Experimental Extended X-ray Absorption Fine Structure Research Articles

Adsorption of U(VI) on Stoichiometric and Oxidised Mackinawite: a DFT Study.

Naturally occurring minerals, such as the iron sulfide mackinawite, play a key role in the remediation of uranium from groundwater systems. Here, density functional theory (DFT) is used to investigate the interaction of uranium with the most stable surface of stoichiometric mackinawite, {001}-S. The high reactivity of the mineral toward oxygen may affect its ability to sequester uranium; therefore, two models of oxidized mackinawite are also used to study the effect of surface oxidation on adsorption. Weak adsorption of mononuclear uranyl(VI) complexes is found on stoichiometric mackinawite; however, equivalent adsorption modes on the oxidized mackinawite models generally exhibit stronger adsorption. Some of the most energetically stable DFT structures are found to match well with experimental extended X-ray absorption fine structure (EXAFS) data. The implications for the proposed use of mackinawite as a scavenger material for uranium in groundwater systems are discussed.

Analysis of Anharmonic EXAFS Spectra of Crystalline Nickel Using High-order Debye-Waller Factors

The extended X-ray absorption fine structure (EXAFS) has been developed into a powerful technique and is widely applied to determine many structural parameters and dynamic properties of materials. The EXAFS technique is now the technique of choice in many materials science investigations, and the EXAFS data analysis is being performed in many laboratories spread around the world. In this work, the anharmonic EXAFS spectra of crystalline nickel (Ni) has been analyzed based on the quantum anharmonic correlated Einstein model. The anharmonic EXAFS oscillation presented in terms of the Debye-Waller factors using the cumulant expansion approach up to the fourth-order. This calculation model has been developed from the high-order anharmonic effective potential that described the contribution of their nearest-neighbor atoms to the pair interaction potential. The analytical expressions of the anharmonic EXAFS cumulants are not only explicit forms but also satisfy all of their fundamental properties in temperature dependence. The analysis of the anharmonic EXAFS spectra was performed by evaluating the contributions of the cumulants to the amplitude reduction and the phase shift of the anharmonic EXAFS oscillation. The numerical results for Ni were in good agreement with those obtained using the other theoretical methods and experiment at various temperatures, which are useful for analyzing the experimental EXAFS data of the metal crystals.

Bond Covalency and Oxidation State of Actinide Ions Complexed with Therapeutic Chelating Agent 3,4,3-LI(1,2-HOPO).

The hydroxypyridinone ligand 3,4,3-LI(1,2-HOPO) is a promising agent for biological decorporation of radionuclides, and allows spectroscopic detection of many lanthanide (Ln) and actinide (An) species via sensitized luminescence. Despite the manifest uses of this ligand, the structural and thermodynamic properties of its complexes across the An series remain understudied. Theoretical investigations of the binding of An(III) and An(IV) ions, from actinium to einsteinium, by the 3,4,3-LI(1,2-HOPO) ligand, as well as experimental extended X-ray absorption fine structure (EXAFS) studies on the trivalent americium, curium, and californium complexes were employed to address the resulting structures, thermodynamic parameters, redox properties, and corresponding electronic configurations. An(IV) ions were found to form much stronger complexes than An(III) ions, consistent with experimental measurements. Complexation of both An(III) and An(IV) ions generally becomes more favorable for heavier actinides, reflecting increased energy degeneracy driven covalency and concomitant orbital mixing between the 5f orbitals of the An ions and the π orbitals of the ligand. Notably, the ability of this ligand to either accept or donate electron density as needed from its pyridine rings is found to be key to its extraordinary stability across the actinide series.

Solution structures of chloroquine–ferriheme complexes modeled using MD simulation and investigated by EXAFS spectroscopy

The interaction of chloroquine (CQ) and the μ-oxo dimer of iron(III) protoporphyrin IX (ferriheme) in aqueous solution was modeled using molecular dynamics (MD) simulations. Two models of the CQ-(μ-oxo ferriheme) complex were investigated, one involving CQ π-stacked with an unligated porphyrin face of μ-oxo ferriheme and the other in which CQ was docked between the two porphyrin rings. The feasibility of both models was tested by fitting computed structures to the experimental extended X-ray absorption fine structure (EXAFS) spectrum of the CQ-(μ-oxo ferriheme) complex in frozen aqueous solution. The docked model produced better agreement with experimental data, suggesting that this is the more likely structure in aqueous solution. The EXAFS fit indicated a longer than expected Fe–O bond of 1.87Å, accounting for the higher than expected magnetic moment of the complex. As a consequence, the asymmetric Fe–O–Fe stretch shifts much lower in frequency and was identified in the precipitated solid at 744cm−1 with the aid of the O18 isomer shift. Three important CQ-ferriheme interactions were identified in the docked structure. These were a hydrogen bond between the oxide bridge of μ-oxo ferriheme and the protonated quinolinium nitrogen atom of CQ; π-stacking between the quinoline ring of CQ and the porphyrin rings; and a close contact between the 7-chloro substituent of CQ and the porphyrin methyl hydrogen atoms. These interactions can be used to rationalize previously observed structure–activity relationships for quinoline–ferriheme association.

ISOTOPIC EFFECT IN DEBYE–WALLER FACTOR OF CRYSTALLINE GERMANIUM

The statistical moment method has been used to study the effect of isotopic mass difference on extended X-ray absorption fine structure (EXAFS) Debye–Waller factor of crystalline germanium. The effects on the parallel mean-square relative displacement and the atomic mean square displacements have been considered. This research also exposed that isotopic effect is noticeable where the correlated atomic motion is concerned. Numerical calculations have been performed for two isotopes 70 Ge and 76 Ge in range of temperature from 0 K to 600 K. Our results are compared with available experimental EXAFS data [J. Purans et al., Phys. Rev. Lett.100 (2008) 055901] as well as with lattice dynamics calculations [A. Sanson, Solid State Sci.12 (2010) 1988] and the good agreements are found.

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.

Theoretical and experimental studies of the atomic structure of oxygen-rich amorphous silicon oxynitride films

In this work we used an empirical potential model in order to describe the bulk structure of the oxygen-rich Si-O-N amorphous system. From the atomic configuration obtained by Monte Carlo simulations, the local order structure and the pair correlation function are determined. The results show that the basic structure of the amorphous is well described by a random distribution of tetrahedra with a central Si atom bonded to nitrogen and oxygen atoms. The Fourier transform of the extended x-ray-absorption fine structure (EXAFS) signal obtained by ab initio multiple-scattering calculations, using the theoretical atomic structure as input, shows good agreement with the experimental EXAFS analysis performed at the silicon K edge.

Investigation of the structure of β-tantalum

The local structure of β-tantalum was investigated by comparing experimental extended X-ray absorption fine structure (EXAFS) measurements with calculated spectra of proposed models. Four possible structure candidates were examined: a β-Uranium based structure, a distorted A15 structure, a bcc-Ta based superlattice structure with N interstitials and a simple hcp structure. The local structural measurements were found to be consistent with the β-Uranium based model containing 30 atoms per unit cell and having the space group P4 2/mnm. The thermal effect analysis on X-ray diffraction and EXAFS spectra, which reveals that β-Ta is highly disordered, agrees with the low symmetry and anisotropic system of the β-U model.

Systematic deviations between theoretical and experimental EXAFS functions: Possible evidence of interstitial scattering outside the muffin-tin radius

Extended x-ray absorption fine structure (EXAFS) analysis utilizing theoretical standards generated by the FEFF6 and FEFF7 codes often suffers from small systematic deviations on the high-$r$ side of the first neighbor peak in the Fourier transform. Similar deviations may also occur for other codes that are based on nonself-consistent muffin-tin potentials. These deviations substantially decrease the goodness of fit, and in more complex crystal systems which have more than one peak in the first neighbor shell, may change the resulting fit parameters significantly. We have carefully investigated four simple systems: Ag, Au, Pb, and RbBr, each of which has only one bond length in the first neighbor shell. Fits using theoretical functions show deviations on the high-$r$ side of the peak; in k-space, the problem is associated with structure in the effective backscattering amplitude function $F(k),$ calculated by FEFF, particularly in the low-$k$ region below $8 {\AA{}}^{\ensuremath{-}1}.$ We compare the fits obtained using FEFF functions and experimentally determined EXAFS standards. The deviations on the high-$r$ side of the first peak are important for an accurate analysis of complex materials with several closely spaced neighbors or systems with distorted local environments, because such differences may be mistaken for additional or displaced neighbors. This is illustrated by fitting the first Ag-Ag shell for Ag metal to a sum of two peaks. A good fit can be achieved, but yields the unphysical result that a few long Ag-Ag bonds at 3.15 \AA{} exist. Models to date are based on the spherical muffin-tin approximation which ignore the nonsphericity of the true potential about each atom and treat the interstitial region as a constant potential outside the muffin-tin radii. To crudely include some anisotropy we have used H atoms at interstitial sites as a surrogate for scattering in the interstitial region and show that an additional peak occurs at exactly the region in r-space where the deviation between FEFF and experimental data is largest for Ag.

Analysis of extended X-ray absorption fine structure spectra using annealing evolutionary algorithms

An annealing evolutionary algorithm (AEA), which combines aspects of genetic algorithms and simulated annealing, is proposed to find the global minimum of a non-linear least square function for spectral fitting. By application of the algorithm to the fitting of structural parameters from experimental extended X-ray absorption fine structure (EXAFS) spectra of two Cu samples, it was found that reasonable results were obtained. Comparing with genetic algorithms and EXCURVE88, the AEA method is faster and more accurate in analysis of EXAFS spectra.

X-ray-absorption spectroscopy of Nd3+-exchanged beta -alumina crystal.

The results of x-ray-absorption spectroscopy investigations of ${\mathrm{Nd}}^{3+}$ ions in a nearly fully exchanged (93%) sodium \ensuremath{\beta}-alumina crystal are reported. The ${\mathrm{Nd}}^{3+}$ local environment is reconstructed using a multishell best fit procedure and is compared with existing structural models. The experimental extended x-ray-absorption fine-structure (EXAFS) spectra are also compared with model ab initio FEFF6 calculations based on the x-ray-diffraction data for the ${\mathrm{Nd}}^{3+}$ ions located at the BR(2d) and interstitial A(6h) sites of \ensuremath{\beta}-alumina. Neodymium ions are mainly found near the BR(2d) sites of the conduction plane, where they are strongly bonded to three O(5) oxygens located in the same plane and shifted by \ensuremath{\sim}0.6 \AA{} from the crystallographic positions occupied in sodium \ensuremath{\beta}-alumina. The atoms located at the spinel blocks below and above the conduction plane produce negligible contribution to the total Nd ${\mathit{L}}_{3}$ edge EXAFS signal due to the polarization effect and, mainly, to thermal and/or static disorder. The similarity of the local structure around the ${\mathrm{Nd}}^{3+}$ ions in the \ensuremath{\beta}- and ${\mathrm{\ensuremath{\beta}}}^{\mathrm{\ensuremath{''}}}$-alumina crystals is also discussed. \textcopyright{} 1996 The American Physical Society.

Dependence of Phase Shift on Chemical Environment in Extended X‐Ray Absorption Fine Structure

AbstractThe coefficient of the term linearly dependent on K, αj in the phase shift is calculated from the theoretical phase functions of Teo and Lee and from experimental extended X‐ray absorption fine structure (EXAFS) data for 3 d transition metal systems of manganese, cobalt, and copper. Attempts are made to explain the behaviour of the phase shift of a given atom pair in different chemical surroundings. The dependence of αj on chemical shift and partial charge is also studied.

Analysis of experimental extended x-ray-absorption fine-structure (EXAFS) data using calculated curved-wave, multiple-scattering EXAFS spectra.

We present an EXAFS analysis method that is accurate and generally applicable and can be implemented on a fast microcomputer within a reasonable amount of computation time. The analysis is based on the comparison between a calculated EXAFS spectrum of a parametrized model with the experimental spectrum and the refinement of the model parameters. The calculated EXAFS spectrum is evaluated taking into account the curved-wave nature of the photoelectron and multiple scattering up to and including third-order collinear scattering. Such an expansion treats accurately all multiple-scattering contributions that contribute to the Fourier transform of the EXAFS spectrum up to the fourth-neighbor distance. The comparison between theory and experiment is thus limited to this distance. In this calculation we schematically express the contributions of the various scattering configurations \ensuremath{\eta} in the form ${\mathrm{\ensuremath{\chi}}}_{0}^{\mathrm{\ensuremath{\eta}}}$=${\mathit{F}}_{\mathrm{\ensuremath{\eta}}}$(k)sin[${\mathit{kL}}_{\mathrm{\ensuremath{\eta}}}$+${\mathrm{\ensuremath{\Theta}}}_{\mathrm{\ensuremath{\eta}}}$(k)] and expand to lowest order the amplitude ${\mathit{F}}_{\mathrm{\ensuremath{\eta}}}$ and the phase ${\mathrm{\ensuremath{\Theta}}}_{\mathrm{\ensuremath{\eta}}}$ functions in terms of all structural and potential parameters. This expansion is quite accurate and significantly speeds up the computation. We discuss a set of parameters which seems to account for the limitations in the employed theory, providing a very good fit between theory and experiment. The analysis method and the parameters have been implemented successfully on a number of systems. We present here the analysis of the copper EXAFS spectrum. The experimental data contain 20 independent experimental points; yet we obtain a very good fit with only six parameters. The results also show the importance of both double and triple collinear scattering as well as the importance of noncollinear double scattering.