Some applications of statistical tests in analysis of EXAFS and SEXAFS data

Revisiting the Extended X-ray Absorption Fine Structure Fitting Procedure through a Machine Learning-Based Approach

A novel approach for the analysis of extended X-ray absorption fine structure (EXAFS) spectra is developed exploiting an inverse machine learning-based algorithm. Through this approach, it is possible to explore and account for, in a precise way, the nonlinear geometry dependence of the photoelectron backscattering phases and amplitudes of single and multiple scattering paths. In addition, the determined parameters are directly related to the 3D atomic structure, without the need to use complex parametrization as in the classical fitting approach. The applicability of the approach, its potential and the advantages over the classical fit were demonstrated by fitting the EXAFS data of two molecular systems, namely, the KAu (CN)₂ and the [RuCl₂(CO)₃]₂ complexes.

Tracking the Influence of Thermal Expansion and Oxygen Vacancies on the Thermal Stability of Ni-Rich Layered Cathode Materials

The ever-growing demand for high-energy lithium-ion batteries in portable electronics and electric vehicles has triggered intensive research efforts over the past decade. An efficient strategy to boost the energy and power density of lithium-ion batteries is to increase the Ni content in the cathode materials. However, a higher Ni content in the cathode materials gives rise to safety issues. Herein, thermal expansion and oxygen vacancies are proposed as new critical factors that affect the thermal stability of charged Ni-rich cathode materials based on a systematic synchrotron-based X-ray study of Li0.33Ni0.5+ x Co0.2Mn0.3- x O2 (x = 0, 0.1, 0.2) cathode materials during a heating process. Charged cathode materials with higher Ni contents show larger thermal expansion, which accelerates transition metal migration to the Li layers. Oxygen vacancies are formed and accumulate mainly around Ni ions until the layered-to-spinel phase transition begins. The oxygen vacancies also facilitate transition metal migration to the Li layers. Thermal expansion and the presence of oxygen vacancies decrease the energy barrier for cation migration and facilitate the phase transitions in charged cathode materials during the heating process. These results provide valuable guidance for developing new cathode materials with improved safety characteristics.

The stability of Pd/TS-1 and Pd/silicalite-1 for catalytic oxidation of methane – understanding the role of titanium

The stability of Pd/TS-1 and Pd/silicalite-1 catalysts was assessed at 400 °C and an approximate relative humidity (RH) of 80% for catalytic combustion of fugitive methane emissions, aiming to understand the role of titanium in the stability of the catalysts.

Whole-nanoparticle atomistic modeling of the schwertmannite structure from total scattering data

Schwertmannite is a poorly crystalline nanometric iron sulfate oxyhydroxide. This mineral shows a structural variability under different environments. Because of that, the determination of its structure and, consequently, of its physical–chemical properties is quite challenging. This article presents a detailed structural investigation of the structure of schwertmannite conducted under different approaches: X-ray absorption spectroscopy, Rietveld refinement, and a combined reverse Monte Carlo and Debye function analysis of the whole nanoparticle structure. The schwertmannite model presented here is, to the auhors' knowledge, the most complete model so far reported.

Arsenate and Selenate Scavenging by Basaluminite: Insights into the Reactivity of Aluminum Phases in Acid Mine Drainage

Basaluminite precipitation may play an important role in the behavior of trace elements in water and sediments affected by acid mine drainage and acid sulfate soils. In this study, the affinity of basaluminite and schwertmannite for arsenate and selenate is compared, and the coordination geometries of these oxyanions in both structures are reported. Batch isotherm experiments were conducted to examine the sorption capacity of synthetic schwertmannite and basaluminite and the potential competitive effect of sulfate. In addition, synchrotron-based techniques such as differential pair distribution function (d-PDF) analysis and extended X-ray absorption fine structure (EXAFS) were used to determine the local structure of As(V) and Se(VI) complexes. The results show that oxyanion exchange with structural sulfate was the main mechanism for removal of selenate, whereas arsenate was removed by a combination of surface complexes and oxyanion exchange. The arsenate adsorption capacity of basaluminite was 2 times higher than that of schwertmannite and 3 times higher than that of selenate in both phases. The sulfate:arsenate and sulfate:selenate exchange ratios were 1:2 and 1:1, respectively. High sulfate concentrations in the solutions did not show a competitive effect on arsenate sorption capacity but had a strong impact on selenate uptake, suggesting some kind of specific interaction for arsenate. Both d-PDF and EXAFS results indicated that the bidentate binuclear inner sphere was the most probable type of ligand for arsenate on both phases and for selenate on schwertmannite, whereas selenate forms outer-sphere complexes in the aluminum octahedral interlayer of basaluminite. Overall, these results show a strong affinity of poorly crystalline aluminum phases such as basaluminite for As(V) and Se(VI) oxyanions, with adsorption capacities on the same order of magnitude as those of iron oxides. The results obtained in this study are relevant to the understanding of trace element behavior in environments affected by acid water, potentially opening new research lines focused on remediation by natural attenuation processes or engineered water treatment systems.

The nanoscale structure and unoccupied valence electronic states in FeSe1-xTex chalcogenides probed by X-ray absorption measurements

We have studied the nanoscale structure and unoccupied electronic states in FeSe1-xTex by a combined analysis of Se K, Te L1 and Fe K-edges X-ray absorption measurements. Extended X-ray absorption fine structure (EXAFS) results show that iron-chalcogen (Fe-Se and Fe-Te) distances in ternary FeSe1-xTex are similar to those measured for binary FeSe and FeTe. The local Fe-Se/Te distances determined by different absorption edges fit well in the characteristic Z-plot of random alloys, providing unambiguous support to the inhomogeneous nanoscale structure of the ternary FeSe1-xTex system. X-ray absorption near-edge structure (XANES) spectra reveal a gradual evolution of the unoccupied valence electronic states as a function of Te-substitution in FeSe1-xTex. The Fe 3d-Se 4p/Te 5p hybridization is found to decrease with Te-substitution, accompanied by an increase in unoccupied Se 4p states and a decrease in unoccupied Te 5p states. The results are discussed in the frame of local inhomogeneity in the FeSe1-xTex system driven by random alloying of Se/Te atoms.

Molybdenum site structure of MOSC family proteins

Mo K-edge X-ray absorption spectroscopy has been used to probe as-isolated structures of the MOSC family proteins pmARC-1 and HMCS-CT. The Mo K-edge near-edge spectrum of HMCS-CT is shifted ~2.5 eV to lower energy compared to the pmARC-1 spectrum, which indicates that as-isolated HMCS-CT is in a more reduced state than pmARC-1. Extended X-ray absorption fine structure analysis indicates significant structural differences between pmARC-1 and HMCS-CT, with the former being a dioxo site and the latter possessing only a single terminal oxo ligand. The number of terminal oxo donors is consistent with pmARC-1 being in the Mo(VI) oxidation state and HMCS-CT in the Mo(IV) state. These structures are in accord with oxygen-atom-transfer reactivity for pmARC-1 and persulfide bond cleavage chemistry for HMCS-CT.

Lead is not off center in PbTe: the importance of r-space phase information in extended x-ray absorption fine structure spectroscopy

PbTe is a well-known thermoelectric material. Recent x-ray total scattering studies suggest that Pb moves off center along 100 in PbTe, by ∼0.2  Å at 300 K, producing a split Pb-Te pair distribution. We present an extended x-ray absorption fine structure spectroscopy (EXAFS) study of PbTe (and Tl doped PbTe) to determine if Pb or Te is off center. EXAFS provides sensitive r- or k-space phase information which can differentiate between a split peak for the Pb-Te distribution (indicative of off-center Pb) and a thermally broadened peak. We find no evidence for a split peak for Pb-Te or Te-Pb. At 300 K, the vibration amplitude for Pb-Te (or Te-Pb) is large; this thermally induced disorder is indicative of weak bonds, and the large disorder is consistent with the low thermal conductivity at 300 K. We also find evidence of an anharmonic potential for the nearest Pb-Te bonds, consistent with the overall anharmonicity found for the phonon modes. This effect is modeled by a "skew" factor (C3) which significantly improves the fit of the Pb-Te and Te-Pb peaks for the high temperature EXAFS data; C3 becomes significant above approximately 150-200 K. The consequences of these results will be discussed.

Surface-mediated synthesis and spectroscopic characterization of tantalum clusters on silica

Tantalum clusters were synthesized on the surface of porous silica by treatment of adsorbed Ta(CH(2)Ph)(5) in H(2) at temperatures in the range of 523-723 K. The surface species were characterized by UV-vis, far-infrared, and extended X-ray absorption fine-structure (EXAFS) spectroscopies, each of which provided evidence of Ta-Ta bonds similar to those in well-characterized molecular tantalum clusters. The Ta-Ta distance determined by EXAFS spectroscopy was 2.93 A. The chemistry of the cluster synthesis is similar to that of syntheses of similar tantalum clusters in solution. The supported clusters formed at 523 K are characterized by an EXAFS first-shell Ta-Ta coordination number of nearly 2, indicative of tri-tantalum clusters, although it is expected that a mixture of clusters was present, and reduction in H(2) at higher temperatures led to larger tantalum clusters. This is the first example of the surface-mediated synthesis of an early transition metal cluster, and the supported clusters reported here are the first to have been characterized by all three of the spectroscopic methods mentioned above. The similarity of the surface synthesis to that in solution points to opportunities to extend this new class of material to other early transition metal clusters on various supports.

Dependence of Copper Species on the Nature of the Support for Dispersed CuO Catalysts

Copper catalysts prepared by chemisorption-hydrolysis technique over silica (Cu/Si) and silica-alumina (Cu/SiAl) supports were studied to understand the role of the support on the nature and surface properties of the copper species stabilized on their surfaces. The morphological and surface properties of the copper phases have been characterized by complementary techniques, such as HRTEM, EXAFS-XANES, EPR, XPS, and FTIR. For the FTIR investigation, molecular probes (CO and NO) were also adsorbed on the surfaces to test the reactivity of the copper species. Moreover, the catalytic performances of the two catalysts have been compared in the HC-SCR reaction (NO reduction by C(2)H(4)) performed in highly oxidant conditions. The superior activity and selectivity of the supported silica-alumina catalyst with respect to that supported on silica could be related with the different nature of the copper species stabilized on the two supports, as emerged from the results obtained from the spectroscopic investigations. Small and well-dispersed CuO particles were present on silica, whereas isolated copper ions predominated on silica-alumina, likely in regions rich in alumina that made some exchangeable sites available, as indicated by FTIR spectra of adsorbed CO. The less positive global charge of copper species on Cu/SiAl than in Cu/Si has been confirmed by EPR, XPS, and EXAFS-XANES analyses.

An EXAFS study of the formation of a nanoporous metal–organic framework: evidence for the retention of secondary building units during synthesis

EXAFS data measured from amorphous intermediates and crystallisation solutions provides the first evidence that trimeric iron oxide secondary building units remain intact during crystallisation of the metal-organic framework MIL-89 from starting materials to products.

X-ray Diffraction and EXAFS Studies of Hydroxo−Cu(II) Complexes Based on a Calix[6]arene-N3 Ligand: Evidence for a Mononuclear−Dinuclear Equilibrium Controlled by Supramolecular Features

The formation of hydroxo complexes based on a calix[6]trisimidazole ligand is described. Deprotonation of the mononuclear Cu(II)-aqua complex gives rise to a dinuclear bis(mu-hydroxo) complex that has been characterized by X-ray diffraction analysis. Spectroscopic studies (EPR and UV-vis), conducted in dichloromethane solutions in the presence of various coordinating cosolvents (DMF, EtOH, or RCN) or with acetamide, revealed the coexistence of a mononuclear hydroxo species. The latter could be trapped by acetic acid to provide an acetato-Cu(II) complex that presents close spectroscopic features. An EXAFS study first conducted on the hydroxo-Cu(II) complex led to an excellent fit for the dinuclear core. It then allowed for the characterization of the mononuclear acetato complex with an acetamide guest included in the calixarene cavity. Hence, this study illustrates the flexibility of calixarene-based ligands and the role of the second coordination sphere in the stabilization of acidic or basic Cu(II) complexes.

An X-ray Absorption Study of Two VOCl3-Modified Silicas: Evidence for Chloride−Silica Interactions

The structures of the sites formed in the gas-solid reactions of VOCl3 with the surfaces of a fumed silica (Aerosil) and a silica gel (Sylopol) were investigated by using X-ray absorption spectroscopy. XANES and EXAFS analysis at the vanadium K-edge reveal that the sites have a uniform first coordination sphere regardless of the origin or the extent of hydroxylation of the silica support (controlled by thermal treatment in vacuo at 100 and 500 degrees C). Analysis of the second coordination sphere was limited by the lack of structural uniformity. EXAFS curve-fitting confirmed that the sites are [triple bond]SiOVOCl2, but revealed an unexpected asymmetry in the V-Cl bond distances. The latter is suggested to be a manifestation of silicon-chloride interactions.

On the Competition for Available Zinc

Extended x-ray absorption fine structure (EXAFS) spectroscopy was combined with thermodynamic and kinetic approaches to investigate zinc binding to a zinc finger (C2H2) and a tetrathiolate (C4) peptide. Both peptides represent structural zinc sites of proteins and rapidly bind a single zinc ion with picomolar dissociation constants. In competition with EDTA the transfer of peptide-bound zinc ions proved to be 6 orders of magnitude faster than predicted for a dissociation-association mechanism thus requiring ligand exchange mechanisms via peptide-zinc-EDTA complexes. EXAFS spectra of C2H2 showed the expected Cys2His2-ligand geometry when fully loaded with zinc. For a 2-fold excess of peptide, however, the existence of zinc-bridged peptide-peptide complexes with dominating sulfur coordination could be clearly shown. Whereas zinc binding kinetics of C2H2 appeared as a simple second order process, the suggested mechanism for C4 comprises a zinc-bridged Zn-(C4)2 species as well as a Zn-C4 species with less than 4 metal-bound thiolates, which is supported by EXAFS results. A rapid equilibrium of bound and unbound states of individual ligands might explain the kinetic instability of zinc-peptide complexes, which enables fast ligand exchange during the encounter of occupied and unoccupied acceptor sites. Depending on relative concentrations and stabilities, this results in a rapid transfer of zinc ions in the virtual absence of free zinc ions, as seen for the zinc transfer to EDTA, or in the formation of zinc-bridged complexes, as seen for both peptides with excess of peptides over available zinc.

Exploiting the conformational flexibility of leghemoglobin: a framework for examination of heme protein axial ligation

We have exploited the intrinsic conformational flexibility of leghemoglobin to reengineer the heme active site architecture of the molecule by replacement of the mobile His61 residue with tyrosine (H61Y variant). The electronic absorption spectrum of the ferric derivative of H61Y is similar to that observed for the phenolate derivative of the recombinant wild-type protein (rLb), consistent with coordination of Tyr61 to (high-spin) iron. EXAFS data clearly indicate a 6-coordinate heme geometry and a Fe-O bond length of 185pm. MCD and EPR spectroscopies are consistent with this assignment and support ligation by an anionic (tyrosinate) group. The alteration in heme ligation leads to a 148mV decrease in the reduction potential for H61Y (-127+/-5mV) compared to rLb and destabilisation of the functional oxy-derivative. The results are discussed in terms of our wider understanding of other heme proteins with His-Tyr ligation.

Coordination geometries of metal ions in d- or l-captopril-inhibited metallo-beta-lactamases

d- and l-captopril are competitive inhibitors of metallo-beta-lactamases. For the enzymes from Bacillus cereus (BcII) and Aeromonas hydrophila (CphA), we found that the mononuclear enzymes are the favored targets for inhibition. By combining results from extended x-ray absorption fine structure, perturbed angular correlation of gamma-rays spectroscopy, and a study of metal ion binding, we derived that for Cd(II)1-BcII, the thiolate sulfur of d-captopril binds to the metal ion located at the site defined by three histidine ligand residues. This is also the case for the inhibited Co(II)1 and Co(II)2 enzymes as observed by UV-visible spectroscopy. Although the single metal ion in Cd(II)1-BcII is distributed between both available binding sites in both the uninhibited and the inhibited enzyme, Cd(II)1-CphA shows only one defined ligand geometry with the thiolate sulfur coordinating to the metal ion in the site composed of 1 Cys, 1 His, and 1 Asp. CphA shows a strong preference for d-captopril, which is also reflected in a very rigid structure of the complex as determined by perturbed angular correlation spectroscopy. For BcII and CphA, which are representatives of the metallo-beta-lactamase subclasses B1 and B2, we find two different inhibitor binding modes.

Metal ion binding and coordination geometry for wild type and mutants of metallo-beta -lactamase from Bacillus cereus 569/H/9 (BcII): a combined thermodynamic, kinetic, and spectroscopic approach

One high affinity (nm) and one low affinity (microM) macroscopic dissociation constant for the binding of metal ions were found for the wild-type metallo-beta-lactamase from Bacillus cereus as well as six single-site mutants in which all ligands in the two metal binding sites were altered. Surprisingly, the mutations did not cause a specific alteration of the affinity of metal ions for the sole modified binding site as determined by extended x-ray absorption fine structure (EXAFS) and perturbed angular correlation of gamma-rays spectroscopy, respectively. Also UV-visible absorption spectra for the mono-cobalt enzymes clearly contain contributions from both metal sites. The observations of the very similar microscopic dissociation constants of both binding sites in contrast to the significantly differing macroscopic dissociation constants inevitably led to the conclusion that binding to the two metal sites exhibits negative cooperativity. The slow association rates for forming the binuclear enzyme determined by stopped-flow fluorescence measurements suggested that fast metal exchange between the two sites for the mononuclear enzyme hinders the binding of a second metal ion. EXAFS spectroscopy of the mono- and di-zinc wild type enzymes and two di-zinc mutants provide a definition of the metal ion environments, which is compared with the available x-ray crystallographic data.

Synthesis, crystal structure, EXAFS, and magnetic properties of catena [mu-tris(1,2-bis(tetrazol-1-yl)propane-N1,N1')iron(II)] bis(perchlorate). First crystal structure of an iron(II) spin-crossover chain compound

[Fe(btzp)3](ClO4)2 (btzp = 1,2-bis(tetrazol-1-yl)propane) represents the first structurally characterized Fe(II) linear chain compound exhibiting thermal spin crossover. It shows a very gradual spin transition (T1/2 = 130 K) which has been followed by magnetic susceptibility measurements and 57Fe Mössbauer spectroscopy. The structure has been solved at 200 and 100 K by single-crystal X-ray analysis. It crystallizes in the trigonal space group P3c1 with Z = 2 Fe(II) units at both temperatures. The molecular structure consists of chains running along the c axis in which the Fe(II) ions are linked by three N4,N4' coordinating bis(tetrazole) ligands. The main difference between the two forms appears to be in the Fe-N bond lengths, which are 2.164(4) A at 200 K and 2.038(4) A at 100 K. The Fe-Fe separations are 7.422(1) A at 200 K and 7.273(1) A at 100 K. The EXAFS results are consistent with the crystal structure. In both spin states, the FeN6 octahedron is almost regular within the EXAFS resolution. The Fe-N distance is found as 2.16(2) A at 300 K and 2.00(2) A at 40 K. The absence of the "7 A peak" in the EXAFS spectra of [Fe(btzp)3](ClO4)2, in contrast with what has been observed for the [Fe(4-R-1,2,4-triazole)3]-(anion)2 chain compounds, confirms that this peak can be used as the signature of a metal alignment only when it involves a strongly enhanced multiple scattering M-M-M path, with M-M spacing less than 4 A. Irradiation with green light at 5 K has led to the population of the metastable high-spin state for the iron(II) ion. The nature of the spin-crossover behavior has been discussed on the basis of the structural features.

X-ray Absorption Spectroscopic Studies of the Copper(I) Complexes of Crown Ether Appended Bis{(2-pyridyl)ethyl}amines and Their Dioxygen Adducts

An X-ray absorption spectroscopic study of the Cu complexes of the bis{(2-pyridyl)ethyl}-appended monoaza crown ether 1, diaza crown ether 2, and diphenylglycoluril diaza basket 3 is reported. Following detailed analysis of the spectra of the crystallographically characterized model compound tetrapyridyl Cu(II) bis(nitrato pyridine) (4), the contributions of the ring atoms of the coordinating pyridine to the EXAFS were simulated using a multiple-scattering approach and the final parameters obtained by restrained refinement. Oxygenation of the Cu(I) complexes resulted in a large increase of the intensity of the major peak in the phase-corrected Fourier transform. This was interpreted as evidence for a &mgr;-eta(2):eta(2)-peroxo coordination mode of the oxygen between the copper ions, which had changed valence from Cu(I) to Cu(II) as judged from the edge position. This oxygen binding mode is reminiscent of that of hemocyanin, but the Cu-Cu distances are significantly shorter in the model than in the enzyme and vary with solvent. The EXAFS of the oxygenated complexes was simulated in a new approach in which, besides the parameters of the pyridine unit, those of an additional multiple scattering unit describing the geometry of the Cu-O(2)-Cu moiety were also refined.

EXAFS study of zinc coordination in bacitracin A

Bacitracin is a dodecapeptide antibiotic produced by Bacillus sp. The antibacterial activity depends upon the peptide binding a divalent metal. Hitherto, the exact coordination of the cation has not been established. In particular the role played by the sulphur and nitrogen atoms of the thiazoline ring of bacitracin A has not been clear. Here the coordination of Zn2+ by bacitracin A has been studied using extended X-ray absorption fine structure. The experimental data are consistent with a model in which zinc is coordinated by one oxygen and three nitrogen atoms with the sulphur atom of the thiazoline ring not being directly involved in the zinc coordination.