes in solid oxide fuel cells. The samples have been characterized by x-ray diffraction with laboratory x-ray source of Cu Kα radiation and extended x-ray absorption fine structure (EXAFS) spectroscopy measurement at Zr K edge with synchrotron radiation. The XRD spectra have been analyzed to determine the structure of the samples and the EXAFS data have been analyzed to find out relevant local structure parameters of the Zr-O and Zr-Zr shells, viz., bond distances, co-ordinations, and disorder parameters. The effect of change in ionic radius as well as concentration of the dopants on the above parameters has been thoroughly studied. The experimental results, in some cases, have also been corroborated by first principle calculations of the energetics of the systems.

Is histidine dissociation a critical component of the NO/H-NOX signaling mechanism? Insights from X-ray absorption spectroscopy.

The H-NOX (Heme-Nitric oxide/OXygen binding) family of diatomic gas sensing hemoproteins has attracted great interest. Soluble guanylate cyclase (sGC), the well-characterized eukaryotic nitric oxide (NO) sensor is an H-NOX family member. When NO binds sGC at the ferrous histidine-ligated protoporphyrin-IX, the proximal histidine ligand dissociates, resulting in a 5-coordinate (5c) complex; formation of this 5c complex is viewed as necessary for activation of sGC. Characterization of other H-NOX family members has revealed that while most also bind NO in a 5c complex, some bind NO in a 6-coordinate (6c) complex or as a 5c/6c mixture. To gain insight into the heme pocket structural differences between 5c and 6c Fe(ii)-NO H-NOX complexes, we investigated the extended X-ray absorption fine structure (EXAFS) of the Fe(II)-unligated and Fe(II)-NO complexes of H-NOX domains from three species, Thermoanaerobacter tengcongensis, Shewanella woodyi, and Pseudoalteromonas atlantica. Although the Fe(II)-NO complex of TtH-NOX is formally 6c, we found the Fe-N(His) bond is substantially lengthened. Furthermore, although NO binds to SwH-NOX and PaH-NOX as a 5c complex, consistent with histidine dissociation, the EXAFS data do not exclude a very weakly associated histidine. Regardless of coordination number, upon NO-binding, the Fe-N(porphyrin) bond lengths in all three H-NOXs contract by ~0.07 Å. This study reveals that the overall heme structure of 5c and 6c Fe(II)-NO H-NOX complexes are substantially similar, suggesting that formal histidine dissociation may not be required to trigger NO/H-NOX signal transduction. The study has refined our understanding of the molecular mechanisms underlying NO/H-NOX signaling.

In Situ X-ray Absorption Spectroscopic Study of the Adsorption of Ni2+on Fe3O4Nanoparticles in Supercritical Aqueous Fluids

In situ X-ray absorption spectroscopy (XAS) measurements were made on Fe3O4 nanoparticles in supercritical aqueous fluids to study their reactivity with Ni2+ ions and to investigate the structural properties of the reacted nanoparticles. XAS spectra were measured from Ni2+ added to an aqueous solution containing Fe3O4 nanoparticles at temperatures up to 500 °C. The XANES and the EXAFS data indicate that reactivity of Fe3O4 nanoparticles with Ni2+ ions is negligible to 300 °C but becomes significant in the 400–500 °C temperature range. Analysis of Ni K-edge extended X-ray absorption fine structure (EXAFS) using an atomic cluster model based on the spinel structure shows that Ni2+ adsorbs predominantly on octahedral sites of the surface of nanoparticles in aqueous fluids at 400–500 °C. The EXAFS structural results are consistent with diffusion of Ni into the near-surface region of the Fe3O4 nanoparticles in the aqueous fluid at 400 and 500 °C.

EXAFS study of binuclear hydroxo-bridged copper(II) complexes

Extended X-ray absorption fine structure (EXAFS) measurements have been recorded at the K-edge of copper in binuclear monohydroxo-bridged copper(II) complexes [(bpy)2Cu–OH–Cu(bpy)2](ClO4)3 (1) and [(phen)2Cu–OH–Cu(phen)2](C1O4)3 (2) and dihydroxo-bridged copper(II) complexes [Cu2(μ–OH)2(bipy)2]SO4 · 5H2O (3) and [Cu2(μ–OH)2(phen)2]SO4 · 5H2O (4) (where bpy and phen are 2,2′-bipyridine and 1,10-phenanthroline, respectively) using the dispersive EXAFS beamline at 2 GeV Indus-2 synchrotron source at RRCAT, Indore, India. The EXAFS data have been analyzed using the software, Athena and Artemis. Theoretical models have been generated for 1 and 3 using available crystallographic data and then fitted to their experimental EXAFS data to obtain the structural parameters, which include bond-lengths, coordination numbers, and thermal disorders. The results obtained have been found to be comparable with their crystallographic results. As the crystallographic data for 2 and 4 are not available in the literature, we have determined their structural parameters by fitting their experimental EXAFS data with the same theoretical models which were generated for their corresponding analogous complexes 1 and 3, respectively. The structural parameters thus determined have been reported. Also, on the basis of the analysis of the EXAFS data, these four complexes have been shown to be binuclear, i.e. they contain two metals. Further, the values of the chemical shifts suggest that copper is in +2 oxidation state in these complexes.

Extended X-ray absorption fine structure studies of magnetic nanoparticles

We have synthesized nickel by means of pulsed laser ablation. A nickel disc was used for ablation with the focused output of fundamental harmonic from Nd:YAG laser. X-ray diffraction result shows that the synthesized nanoparticles are of pure metallic nickel with a face-centred cubic structure and the average particle size is 35 nm. The extended X-ray absorption fine structure (EXAFS) studies of pure nickel foil and the synthesized nanoparticles show similar structures. The position of the main peak is same in these nanoparticles with reference to the nickel foil. The only difference was observed in the reduction of the amplitude. The nearest-neighbour distance is similar as for pure nickel foil. The Debye–Waller factor is also similar. There is no trace of oxide and hydroxide in the EXAFS data, suggesting that the synthesized nanoparticles contain only nickel metal.

Coordination Chemistry Study of Hydrated and Solvated Lead(II) Ions in Solution and Solid State

The coordination chemistry of lead(II) in the oxygen donor solvents water, dimethylsulfoxide (dmso, Me(2)SO), N,N-dimethylformamide (dmf), N,N-dimethylacetamide (dma), N,N'-dimethylpropyleneurea (dmpu), and 1,1,3,3-tetramethylurea (tmu), as well as in the sulfur donor solvent N,N-dimethylthioformamide (dmtf), has been investigated by extended X-ray absorption fine structure (EXAFS) and/or large angle X-ray scattering (LAXS) in solution, and by single crystal X-ray diffraction and/or EXAFS of solid hydrates and solvates. Lead(II) may either form hemidirected complexes with large bond distance distribution and an apparent gap for excess electron density, or holodirected ones with a symmetric coordination sphere with normal bond distance distribution, depending on the strength of antibonding lead 6s/ligand np molecular orbital interactions and ligand-ligand interactions. The crystallographic data show that the solid lead(II) perchlorate and trifluoromethanesulfonate hydrate structures are hemidirected, while the solid lead(II) solvates of dma and dmpu have regular octahedral configuration with holodirected geometry and mean Pb-O bond distances in the range 2.50-2.52 Å. EXAFS data on the hydrated lead(II) ion in aqueous solution show broad bond distance distribution and a lack of inner-core multiple scattering contributions strongly indicating a hemidirected structure. The Pb-O bond distances found both by EXAFS and LAXS, 2.54(1) Å, point to a six-coordinate hydrated lead(II) ion in hemidirected fashion with an unevenly distributed electron density. The results obtained for the dmso solvated lead(II) ion in solution are ambiguous, but for the most part support a six-coordinate hemidirected complex. The mean Pb-O bond distances determined in dmf and dma solution by LAXS, 2.55(1) and 2.48(1) Å, respectively, indicate that in both solvate complexes lead(II) binds six solvent molecules with the former complex being hemidirected whereas the latter is holodirected. The dmpu and tmu solvated lead(II) ions have a regular holodirected octahedral configuration, as expected given their space-demanding characteristics and ligand-ligand intermolecular interactions. The dmtf solvated lead(II) ion in solution is most likely five-coordinate in a hemidirected configuration, with a mean Pb-S bond distance of 2.908(4) Å. New and improved ionic radii for the lead(II) ion in 4-8-coordination in hemi and holodirected configurations are proposed using crystallographic data.

Reverse Monte Carlo simulations of an amorphous Se 0.90S 0.10 alloy produced by mechanical alloying combining XRD and EXAFS data

The local atomic order of an amorphous Se 0.90S 0.10 alloy produced by Mechanical Alloying was studied by reverse Monte Carlo simulations combining X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) data obtained on Se K edge. From the simulations structural properties such as average interatomic distances and average coordination numbers were determined and compared with the values extracted using only XRD data in the simulations. In addition, the bond-angle distribution functions Θ ijℓ (cos θ) were obtained, and they indicate the existence of Se n clusters in the alloy and also the substitution of Se atoms by S atoms in some of these clusters.

Reverse Monte Carlo refinements of local displacive order in perovskites:AgNbO3 case study

Reverse Monte Carlo refinements with combined input from neutron/x-raytotal scattering and extended x-ray absorption fine structure (EXAFS)were applied to analyze local atomic displacements in perovskite-relatedAgNbO3. Thiscompound exhibits complex displacive order–disorder behavior that determines the unique dielectric propertiesof AgNbO3-based ceramics. Our results revealed that the total scattering and EXAFSdata collected from polycrystalline samples were insufficient to reproducethe correlated local Nb displacements which are evident from the diffusescattering observed in electron diffraction. A credible representation of theAgNbO3 structure was obtained by enforcing these correlations via restraints on the atomicmoves, thus ensuring that the refined atomic ensemble not only satisfied the totalscattering and EXAFS data (a total of five datasets) but also reproducedthe shape of the observed electron diffuse scattering. Such constrained RMCrefinements revealed two-site positional disorder for each of the two non-equivalentAg crystallographic positions. The refinements confirmed that all Ag cations inAgNbO3 exhibit similar local Ag–O coordination environments as opposed to the two distinct Agcoordinations in the average Pbcm structure. These results support the existence of Agorder–disorder behavior similar to that observed for Nb.

X-ray Absorption Spectroscopy and Reactivity of Thiolate-Ligated FeIII−OOR Complexes

The reaction of a series of thiolate-ligated iron(II) complexes [Fe(II)([15]aneN(4))(SC(6)H(5))]BF(4) (1), [Fe(II)([15]aneN(4))(SC(6)H(4)-p-Cl)]BF(4) (2), and [Fe(II)([15]aneN(4))(SC(6)H(4)-p-NO(2))]BF(4) (3) with alkylhydroperoxides at low temperature (-78 °C or -40 °C) leads to the metastable alkylperoxo-iron(III) species [Fe(III)([15]aneN(4))(SC(6)H(5))(OOtBu)]BF(4) (1a), [Fe(III)([15]aneN(4))(SC(6)H(4)-p-Cl)(OOtBu)]BF(4) (2a), and [Fe(III)([15]aneN(4))(SC(6)H(4)-p-NO(2))(OOtBu)]BF(4) (3a), respectively. X-ray absorption spectroscopy (XAS) studies were conducted on the Fe(III)-OOR complexes and their iron(II) precursors. The edge energy for the iron(II) complexes (∼7118 eV) shifts to higher energy upon oxidation by ROOH, and the resulting edge energies for the Fe(III)-OOR species range from 7121-7125 eV and correlate with the nature of the thiolate donor. Extended X-ray absorption fine structure (EXAFS) analysis of the iron(II) complexes 1-3 in CH(2)Cl(2) show that their solid state structures remain intact in solution. The EXAFS data on 1a-3a confirm their proposed structures as mononuclear, 6-coordinate Fe(III)-OOR complexes with 4N and 1S donors completing the coordination sphere. The Fe-O bond distances obtained from EXAFS for 1a-3a are 1.82-1.85 Å, significantly longer than other low-spin Fe(III)-OOR complexes. The Fe-O distances correlate with the nature of the thiolate donor, in agreement with the previous trends observed for ν(Fe-O) from resonance Raman (RR) spectroscopy, and supported by optimized geometries obtained from density functional theory (DFT) calculations. Reactivity and kinetic studies on 1a- 3a show an important influence of the thiolate donor.

ChemInform Abstract: EXAFS Studies of Aqueous Solutions of Rubidium Bromide

We report the results of extended X-ray absorption fine structure (EXAFS) measurements performed on aqueous solutions of rubidium bromide (RbBr) at room temperature. The measurements were made at the Br and Rb K-edges. Average Rb+–OH2, Br− – OH2 and Rb–Br distances were determined from the quantitative analysis of the EXAFS data.

The ionic conductivity and local environment of cations in Bi 9ReO 17

The influence of temperature on the structure of Bi 9ReO 17 has been investigated using differential thermal analysis, variable temperature X-ray diffraction and neutron powder diffraction. The material undergoes an order–disorder transition at ∼1000 K on heating, to form a fluorite-related phase. The local environments of the cations in fully ordered Bi 9ReO 17 have been investigated by Bi L III- and Re L III-edge extended X-ray absorption fine structure (EXAFS) measurements to complement the neutron powder diffraction information. Whereas rhenium displays regular tetrahedral coordination, all bismuth sites show coordination geometries which reflect the importance of a stereochemically active lone pair of electrons. Because of the wide range of Bi–O distances, EXAFS data are similar to those observed for disordered structures, and are dominated by the shorter Bi–O bonds. Ionic conductivity measurements indicate that ordered Bi 9ReO 17 exhibits reasonably high oxide ion conductivity, corresponding to 2.9×10 −5 Ω −1 cm -1 at 673 K, whereas the disordered form shows higher oxide ion conductivity (9.1×10 −4 Ω −1 cm −1 at 673 K).

ChemInform Abstract: Evidence of Bilayer Structure in V2O5 Xerogel.

Polarized X-ray absorption spectroscopy has been used to study the short-range structure of deposited films of V2O5 xerogel. The material is characterized by a layer of VO5 units with the V−O apical bond perpendicular to the basal (xy) plane. We have focused our attention along the z axis. Experiments were carried out by extended X-ray absorption fine structure (EXAFS) spectroscopy in a grazing incidence geometry and showed evidence for close interactions between neighboring layers of V2O5. The structure is described by two sheets of V2O5 facing each other. Fitting of the EXAFS data has confirmed the existence of a vanadium−vanadium interaction between two different V2O5 layers and an oxygen bridge between them.

U(VI) Reduction to Mononuclear U(IV) by Desulfitobacterium Species

The bioreduction of U(VI) to U(IV) affects uranium mobility and fate in contaminated subsurface environments and is best understood in Gram-negative model organisms such as Geobacter and Shewanella spp. This study demonstrates that U(VI) reduction is a common trait of Gram-positive Desulfitobacterium spp. Five different Desulfitobacterium isolates reduced 100 microM U(VI) to U(IV) in <10 days, whereas U(VI) remained soluble in abiotic and heat-killed controls. U(VI) reduction in live cultures was confirmed using X-ray absorption near-edge structure (XANES) analysis. Interestingly, although bioreduction of U(VI) is almost always reported to yield the uraninite mineral (UO(2)), extended X-ray absorption fine structure (EXAFS) analysis demonstrated that the U(IV) produced in the Desulfitobacterium cultures was not UO(2). The EXAFS data indicated that the U(IV) product was a phase or mineral composed of mononuclear U(IV) atoms closely surrounded by light element shells. This atomic arrangement likely results from inner-sphere bonds between U(IV) and C/N/O- or P/S-containing ligands, such as carbonate or phosphate. The formation of a distinct U(IV) phase warrants further study because the characteristics of the reduced material affect uranium stability and fate in the contaminated subsurface.

Nanoscale disorder and local electronic properties ofCaCu3Ti4O12: An integrated study of electron, neutron, and x-ray diffraction, x-ray absorption fine structure, and first-principles calculations

We report a combined experimental and theoretical study of ${\text{CaCu}}_{3}{\text{Ti}}_{4}{\text{O}}_{12}$. Based on our experimental observations of nanoscale regions of Ca-Cu antisite defects in part of the structure, we carried out density-functional theory (DFT) calculations that suggest a possible electronic mechanism to explain the gigantic dielectric response in this material. The defects are evident in atomically resolved transmission electron microscopy measurements, with supporting evidence from a quantitative analysis of the electron diffraction and DFT which suggests that such defects are reasonable on energetic grounds. To establish the extent of the defects, bulk average measurements of the local structure were carried out: extended x-ray absorption fine structure (EXAFS), atomic pair-distribution function analysis of neutron powder-diffraction data, and single-crystal x-ray crystallography. The EXAFS data are consistent with the presence of the nanoclustered defects with an estimate of less than 10% of the sample being disordered while the neutron powder-diffraction experiments place an upper of $\ensuremath{\sim}5\mathrm{%}$ on the proportion of the sample in the defective state. Because of the difficulty of quantifying nanoscale defects at such low levels, further work will be required to establish that this mechanism is operative in ${\text{CaCu}}_{3}{\text{Ti}}_{4}{\text{O}}_{12}$ but it presents a nontraditional plausible avenue for understanding colossal dielectric behavior.

Local atomic structure in tetragonal pure ZrO2nanopowders

The local atomic structures around the Zr atom of pure (undoped) ZrO2nanopowders with different average crystallite sizes, ranging from 7 to 40 nm, have been investigated. The nanopowders were synthesized by different wet-chemical routes, but all exhibit the high-temperature tetragonal phase stabilized at room temperature, as established by synchrotron radiation X-ray diffraction. The extended X-ray absorption fine structure (EXAFS) technique was applied to analyze the local structure around the Zr atoms. Several authors have studied this system using the EXAFS technique without obtaining a good agreement between crystallographic and EXAFS data. In this work, it is shown that the local structure of ZrO2nanopowders can be described by a model consisting of two oxygen subshells (4 + 4 atoms) with different Zr—O distances, in agreement with those independently determined by X-ray diffraction. However, the EXAFS study shows that the second oxygen subshell exhibits a Debye–Waller (DW) parameter much higher than that of the first oxygen subshell, a result that cannot be explained by the crystallographic model accepted for the tetragonal phase of zirconia-based materials. However, as proposed by other authors, the difference in the DW parameters between the two oxygen subshells around the Zr atoms can be explained by the existence of oxygen displacements perpendicular to thezdirection; these mainly affect the second oxygen subshell because of the directional character of the EXAFS DW parameter, in contradiction to the crystallographic value. It is also established that this model is similar to another model having three oxygen subshells, with a 4 + 2 + 2 distribution of atoms, with only one DW parameter for all oxygen subshells. Both models are in good agreement with the crystal structure determined by X-ray diffraction experiments.

NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P.

Functionally critical metals interact with RNA through complex coordination schemes that are currently difficult to visualize at the atomic level under solution conditions. Here, we report a new approach that combines NMR and XAS to resolve and characterize metal binding in the most highly conserved P4 helix of ribonuclease P (RNase P), the ribonucleoprotein that catalyzes the divalent metal ion-dependent maturation of the 5' end of precursor tRNA. Extended X-ray absorption fine structure (EXAFS) spectroscopy reveals that the Zn(2+) bound to a P4 helix mimic is six-coordinate, with an average Zn-O/N bond distance of 2.08 A. The EXAFS data also show intense outer-shell scattering indicating that the zinc ion has inner-shell interactions with one or more RNA ligands. NMR Mn(2+) paramagnetic line broadening experiments reveal strong metal localization at residues corresponding to G378 and G379 in B. subtilis RNase P. A new "metal cocktail" chemical shift perturbation strategy involving titrations with , Zn(2+), and confirm an inner-sphere metal interaction with residues G378 and G379. These studies present a unique picture of how metals coordinate to the putative RNase P active site in solution, and shed light on the environment of an essential metal ion in RNase P. Our experimental approach presents a general method for identifying and characterizing inner-sphere metal ion binding sites in RNA in solution.

Local dynamical properties of crystalline germanium and their effects in extended x-ray absorption fine structure

The local dynamics of crystalline germanium has been investigated by molecular-dynamics simulations. The radial distribution functions of the first six coordination shells, as well as their parallel and perpendicular mean-square relative displacements, have been determined as a function of temperature. The agreement with the available extended x-ray absorption fine-structure data is very good. Original insights on the outer shells have been achieved. In particular, differently from the first shell, the bond thermal expansion of the outer shells is mainly due to the shift of the maximum of the distance distribution while the contribution of the distribution asymmetry is smaller than 15%.