FEFF Calculations Research Articles

Local Structure studies of Schiff base dependent Cadmium complex

Cadmium complex with Schiff-base ligand has been receiving significant interest due to its wide variety of biological activities, such as antitumor, antibacterial, antifungal, antiviral etc properties. The present paper deals with the Synthesis of Cadmium complex prepared by Schiff base ligand in the 2:1 (ligand: metal) equimolar ratio. The ligand was derived from 2-Aminopropanoic acid. The synthesized complex was used to characterize by X-ray absorption fine structure spectroscopy at cadmium K-edge. The studies revealed its octahedral coordination geometry with + 2 oxidation state of cadmium in the complex. The processed data of the complex was used to fit with the theoretical model generated from standard crystallographic data using FEFF calculations.

Onion-like Carbon (OLC), Iron, Cobalt and Nitrogen X-Ray Absorption Spectroscopy (XAS) Data Analysis

This project was about analyzing the data of the X-Ray Absorption Spectroscopy (XAS) of several synthesis of modified Onion-like Carbon (OLC) nanoparticles with nitrogen conductive polymers to study different catalysts for the Oxygen Reduction Reaction (ORR). Also, observing differences in the oxidation state, geometry, iron and cobalt bonds, and structures between the samples at different potentials were some of the objectives in this investigation. The PyMca program was used to normalized the samples and transferred the scan’s data. In Athena for the X-Ray Absorption Near Edge Structure (XANES) region, the scans were merged for every sample individually by adjusting the pre-edge, post-edge, spline range in “k”, and the normalization order parameters. Subsequently, Artemis for the Extended X-Ray Absorption Fine Structure (EXAFS) region was used to fit the first and second shell of the samples used in Athena. Here we used a FEFF calculations file from a Cobalt Oxide and Iron Oxide compounds that have similar elements to the ones in our samples. As results, we have been able to fit the N-OLC/FeCo (1:3)-Co and N-OLC/FeCo(1:3)-Fe. In both cases the fits from the first shell were from Co-O and Fe-O bonding interactions and the fits from the second shell were from Co-Co and Fe-Fe bonding interactions between the atoms.

In Situ Determination of Speciation and Local Structure of NaCl-SrCl2 and LiF-ZrF4 Molten Salts.

Understanding the local environment of the metal atoms in salt melts is important for modeling the properties of melts and predicting their behavior and thus helping enable the development of technologies such as molten salt reactors and solar-thermal power systems and new approaches to recycling rare-earth metals. Toward that end, we have developed an in situ approach for measuring the coordination of metals in molten salt coupling X-ray absorption spectroscopy (XAS) and Raman spectroscopy. Our approach was demonstrated for two salt mixtures (1.9 and 5 mol % SrCl2 in NaCl, 0.8 and 5 mol % ZrF4 in LiF) at up to 1100 °C. Near-edge (X-ray absorption near-edge structure, XANES) and extended X-ray absorption fine structure (EXAFS) spectra were measured. The EXAFS response was modeled using ab initio FEFF calculations. Strontium's first shell is observed to be coordinated with chlorine (Sr2+-Cl-) and zirconium's first shell is coordinated by fluorine (Zr4+-F-), both having coordination numbers that decrease with increasing temperature. Multiple zirconium complexes are believed to be present in the melt, which may interfere and distort the EXAFS spectra and result in an anomalously low zirconium first shell coordination number. The use of boron nitride (BN) powder as a salt diluent for XAFS measurements was found to not interfere with measurements and thus can be used for investigations of such systems.

Evidence for the AlZn-Oi defect-complex model for magnetron-sputtered aluminum-doped zinc oxide: A combined X-ray absorption near edge spectroscopy, X-ray diffraction and electronic transport study

Al-doped ZnO and Zn1 − xMgxO films, deposited by magnetron sputtering at substrate temperatures from about 25 °C to 500 °C and exhibiting a strong variation of the carrier concentration, were investigated by X-ray absorption spectroscopy (XAS), analyzing the X-ray absorption near-edge structures. The near-order structure, derived from the X-ray absorption spectra, shows that the dopant Al was built-in onto Zn lattice sites, independently of the deposition temperature up to 450 °C. FEFF calculations confirm the lattice location of the dopant on zinc lattice sites. The formation of secondary (spinel) phases occurs only at deposition temperatures above 450 °C, more pronounced for the Zn1 − xMgxO:Al films. In contrast to the XAS measurements, the electrical parameters of the films—carrier concentration and Hall mobility—exhibit a strong dependence on the substrate temperature, with a variation of the electron concentration by a factor of 4.5 from 25 °C to about 300 °C. This shows that the XAS method is significantly less sensitive compared to electrical measurements for the characterization of electrically active dopant elements. This fact is tentatively explained by the formation of oxygen interstitial defects Oi during deposition, annealing out at low temperatures, and by the formation of defect complexes of dopant atoms with intrinsic lattice defects, like Al-Oi or Al-Mg-Oi, which induce the observed electrical effects but are not detectable by XAS methods.

Electronic properties of a PrPC-Cu(ii) complex as a marker of 5-fold Cu(ii) coordination.

Human prion protein is a subject of extensive study, related in particular to the molecular basis of neurodegenerative disease development and prevention. This protein has two main domains: the membrane C-terminal, structured domain as well as the unstructured N-terminal domain. While PrPC (23-231) has up to eight Cu(ii) binding sites in the N-terminal domain, it includes a characteristic, conservative octarepeat region PHGGGWGQ, which was studied by means of X-ray absorption near edge spectroscopy. The measurements were conducted at the SuperXAS beamline (SLS, PSI, Villigen). For the initial 1 : 1 protein-to-Cu(ii) ratio, the two main Cu(ii) binding modes were identified using linear combination fitting and ab initio FEFF calculations for X-ray spectra. Their electronic structures indicated that Cu(ii) coordinated by strong π-donors could effectively suppress the pre-edge structure due to the filling of empty Cu(ii) d-states. The suppression was correlated with the charge transfer effect and filling of the virtual electronic Cu(ii) states. What is more, we showed that the 1s → 4p + LMCT (Ligand-to-Metal-Charge-Transfer) multielectron transition relation with the main edge transition could be used as a marker for preliminary comparison of an unknown organic compound to a reference. The presented results permitted a possible explanation of the mechanism of choosing the preferred Cu(ii) modes in PrPC-Cu(ii) coordination processes and of the complex stability from the electronic point of view.

Spectroscopic and theoretical investigation of the [Fe2(bdt)(CO)6] hydrogenase mimic and some catalyst intermediates.

In [Fe-Fe] hydrogenase mimic systems the ene-1,2-dithiolene ligands play an important role in the stabilisation of the redox-active metal center. This is demonstrated by the benzenedithiolene (bdt) analogue, featuring six terminal carbonyl ligands connected to a di-iron metal center, i.e. [Fe2(bdt)(CO)6]. Here we present a combined experimental and theoretical study that elucidates key intermediates [Fe2(bdt)(CO)6]1- and [Fe2(bdt)(μ-CO)(CO)5]2- in the electrocatalytic production of dihydrogen. A DFT study shows that [Fe2(bdt)(CO)6]1- is the kinetic product after the first one electron reduction, while the previously proposed bridging intermediate species [Fe2(bdt)(μ-CO)(CO)5]1- is kinetically inaccessible. The doubly reduced species [Fe2(bdt)(μ-CO)(CO)5]2- was for the first time structurally characterized using EXAFS. XANES analysis confirms the existence of reduced iron zero species and confirms the distorted geometry that was suggested by the DFT calculations. Combining IR, UV-vis and XAS spectroscopic results with TD-DFT and FEFF calculations enabled us to assign the key-intermediate [Fe2(bdt)(CO)6]2-. This study emphasizes the strengths of combining computational chemistry with advanced spectroscopy techniques.

Automated generation and ensemble-learned matching of X-ray absorption spectra

X-ray absorption spectroscopy (XAS) is a widely used materials characterization technique to determine oxidation states, coordination environment, and other local atomic structure information. Analysis of XAS relies on comparison of measured spectra to reliable reference spectra. However, existing databases of XAS spectra are highly limited both in terms of the number of reference spectra available as well as the breadth of chemistry coverage. In this work, we report the development of XASdb, a large database of computed reference XAS, and an Ensemble-Learned Spectra IdEntification (ELSIE) algorithm for the matching of spectra. XASdb currently hosts more than 800,000 K-edge X-ray absorption near-edge spectra (XANES) for over 40,000 materials from the open-science Materials Project database. We discuss a high-throughput automation framework for FEFF calculations, built on robust, rigorously benchmarked parameters. FEFF is a computer program uses a real-space Green’s function approach to calculate X-ray absorption spectra. We will demonstrate that the ELSIE algorithm, which combines 33 weak “learners” comprising a set of preprocessing steps and a similarity metric, can achieve up to 84.2% accuracy in identifying the correct oxidation state and coordination environment of a test set of 19 K-edge XANES spectra encompassing a diverse range of chemistries and crystal structures. The XASdb with the ELSIE algorithm has been integrated into a web application in the Materials Project, providing an important new public resource for the analysis of XAS to all materials researchers. Finally, the ELSIE algorithm itself has been made available as part of veidt, an open source machine-learning library for materials science.

Gel-State Dependencies of Brown Patterns of Mn–Fe-Based Prussian Blue Analogues Studied by Combined X-ray Spectroscopies

Abstract The gel-state dependencies of brown patterns of Mn–Fe-based Prussian blue analogues (PBAs) formed in water-glass gels by reaction–diffusion (RD) processes have been studied by using X-ray fluorescence and X-ray absorption near-edge structure spectroscopies. Three tubes containing admixtures of 0.25 M [Fe(CN)6]3− and 0.30 M acetic acid (A and B) or boric acid (C) in water-glass (9.1 (A) and 7.4 (B and C) mass%) were brought into contact with 0.20 M MnSO4 solution. Tube A formed periodic (but not genuine Liesegang) bands, whereas tubes B and C formed light-brown bands in the turbid zone (TZ). A lowered amount of water-glass (A → B) resulted in a more fluctuant distribution of the PBAs. [Mn(H2O)6]2+ ions were also present in the TZ of tube B and their content increased with distance from the gel-junction after stopping the RD process. Addition of boric acid (C) suppressed the RD processes in the gel, slowing down the formation of PBAs. It is likely that the areas of low PBA content in the TZ of tubes B and C generate the light-brown bands. FEFF calculations suggest that the most likely local structures of the predominant PBAs in tubes A/B and C are Mn(NCFe)2O4K2 and Mn(NCFe)2O4, respectively.

NEXAFS and XPS of p-Aminobenzoic Acid Polymorphs: The Influence of Local Environment

Nitrogen K-edge XPS and NEXAFS of the two polymorphic forms of para- aminobenzoic acid (PABA) are significantly different reflecting variation in hydrogen bonding. Alteration in hydrogen bonding at the amino group leads to a shift to high energy for both the XPS N 1s core level and the 3π* NEXAFS resonance with β-PABA. Participation of the amine group in the aromatic system causes the 1π* resonance to be sensitive to the nature of the intermolecular bonding at the para-carboxylic acid group, and a shift to low energy for α- PABA is observed due to hydrogen-bonded carboxylic acid dimer formation. FEFF calculations also successfully reproduce both the energy and intensity variations observed for the σ* shape resonance associated with the C-N bond, with the majority of the decrease in energy observed for b-PABA arising from the longer C-N bond.

NEXAFS Chemical State and Bond Lengths of p-Aminobenzoic Acid in Solution and Solid State

Solid-state and solution pH-dependent NEXAFS studies allow direct observation of the electronic state of para-aminobenzoic acid (PABA) as a function of its chemical environment, revealing the chemical state and bonding of the chemical species. Variations in the ionization potential (IP) and 1s→π* resonances unequivocally identify the chemical species (neutral, cationic, or anionic) present and the varying local environment. Shifts in σ* shape resonances relative to the IP in the NEXAFS spectra vary with C-N bond length, and the important effect of minor alterations in bond length is confirmed with nitrogen FEFF calculations, leading to the possibility of bond length determination in solution.

X-ray absorption spectroscopy study of Cu(II) coordination in the interlayer of montmorillonite

Cu(II) coordination in the interlayer of an expandable clay mineral montmorillonite is studied using X-ray absorption spectroscopy (XAS) along with electron paramagnetic resonance (EPR) and X-ray diffraction (XRD). Ab initio calculations are performed using FEFF code to reproduce the X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) portion of the experimentally measured XAS spectra. Cu(II) coordination changes depending on the Cu(II) loading and hydration state of the interlayer. XRD shows that the Cu-saturated montmorillonite has d001-spacing values corresponding to the interlayer thickness of four and one water layer(s) for the hydrated and dehydrated interlayers, respectively. EPR shows that Cu(II) in the fully hydrated, unsaturated interlayer behaves similarly to free Cu(II) ion in a bulk aqueous solution, while Cu(II) forms a square planar complex in the dehydrated interlayer. Cu(II) in the fully hydrated, Cu-saturated montmorillonite has a characteristic singlet 1st derivative XANES spectrum. FEFF calculations show that this singlet feature originates from a quasi-regular octahedral coordination of water molecules around the interlayer Cu(II) atom. All other samples and model compounds including the dry Cu-saturated montmorillonite, wet and dry unsaturated montmorillonite, aqueous Cu(II), cupric nitrate salt (Cu(NO3)2·4.5H2O), and Cu(II) hydroxide precipitates have doublet 1st derivative XANES spectra. FEFF calculations suggest that the doublet features arise from an axially elongated octahedral coordination under the Jahn–Teller effect or square planar coordination. FEFF calculations of the EXAFS spectra as a function of the axial oxygen bond length demonstrate that a destructive interference between backscattering from equatorial oxygen (Oeq) and that from axial oxygen (Oax) atoms leads to an apparent coordination number (CN) less than six expected for the tetragonal coordination, with the farther, loosely bound axial oxygen atoms making a minor, yet negative contribution to the CN determined by the EXAFS analysis. This study shows that Cu(II) has interchangeable octahedral, tetragonal, and square planar coordinations in the interlayer of montmorillonite, depending on Cu(II) loading and degree of hydration. The quasi-regular octahedral coordination of the interlayer Cu(II) in montmorillonite is a new finding of this study.

Strain modulated anisotropic electronic charge transfer in perovskite Pr0.67 Sr0.33 MnO3 thin films

Strain-modulated anisotropic electronic charge transfers in perovskite ${\mathrm{Pr}}_{0.67}$${\mathrm{Sr}}_{0.33}$${\mathrm{MnO}}_{3}$ thin films were investigated using polarization dependent x-ray absorption near-edge structure at the Mn $K$ absorption edge and half-integer diffraction. The strain from the lattice mismatch between the film and the substrate affects the ${\mathrm{MnO}}_{6}$ octahedron tilt pattern in thin films, which modifies the Mn-O bond length and bond angles, and charge transfer properties. The probability of charge transfer from O to Mn is anisotropic along the in-plane and out-of-plane directions, which is enhanced in the direction with compressive strain due to a larger overlap of Mn 3$d$ and O 2$p$ orbitals as a result of a shorter Mn-O bond length. These results were further verified using the ab initio FEFF calculations and Curie temperature calculation.

Delocalization and occupancy effects of 5f orbitals in plutonium intermetallics using L3-edge resonant X-ray emission spectroscopy

Although actinide (An) L3-edge X-ray absorption near-edge structure (XANES) spectroscopy has been very effective in determining An oxidation states in insulating, ionically bonded materials, such as in certain coordination compounds and mineral systems, the technique fails in systems featuring more delocalized 5f orbitals, especially in metals. Recently, actinide L3-edge resonant X-ray emission spectroscopy (RXES) has been shown to be an effective alternative. This technique is further demonstrated here using a parameterized partial unoccupied density of states method to quantify both occupancy and delocalization of the 5f orbital in α-Pu, δ-Pu, PuCoGa5, PuCoIn5, and PuSb2. These new results, supported by FEFF calculations, highlight the effects of strong correlations on RXES spectra and the technique's ability to differentiate between f-orbital occupation and delocalization.

Determination of conduction and valence band electronic structure of La2Ti2O7 thin film

The electronic structure of a La2Ti2O7-layered perovskite thin film was determined by resonant inelastic X-ray scattering (RIXS) measurements and FEFF calculations. It was found that the empty Ti and La d-band states dominate the conduction band of the structure, whereas the top edge of the valence band is mainly composed of filled O-p states. Furthermore, there is a pronounced overlap between occupied La-p states and O-s states, which are located deeper in the valence band.

Point defects in gallium nitride: X-ray absorption measurements and multiple scattering simulations

We have studied the formation of nitrogen-related point defects in gallium nitride (GaN) using near-edge x-ray absorption fine-structure (NEXAFS) spectroscopy and ab initio FEFF calculations. The presence of several point defects, created within the GaN matrix by low-energy ion-bombardment, has been detected by NEXAFS measurements around N K-edge. FEFF simulations that take into account the formation of nitrogen antisites, interstitials, and vacancies around absorbing nitrogen atoms are consistent with NEXAFS results. The position of energy levels created by these defects within the energy gap of GaN, obtained by both NEXAFS measurements and FEFF simulations, are in good agreement with theoretical predictions.

EXAFS characterization of TiVCrMn hydrogen storage alloy upon hydrogen absorption–desorption cycles

Extended X-ray absorption fine structure (EXAFS) measurements at room temperature at the Ti, V, and Cr K absorption edges were applied to a TiVCrMn alloy subjected to 300 cycles of hydrogen absorption-desorption. The model of the cubic symmetry and atom random distribution is used to fit the EXAFS spectra. The FEFF calculations show relatively good agreement using this model. The EXAFS analysis reveals the variation of local structure of the TiVCrMn alloy with cycling. Aside from the Ti–Cr and Cr–Cr distances, noticeable changes in the other bond lengths were observed during cycling, which can be due to the entrance of hydrogen and lattice contraction in the alloy cells.

An activity and XANES study of Mn-promoted, Fe-based Fischer–Tropsch catalysts

Iron-based Fischer–Tropsch (FT) catalysts with a mol-based formula of (100 − x)Fe/ xMn/5Cu/17SiO 2 ( x ≤ 20), were prepared using co-precipitation methods. The calcined catalysts were first activated in H 2 for 12 h, then reacted in flowing syngas at 1.8 atm, 280 °C, and a 2:1 ratio of H 2:CO. The fresh and reacted catalysts were characterized using X-ray absorption near-edge structure (XANES) to determine changes in the oxidation state and the atomic-level environment of the Fe and Mn atoms. XANES spectra of the fresh calcined and reacted catalyst were taken using the K edges of Fe (7.112 KeV) and Mn (6.540 KeV) for various Mn-metal loadings ( x = 0, 5, 20). The FT activity significantly increased with Mn promotion, indicating significant Fe–Mn interactions. The least squares fitting of the reacted catalyst shows that higher Mn loadings lead to decreased Fe x C concentration and increased Fe 3O 4 concentration. Principal Component Analysis (PCA) of Fe indicates that the Fe 2O 3, Fe 3O 4, θ-Fe 3C phases were present in either the calcined or reacted catalyst. One additional Fe-containing phase was present in the catalyst but was not identified using the Fe standards. The PCA of Mn showed the presence of Mn 2O 3, as well as one additional Mn-containing phase. The Mn XANES of the reacted 95Fe5Mn and 80Fe20Mn catalysts show that Mn was a mixture of the 2+ and 3+ oxidation states. The average oxidation state of Mn in the reacted 95Fe5Mn catalyst was 2.24 ± 0.07, consistent with the formation of an additional phase, identified as (Fe 1− y Mn y ) 3O 4. FEFF calculations have shown relatively good agreement for Mn-substitution of octahedral Fe-sites in Fe 3O 4 (28664-ICSD), specifically in the pre-edge region; corresponding to the composition (Fe 1− y Mn y ) 3O 4. Fe-based FT catalysts deactivate when carbon deposition occurs on larger iron carbide clusters. This study has shown less carbon deposition, Fe x C formation, and higher CO hydrogenation activity with the Mn-promoted catalysts. This indicates that (Fe 1− y Mn y) 3O 4 was responsible for the formation of smaller clusters of Fe x C, which were more active for CO hydrogenation and were less prone to deactivation through carbon deposition.

Not all chromates show the same pre-edge feature. Implications for the modelling of the speciation of Cr in environmental systems

High-resolution XANES spectra for various chromates show that their pre-edge feature varies dramatically with Cr-polymerization. Ab-initio FEFF calculations reproduces those observed experimental trends. Those variations can be easily explained with Pauling's bond valence rules. As chromates are used to model the fraction of toxic Cr(VI) in samples of environmental importance (among others), a careful choice of the chromate model compound is essential for a reliable model of the Cr-speciation in "unknown" samples.

Modeling of XANES-spectra with the FEFF-program

The aim of this project is the calculation of the absorption coefficient μ of x-ray absorption spectra as a function of energy and a comparison with experimental data. A characteristic fine structure can be found in x-ray absorption spectra (XAS) consisting of the XANES (X-Ray Absorption Near Edge Structure) and the EXAFS (Extended X-Ray Absorption Fine Structure) region. XANES is characterized by multiple scattering and provides information about coordination chemistry and bonding angles of the irradiated sample. The program FEFF 8.4 was used for the calculations of the absorption K-edge spectra. FEFF was generated for ab initio multiple scattering calculations of X-ray Absorption Fine Structure (XAFS) of atom-clusters. The code yields scattering amplitudes, phases and other quantities. We computed μ at the K-edge of several elements like Ti, S and Fe. For this purpose, clusters of Na2SO4, Ba2TiO4, FeS2, CaSO2 2(H 2O) were used, working with several space groups. Some of the calculations are consistent with the results of the experiments, but others show energy shifts in the range of some eV. In summary, the FEFF calculations and the experimental data exhibit similarities as well as deviations. By using trimming parameters, deviations could be eliminated to a certain extent, which will be presented.

Chromium speciation in oxide-type compounds: application to minerals, gems, aqueous solutions and silicate glasses

Cr K-edge XANES spectra were obtained for a variety of Cr-bearing model compounds containing Cr(II), Cr(III), Cr(IV), Cr(V) and Cr(VI), in which the Cr-site symmetry is D4h, Oh and Td. The centroid position of the pre-edge feature is a better indicator of the Cr valence than the edge position. In Cr-rich oxides, higher-energy transitions must be excluded in order to refine a robust valence for Cr. The pre-edge for chromates is not unique and varies as a function of the CrO4 2− moiety distortion, which is often related to Cr-polymerization (monochromate vs. dichromate). Both the analogy with the Mn K-pre-edge information and ab initio FEFF calculations of the pre-edge feature for Cr(III) and Cr(VI) confirm the experimental trends. This methodology is applied to the Cr K-edge pre-edge feature collected in gems (emerald, spinel and ruby), the layered minerals fuchsite and kammererite, two Cr-bearing aqueous solutions and a set of sodo-calcic silicate glasses used for bottling sparkling white wine. In emerald and fuchsite, the Cr-site is differently distorted than its ruby or spinel counterpart. In a Cr(III)-bearing aqueous solution and sodo-calcic glass, no evidence for Cr(III) with Td and C3v symmetry is detected. However, minor amounts of chromate moieties (most likely monomeric) are detected in a glass synthesized in air. Preliminary spectra for the wine bottle glass suggest that only trace amounts of chromates might possibly be present in these glasses.