Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Evidence of a cubic iron sub-lattice in t-CuFe2O4 demonstrated by X-ray Absorption Fine Structure.

ABSTRACT: Copper ferrite, belonging to the wide and technologically relevant class of spinel ferrites, was grown in the form of t-CuFe2O4 nanocrystals within a porous matrix of silica in the form of either an aerogel or a xerogel, and compared to a bulk sample. Extended X-ray absorption fine structure (EXAFS) spectroscopy revealed the presence of two different sub-lattices within the crystal structure of t-CuFe2O4, one tetragonal and one cubic, defined by the Cu2+ and Fe3+ ions respectively. Our investigation provides evidence that the Jahn-Teller distortion, which occurs on the Cu2+ ions located in octahedral sites, does not affect the coordination geometry of the Fe3+ ions, regardless of their location in octahedral or tetrahedral sites.

SUBMITTER: Caddeo F

PROVIDER: S-EPMC5768695 | biostudies-other | 2018 Jan

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Evidence of a cubic iron sub-lattice in t-CuFe2O4 demonstrated by X-ray Absorption Fine Structure.

Caddeo Francesco F Loche Danilo D Casula Maria F MF Corrias Anna A

Scientific reports 20180115 1

Copper ferrite, belonging to the wide and technologically relevant class of spinel ferrites, was grown in the form of t-CuFe2O4 nanocrystals within a porous matrix of silica in the form of either an aerogel or a xerogel, and compared to a bulk sample. Extended X-ray absorption fine structure (EXAFS) spectroscopy revealed the presence of two different sub-lattices within the crystal structure of t-CuFe2O4, one tetragonal and one cubic, defined by the Cu ...[more]

PMID: 29335500

Similar Datasets

Extended X-Ray Absorption Fine Structure of ZrW2O8: Theory vs. Experiment.

Project description:Extended x-ray absorption fine structure (EXAFS) is well-suited for investigations of structure and disorder of complex materials. Recently, experimental measurements and analysis of EXAFS have been carried out to elucidate the mechanisms responsible for the negative thermal expansion (NTE) in zirconium tungstate (ZrW2O8). In contrast to previous work suggesting that transverse O-displacements are largely responsible, the EXAFS analysis suggested that correlated rotations and translations of octahedra and tetrahedra within the structure are a major source. In an effort to resolve this controversy, we have carried out ab initio calculations of the structure, lattice vibrations, and EXAFS of ZrW2O8 based on real-space multiple-scattering calculations using the FEFF9 code and auxiliary calculations of structure and Debye-Waller factors. We find that the theoretical simulations are consistent with observed EXAFS, and show that both of the above mechanisms contribute to the dynamical structure of ZrW2O8.

| S-EPMC6115524 | biostudies-literature

An extended-X-ray-absorption-fine-structure investigation of diferric transferrins and their iron-binding fragments.

Project description:Iron K-edge extended-X-ray-absorption-fine-structure (e.x.a.f.s.) spectra were recorded for diferric human and rabbit serum transferrins and for diferric chicken ovotransferrin in aqueous solution; for ovotransferrin e.x.a.f.s. spectra from the N-terminal and C-terminal domain fragments were also measured. The overall spectral profiles closely resemble one another, indicating similar iron-binding sites. The simulation of the diferric ovotransferrin spectrum suggests a first co-ordination shell consisting of six low-Z ligands (nitrogen/oxygen), two ligands at a distance of approx. 0.185 nm (1.85 A) and four ligands at approx. 0.204 nm (2.04 A). The two shorter distances may correspond to Fe-O (tyrosine), whereas the longer distance is consistent with Fe-N (histidine) and Fe-O (water). Detailed analysis of the spectra of the N-terminal and C-terminal fragments indicates a difference in the short ligand distance.

| S-EPMC1153050 | biostudies-other

Geometric structure determination of N694C lipoxygenase: a comparative near-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure study.

Project description:The mononuclear nonheme iron active site of N694C soybean lipoxygenase (sLO1) has been investigated in the resting ferrous form using a combination of Fe-K-pre-edge, near-edge (using the minuit X-ray absorption near-edge full multiple-scattering approach), and extended X-ray absorption fine structure (EXAFS) methods. The results indicate that the active site is six-coordinate (6C) with a large perturbation in the first-shell bond distances in comparison to the more ordered octahedral site in wild-type sLO1. Upon mutation of the asparagine to cysteine, the short Fe-O interaction with asparagine is replaced by a weak Fe-(H(2)O), which leads to a distorted 6C site with an effective 5C ligand field. In addition, it is shown that near-edge multiple scattering analysis can give important three-dimensional structural information, which usually cannot be accessed using EXAFS analysis. It is further shown that, relative to EXAFS, near-edge analysis is more sensitive to partial coordination numbers and can be potentially used as a tool for structure determination in a mixture of chemical species.

| S-EPMC2736335 | biostudies-literature

Ab initio self-consistent x-ray absorption fine structure analysis for metalloproteins.

Project description:X-ray absorption fine structure is a powerful tool for probing the structures of metals in proteins in both crystalline and noncrystalline environments. Until recently, a fundamental problem in biological XAFS has been that ad hoc assumptions must be made concerning the vibrational properties of the amino acid residues that are coordinated to the metal to fit the data. Here, an automatic procedure for accurate structural determination of active sites of metalloproteins is presented. It is based on direct multiple-scattering simulation of experimental X-ray absorption fine structure spectra combining electron multiple scattering calculations with density functional theory calculations of vibrational modes of amino acid residues and the genetic algorithm differential evolution to determine a global minimum in the space of fitting parameters. Structure determination of the metalloprotein active site is obtained through a self-consistent iterative procedure with only minimal initial information.

| S-EPMC1635686 | biostudies-literature

X-ray Absorption Fine Structure (XAFS) Studies of Oxide Glasses-A 45-Year Overview.

Project description:X-ray Absorption Fine Structure (XAFS) spectroscopy has been widely used to characterize the short-range order of glassy materials since the theoretical basis was established 45 years ago. Soon after the technique became accessible, mainly due to the existence of Synchrotron laboratories, a wide range of glassy materials was characterized. Silicate glasses have been the most studied because they are easy to prepare, they have commercial value and are similar to natural glasses, but borate, germanate, phosphate, tellurite and other less frequent oxide glasses have also been studied. In this manuscript, we review reported advances in the structural characterization of oxide-based glasses using this technique. A focus is on structural characterization of transition metal ions, especially Ti, Fe, and Ni, and their role in different properties of synthetic oxide-based glasses, as well as their important function in the formation of natural glasses and magmas, and in nucleation and crystallization. We also give some examples of XAFS applications for structural characterization of glasses submitted to high pressure, glasses used to store radioactive waste and medieval glasses. This updated, comprehensive review will likely serve as a useful guide to clarify the details of the short-range structure of oxide glasses.

| S-EPMC5848901 | biostudies-literature

The effect of orbital-lattice coupling on the electrical resistivity of YBaCuFeO5 investigated by X-ray absorption.

Project description:Temperature-dependent X-ray absorption near-edge structures, X-ray linear dichroism (XLD) and extended X-ray absorption fine structure (EXAFS) spectroscopic techniques were used to investigate the valence state, preferred orbital and local atomic structure that significantly affect the electrical and magnetic properties of a single crystal of YBaCuFeO5 (YBCFO). An onset of increase of resistivity at ~180?K, followed by a rapid increase at/below 125?K, is observed. An antiferromagnetic (AFM)-like transition is close to the temperature at which the resistivity starts to increase in the ab-plane and is also observed with strong anisotropy between the ab-plane and the c-axis. The XLD spectra at the Fe L3,2-edge revealed a change in Fe 3d eg holes from the preferential [Formula: see text] orbital at high temperature (300-150?K) to the [Formula: see text] orbital at/below 125?K. The analysis of the Fe K-edge EXAFS data of YBCFO further revealed an unusual increase in the Debye-Waller factor of the nearest-neighbor Fe-O bond length at/below 125?K, suggesting phonon-softening behavior, resulting in the breaking of lattice symmetry, particularly in the ab-plane of Fe-related square pyramids. These findings demonstrate a close correlation between electrical resistivity and coupling of the preferred Fe 3d orbital with lattice distortion of a single crystal of YBCFO.

| S-EPMC6901513 | biostudies-literature

Formation of a Pt-MgO Solid Solution: Analysis by X-ray Absorption Fine Structure Spectroscopy.

Project description:Thermal treatment of Pt nanoparticles or Pt(acac)2 supported on MgO resulted in the formation of a solid solution of Pt-MgO, as evidenced by Pt L3-edge X-ray absorption fine structure spectroscopy. The valence of Pt in the Pt-MgO solid solution was determined to be 4+. A characteristic shrinkage of the Pt-O bond distance was observed in comparison with that of the nearest-neighboring Mg-O bond in MgO, which agreed with the density functional theory (DFT) calculations. The segregation of Pt and MgO proceeded with a further increase in the thermal treatment temperature up to 1273 K. The dispersion of Pt on MgO measured through CO adsorption was much higher than that on Al2O3 or SiO2 owing to the formation of the Pt-MgO solid solution.

| S-EPMC9366959 | biostudies-literature

Hydrogen absorption and desorption on Rh nanoparticles revealed by in situ dispersive X-ray absorption fine structure spectroscopy.

Project description:To unveil the origin of the hydrogen-storage properties of rhodium nanoparticles (Rh NPs), we investigated the dynamical structural change of Rh NPs using in situ dispersive X-ray absorption fine structure spectroscopy (XAFS). The variation of the Rh-Rh interatomic distance and Debye-Waller factor of Rh NPs with a size of 4.0 and 10.5 nm during hydrogen absorption and desorption suggested that they have a different mechanism for hydrogen absorption, which is that the hydrogen absorption on the inner site has a greater contribution than that on a surface for Rh 4.0 nm. In the case of Rh 10.5 nm, it is opposed to Rh 4.0 nm. This study demonstrates a powerful in situ XAFS method for observing small local structural changes of metal nanoparticles and its importance for understanding of the hydrogen-absorption properties of Rh NPs with an interesting hydrogenation mechanism.

| S-EPMC9054127 | biostudies-literature

Extended-X-ray-absorption-fine-structure investigations of zinc in 5-aminolaevulinate dehydratase.

Project description:The zinc co-ordination in 5-aminolaevulinate dehydratase (5-aminolaevulinate hydro-lyase, EC 4.2.1.24) was investigated by recording and interpreting the extended X-ray-absorption fine structure (e.x.a.f.s.) associated with the zinc K-edge. The enzyme has a molecular mass of 280 000 Da and consists of eight subunits of 35 000 Da each; the samples studied contained approx. 1 g-atom of zinc/mol of subunit. Four forms of the enzyme were investigated and details of the zinc environment were elucidated, as follows. In the native enzyme, zinc is considered to be co-ordinated to three sulphur atoms at 0.228(2)nm [2.28(2)A] and a lower-Z atom at 0.192(5)nm [1.92(5)A] (if nitrogen) or 0.189(5)nm [1.89(5)A] (if oxygen). Reaction of the enzyme with the inhibitor 2-bromo-3-(imidazol-5-yl)propionic acid produced significant changes in the e.x.a.f.s., the nature of which are consistent with co-ordination by about three sulphur atoms at 0.222(2)nm [2.22(2)A], a nitrogen atom at 0.193(5)nm [1.93(5)A] and a nitrogen atom from the inhibitor at 0.214(5)nm [2.14(5)A]. Inactivation of the enzyme by air-oxidation of essential thiol groups and binding of the substrate produce slight changes in the e.x.a.f.s. consistent with slight re-arrangement of ligands with additional lighter ligands (nitrogen or oxygen). These results, when combined with previous findings, are taken to indicate that zinc has a structural rather than a direct catalytic role in 5-aminolaevulinate dehydratase.

| S-EPMC1152664 | biostudies-other

Characterization of surfaces presenting covalently immobilized oligopeptides using near-edge X-ray absorption fine structure spectroscopy.

Project description:This study addresses the need for methods that validate the surface chemistry leading to the immobilization of biomolecules and provide information about the resulting structural configurations. We report on the use of near-edge X-ray absorption fine structure spectroscopy (NEXAFS) to characterize a widely employed immobilization chemistry that leads to the covalent attachment of a biologically relevant oligopeptide to a surface. The oligopeptide used in this study is a kinase substrate of the epidermal growth factor receptor (EGFR), a protein that is a common target for cancer therapeutics. By observing changes in the pi* and sigma* orbitals of specific nitrogen and carbon atoms (amide, imide, carbonyl), we are able to follow the sequential reactions leading to immobilization of the oligopeptide. We also show that it is possible to use NEXAFS to extend this characterization method to submonolayer densities that are relevant to biological assays. Such an element-specific chemical characterization of small peptides on surfaces fills an unmet need and establishes NEXAFS as useful technique for characterizing the immobilization of small biomolecules on surfaces.

| S-EPMC2862363 | biostudies-literature