EXAFS Features Research Articles

New insights on Br speciation in volcanic glasses and structural controls on halogen degassing

Abstract The volcanic degassing of halogens, and especially of the heavier Br and I, received increased attention over the last 20 years due to their significant effect on atmospheric chemistry, notably the depletion of stratospheric ozone. While the effect of melt composition on halogen diffusion, solubility, or fluid-melt partitioning in crustal magma chambers has been thoroughly studied, structural controls on halogen incorporation in silicate melts remain poorly known, with only few studies available in simplified borosilicate or haplogranite compositions. Here, we demonstrate that high-energy resolution fluorescence detection X-ray absorption spectroscopy (HERFD-XAS) with a crystal analyzer spectrometer (CAS) is well-suited for the study of Br speciation in natural volcanic glasses which can contain lower Br concentrations than their laboratory analogs. Especially, HERFD-XAS results in sharper and better-resolved XANES and EXAFS features than previously reported and enables detection limits for EXAFS analysis down to 100 ppm when previous studies required Br concentrations above the 1000 ppm level. XANES and EXAFS analyses suggest important structural differences between synthetic haplogranitic glass, where Br is surrounded by Na and next-nearest oxygen neighbors, and natural volcanic glasses of basaltic to rhyodacitic compositions, where Br is incorporated in at least three distinct sites, surrounded by Na, K, or Ca. Similar environments, involving both alkali and alkaline earth metals have already been reported for Cl in Ca-bearing aluminosilicate glass and our study thus underlines that the association of Br with divalent cations (Ca2+) has been underestimated in the past due to the use of simplified laboratory analogs. Overall, similarities in Cl and Br structural environments over a large array of compositions (46–67 wt% SiO2) suggest that melt composition alone may not have a significant effect on halogen degassing and further support the coupled degassing of Cl and Br in volcanic systems.

New lipophilic 3-hydroxy-4-pyridinonate iron(iii) complexes: synthesis and EXAFS structural characterisation

New tris-iron(III) chelates of 3-hydroxy-4-pyridinone ligands derived from maltol (3-hydroxy-2-methyl-4-pyrone) or ethylmaltol (2-ethyl-3-hydroxy-4-pyrone), including a variety of N-aryl (phenyl, 4'-tolyl, 4'-(n-butyl)phenyl, 4'-(n-hexyl)phenyl) and N-benzyl (4'-methylbenzyl, 4'-fluorobenzyl and 4'-(trifluoromethyl)benzylamine) substituents on the nitrogen atom of the pyridinone ring, have been prepared. Characterization by C,H,N elemental analysis and thermogravimetric measurements indicates that most of the complexes are obtained as hydrates of general formula ML3.xH2O. Structural characterization of these difficult to crystallize lipophilic complexes has been achieved by EXAFS spectroscopy. Solutions of iron(III) complexes of maltol, ethylmaltol, 1,2-dimethyl-3-hydroxy-4-pyridinone and 1-phenyl-2-methyl-3-hydroxy-4-pyridinone in methanol-water mixtures were also examined by EXAFS. Distances from the central atom to ligand atoms, within 6 A of the metal, have been determined in the solid and solution samples and the results show that the structure observed in the powder is maintained in solution. The local structure around the metal centre, bond distances and bond angles, does not change significantly with variable lipophilicity, thus indicating that ligands may be tailored according to specific needs without altering their chelation properties. EXAFS data analysis for this set of tris-iron(III) compounds illustrates the important contribution of both intra-ligand and inter-ligand multiple scattering pathways through the metal centre to a peak observed in the FT spectrum at twice the metal ligand distance (approximately 4 A). The present results demonstrate that EXAFS features at twice the metal-ligand distance are valuable in the assignment of molecular geometry and that location of hydration water molecules, by EXAFS analysis, is limited by the geometry of the complexes, in particular for those in which ligands containing phenyl rings are present.

Iron in silicate glasses: a systematic analysis of pre-edge, XANES and EXAFS features

A large number (67) of silicate glasses containing variable amounts of iron oxide were studied by high-resolution XANES spectroscopy at the Fe K-edge to determine an accurate method to derive redox information from pre-edge features. The glass compositions studied mimic geological magmas, ranging from basaltic to rhyolitic, dry and hydrous, with variable quench rates. The studied glasses also include more chemically simple calco-sodic silicate glass compositions. The Fe contents range from 30 wt.% to less than 2000 ppm. For most of the series of composition studied, the pre-edge information varies linearly with redox, even under high-resolution conditions. The average coordination of Fe(II) is often similar to its Fe(III) counterpart except in highly polymerized glasses because of the strong influence exerted by the tetrahedral framework on iron's sites. Natural volcanic glasses (from various volcanoes around the world) show similar variations. The average coordination of Fe(II) is often comprised between 4.5 and 5. Fe(III) shows larger variations in coordination (4 to 6, depending on composition). Bond valence models are proposed to predict the average coordination of Fe based on composition. Molecular dynamics simulations (Born–Mayer–Huggins) potentials were carried out on some compositions to estimate the magnitude of disorder effects (both static and thermal) in the XAFS analysis. XANES calculations based on the MD simulations and FEFF 8.2 show large variations in the local structures around Fe. Also, 5-coordinated Fe(III) is found to be an important moiety in ferrisilicate glasses. For Fe(II), discrepancies between glass and melt are larger and are related to its greater structural relaxation at Tg. Also, a strong destructive interference between network formers and modifiers explain the relatively weak intensity of the next-nearest neighbors contributions in the experimental spectra.

Reverse Monte Carlo simulations of EXAFS spectra: application to the sorption of gold on iron oxy-hydroxides

The sorption of Au at the goethite-water interface is studied. In order to better understand sorption models for cations on mineral surfaces, reverse Monte-Carlo (RMC) simulations were used to analyse EXAFS spectra. A starting model is constructed based on the (110) mineral surface separated by a layer of water molecules. Some of metal cations at the mineral-water interface are replaced by absorbed gold cations. All atomic positions are allowed to vary on both the mineral surface and in the water layer during the RMC simulations. Partial pair distribution functions and corresponding EXAFS spectra are computed and refined by a Metropolis algorithm. The final RMC model matches most EXAFS features (including short- and medium-range environments). The usual EXAFS parameters (coordination number, coordination distance and Debye–Waller factor and higher moments) are retrieved from the partial pair distribution functions by moment analysis. In case of Au at the the goethite-water interface four Au–O coordinations are found at an average distance of 1.99 Å with a second moment of 0.0013 Å2. Two iron next-nearest neighbors show a broad distribution between 3.2 and 3.8 Å with an average coordination distance of 3.49 Å, a coordination number of 3 and a second moment of 0.013 Å2. The results of the RMC simulations are compared with results of conventional EXAFS analysis methods.

An X-ray Spectroscopic Investigation of Bis(dithiolene)molybdenum(IV,V,VI) and -tungsten(IV,V,VI) Complexes: Symmetrized Structural Representations of the Active Sites of Molybdoenzymes in the DMSO Reductase Family and of Tungstoenzymes in the AOR and F(M)DH Families

Molybdenum and tungsten oxotransferase and hydroxylase enzymes catalyze the generalized reaction X + H2O ↔ XO + 2H+ + 2e- involving substrate and product X/XO. All such enzymes contain one or two pterin dithiolene ligands bound to a molybdenum or tungsten atom in the enzyme cofactor. Recent investigations in these laboratories together with earlier work by others have afforded a set of 10 complexes, all structurally characterized by X-ray diffraction, that are relevant to the active sites of several families of enzymes containing two pterin dithiolenes: [MIVO(bdt)2]2- (1, 6), [MV(bdt)2]1- (2, 7), [MIV(OSiButPh2)(bdt)2]1- (3, 8), [MVIO2(bdt)2]2- (4, 9), and [MVIO(OSiButPh2)(bdt)2]1- (5, 10) [M = Mo (1−5), W (6−10); bdt = benzene-1,2-dithiolate(2−)]. In particular, complexes 3 and 5 simulate the reduced and oxidized sites, respectively, of one DMSO reductase. This set of complexes of accurately known structure provides a heretofore unavailable opportunity to examine by X-ray absorption spectroscopy (XAS) the effects of different oxidation states, ligand types, and coordination geometries on absorption edge and EXAFS features. Molybdenum K-edge or tungsten L2,3-edge spectra and EXAFS analysis (using the GNXAS protocol) are reported for 1−10. Systematic shifts of edge energies over the M(IV,V,VI) oxidation states are observed, and features in the second derivative edge spectra are correlated with the number (0−2) of oxo ligands. While the field of molybdenum and tungsten enzymes has been substantially advanced by protein crystallography, there exist variances in metal−dithiolene interactions for a given enzyme and structural differences among closely related enzymes. Further, protein crystallographic results are not always consistent with conclusions from XAS and other spectroscopic studies. These molecules serve as benchmarks or calibrants with respect to the corresponding structural properties of enzyme sites containing two pterin dithiolene cofactor ligands and one or two oxygen-based ligands such as members of the DMSO family of molybdoenzymes and the AOR and F(M)DH families of tungstoenzymes. Because of the internal consistency of EXAFS and X-ray crystallography results, these complexes will prove useful for future comparisons with enzymes of both known and unknown structure and may help to clarify discrepancies seen in protein crystallography.