X-ray absorption near edge structure and extended X-ray absorption fine structure analysis of Fe(II) aqueous and acetone solutions

X-ray absorption spectroscopy measurements were used to determine the structure of the first coordination shell of Fe(II) ions in aqueous and acetone based solutions. Extended X-ray absorption fine structure analysis coupled with ab initio X-ray absorption near edge structure calculations confirms the octahedral coordination of the iron ion in water based solution. Data collected for acetone rich solutions can be reproduced assuming coexistence of the octahedral Fe(H(2)O)(6)(2+) and tetrahedral [FeCl(4)](2-) complexes. Distortion of the tetrahedral coordination of ion was detected in some of the acetone based solutions.     

Zinc(II) porphyrins at the air-water interface as studied by polarized total-reflection X-ray absorption fine structure

The polarized total-reflection X-ray absorption fine structure method was applied to characterize zinc porphyrins at the air-water interface. The X-ray absorption near edge structure exhibited a significant difference depending on the polarization of the X-ray. A shoulder peak of the Zn K-edge corresponding to the 1s-4p(z) transition for a square planar metal complex without axial coordination(s) was observed at 9662 eV, which indicates that the axial coordination sites of zinc porphyrin molecules examined are not fully hydrated at the air-water interface. The molecular orientation of zinc porphyrins was determined by analyzing the polarization dependence of the transition peak intensity. The meso-substituted porphyrin derivative 5,10,15,20-tetraphenylporphyrinatozinc(II) (ZnTPP) orients rather parallel to the solution surface. In contrast to ZnTPP, the zinc(II) protoporphyrin IX (ZnPP) with hydrophilic carboxyl groups at one side of the molecule stands up with respect to the solution surface, and the average tilting angle of the porphyrin plane to the surface was evaluated to be between 57 degrees and 43 degrees. In addition, the axial coordination of ZnPP is modified depending on the surface concentration, in which the axial hydration to the zinc center is effectively inhibited in the compressed surface layer.     

Calculation of near-edge X-ray absorption fine structure with the CIS(D) method

We report an investigation into the calculation of near-edge X-ray absorption fine structure with the CIS(D) method. Core excitation energies computed with time-dependent density functional theory using standard exchange-correlation functionals are systematically underestimated. CIS(D) predicts core excitation energies that are closer to experiment. However, excitation energies for Rydberg states are too low with respect to valence states, and for some systems spectra that are qualitatively incorrect are obtained. A scaled opposite spin only approach is proposed that reduces the error in the computed core excitation energies, and results in spectra that are in good agreement with experiment.     

X-ray structure of physiological copper(II)-bis(L-histidinato) complex

The isolation and the X-ray crystal structure of physiological copper(II)-L-histidine complex are reported. The neutral five-coordinate complex shows distorted square pyramidal geometry with bidentate and tridentate L-histidine ligands. The basic character of the pendent imidazole group and H-bonding interactions of bidentate L-histidine ligand are important for copper transport. The unique structural features help explain the origin of its thermodynamic stability and kinetic reactivity in human blood along with the ternary copper(II)-amino acid complexes. The role of L-histidine in interaction with copper(II)-albumin, in cellular uptake of copper, and in treatment of Menkes disease can be studied using these results.     

Extended X-ray absorption fine structure (EXAFS) characterisation of dilute palladium homogeneous catalysts

Highly dilute EXAFS characterisation for the elucidation of species involved in Heck chemistry is demonstrated; the major "monomer" species of Herrmann's acetate-bridged phosphapalladadacycle is characterised and species present during the course of a 50 ppm [Pd] Pd(OAc)2/PBu(t)3 catalysed Heck reaction are presented.     

Full quantitative multiple-scattering analysis of X-ray absorption spectra: application to potassium hexacyanoferrat(II) and -(III) complexes

A recently developed method to the full quantitative analysis of the XAS spectra extending from the absorption edge to the high-energy region is presented. This method is based on the use of two independent approaches to the analysis of the EXAFS and XANES data, the well-known GNXAS and the newly developed MXAN procedures. Herein, we report the application of this technique to two iron complexes of known structure where multiple-scattering effects are prominent, the potassium hexacyanoferrat(II) and -(III) crystals and aqueous solutions. The structural parameters obtained from refinements using the two methods are equal and compare quite well with crystallographic values. Small discrepancies between the experimental and calculated XANES spectra have been observed, and their origin has been investigated in the framework of non-muffin-tin correction. The ligand dependence of the theoretical spectra has been also examined. Analysis of the whole energy range of the XAS spectra has been found to be useful in elucidating both the type of ligands and the geometry of iron sites. These results are of particular use in studying the geometrical environment of metallic sites in proteins and complexes of chemical interest.     

Determination of structures of cobalt(II)-chloro complexes in hydrochloric acid solutions by X-ray absorption spectroscopy at 298 K

The anion exchange reaction is fundamental to the adsorption and desorption of a specific species from a solution phase to an extracting phase, and it is widely used for separation and waste fluid treatment in industrial fields. However, the details of the anion exchange reaction are poorly understood. Quantitative thermodynamic analysis needs a precise solution condition before and after the exchange reaction. Identification of species adsorbed on the anion exchanger is also necessary because there are multiple species in the solution phase in general. Cobalt is a base metal that is widely used in modern society. One of the authors determined the distribution of cobalt-chloro complexes in hydrochloric acid solutions. It is necessary to know what species are adsorbed on anion exchangers for the thermodynamic analysis of the anion exchange reaction. The comparison in structures between the species in the solution phase and adsorbed on anion exchangers reveals what species are adsorbed. Therefore, the determination of the structures of cobalt-chloro complexes in the solution phase is the next step for quantitative analysis. X-ray absorption spectroscopy (XAS) was used for the structure analysis. Factor analysis can decompose extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) spectra consisting of multiple species into individual spectra of single species using the distribution determined using UV-Vis absorption spectra. Fitting EXAFS theoretical models to the decomposed individual spectra determined the structures of three cobalt-chloro complexes: an octahedron of [Co^II(H₂O)₆]²⁺, a distorted octahedron of [Co^II(H₂O)₅Cl]⁺, and a tetrahedron of [Co^IICl₄]^2?. The XANES spectra showed us that the Cl ligand in [Co^II(H₂O)₅Cl]⁺ was attracted to the center atom of Co^II by an electrostatic force, and the bonding system between Cl ligands and Co^II in [Co^IICl₄]^2? involved covalency.

     

X-ray absorption fine structure spectroscopic study of uranium nitrides

Uranium mononitride (UN), sesquinitride (U₂N₃) and dinitride (UN₂) were characterized by extended X-Ray absorption fine structure spectroscopy. Analysis on UN indicate the presence of three uranium shells at distances of 3.46(3), 4.89(5) and 6.01(6) Å and a nitrogen shell at a distance of 2.46(2) Å. For U₂N₃, two absorbing uranium atoms at different crystallographic positions are present in the structure. One of the uranium atoms is surrounded by nitrogen atoms at 2.28(2) Å and by uranium atoms at 3.66(4) and 3.95(4) Å. The second type of uranium atom is surrounded by nitrogen atoms at 2.33(2) and 2.64(3) Å and by uranium atoms at 3.66(4), 3.95(4) and 5.31(5) Å. Results on UN₂ indicate two uranium shells at 3.71(4) and 5.32(5) Å and two nitrogen shells at 2.28(2) and 4.34(4) Å. The lattice parameters of UN, U₂N₃ and UN₂ unit cells were respectively determined to be 4.89(5), 10.62(10) and 5.32(5) Å. Those results are well in agreement with those obtained by X-Ray diffraction analysis.     

X-ray absorption fine structure of artificial antigens for cadmium

Immunoassay technology as a quick and large-scale screening method to detect metal ions in foods and environmental samples has rapidly been developed due to several advantages over conventional instrument-intensive methods. Unlike biomacromolecule, metal ions are haptens without immunogenicity, so successful preparation of artificial antigens is the first critical step for establishing immunoassay methods for them. In the current paper, cadmium ions were conjugated to BSA and OVA, respectively, using bifunctional chelator, p-SCN-Bn-DTPA. The ultraviolet analysis indicated that the maximum absorption peak of Cd–p-SCN-DTPA–BSA and Cd–p-SCN-DTPA–OVA had a small peak shift and an apparent absorbance increase compared to that of BSA and OVA, and the extents of substitution of ?-amino in both conjugates were 51.2% and 58.6%, respectively. In addition, the EXAFS of conjugates implied that Cd²⁺ coordinated with N and O atoms of DTPA in artificial antigens, the coordination type and number of Cd–DTPA, Cd–p-SCN-Bn-DTPA–BSA, Cd–p-SCN-Bn-DTPA–OVA were the same. XANES region and geometries of the three compounds were also same. These results implied that the three antigens had the similar local structure and atomic geometry.This was the first time that the XAFS was attempted for the identification of artificial heavy metal ion antigens.     

Guanine-containing copper(II) complexes: synthesis, X-ray structures and magnetic properties

Three new compounds of formula {[Cu(gua)(H(2)O)(3)](BF(4))(SiF(6))(1/2)}(n) (1), {[Cu(gua)(H(2)O)(3)](CF(3)SO(3))(2).H(2)O}(n) (2) and [Cu(gua)(2)(H(2)O)(HCOO)]ClO(4).H(2)O.1/2HCOOH] (3) [gua = 2-amino-1H-purin-6(9H)-one] showing the unprecedented coordination of neutral guanine, have been synthesised and structurally characterized. The structures of the compounds 1 and 2 contain uniform copper(II) chains of formula [Cu(gua)(H(2)O)(3)](n)(2n+), where the copper atoms are bridged by guanine ligands coordinated via N(3) and N(7). The electroneutrality is achieved by uncoordinated tetrafluoroborate and hexafluorosilicate (1) and triflate (2). Each copper atom in 1 and 2 is five-coordinated in a distorted square pyramidal environment: two water molecules in trans positions and the N(3) and N(7a) nitrogen atoms of two guanine ligands build the basal plane whereas a water molecule fills the axial position. The values of the copper-copper separation across the bridging guanine ligand are 7.183(1) (1) and 7.123(1) A (2). is an ionic salt whose structure is made up of mononuclear [Cu(gua)(2)(H(2)O)(HCOO)](+) cations and perchlorate anions plus water and formic acid as crystallization molecules. The two guanine ligands in the cation are coordinated to the copper centre through the N(9) atom. The copper atom in 3 is four-coordinated with two monodentate guanine molecules in the trans position, a water molecule and a monodenate formate ligand building a quasi square planar surrounding. Magnetic susceptibility measurements for 1 and 2 in the temperature range 1.9-300 K show the occurrence of significant intrachain antiferromagnetic interactions between the copper(ii) ions across the guanine bridge [J = -9.6(1) (1) and -10.3(1) cm(-1) (2) with H = -J summation operator(i)S(i).S(i+1)].     

X-ray crystal and molecular structure of sulphato aquotris(benzotriazole) copper(II)benzotriazole

The complex “Cu(SO₄)(btaH)₄·2H₂O” (btaH = benzotriazole) deposited as deep blue crystals from aqueous CuSO₄·5H₂OH₂SO₄btaH solutions been shown by X-ray diffraction methods to be a monohydrate [Cu(SO₄)(H₂O)(btaH)₃·btaH]. The crystals contain five-coordinate, tetragonal pyramidal Cu(SO₄)(H₂O)(btaH)₃ units and bridging btaH molecules linked together by a three-dimensional array of H-bonding interactions.     

Molecular characterization of brominated persistent pollutants using extended X-ray absorption fine structure (EXAFS) spectroscopy

X-ray absorption fine structure (EXAFS) spectroscopy spectra were collected for three brominated persistent pollutants: 6-bromo-2,4,5-trichlorophenol (BrTriClP), pentabromophenol (PentaBrP) and 3,3′,5,5′-tetrabromobisphenol A (TBBA). The substances were selected to be symmetrical (BrTriClP and TBBA) or asymmetrical (PentaBrP) with respect to the atomic Br positions and to differ in the number of bromine and other halide atoms, as well as their relative positions. The asymmetrical PentaBrP was modelled with special detail as not all bromine atoms have identical coordination environments. The studied substances displayed unique EXAFS spectra, which could be used to determine the molecular structure in fair detail. We conclude that EXAFS spectroscopy is a suitable technique for molecular characterization of the comparatively complex molecules within the class of compounds of brominated organic persistent pollutants. A detailed understanding of the EXAFS spectra of the pure compounds opens up possibilities to study the interactions with soil and sediment matrices by means of EXAFS spectroscopy. Figure Brominated organic persistent pollutants are characterized by EXAFS spectroscopy     

NMR spectroscopic characterization of copper(II) and zinc(II) complexes of indomethacin

Molecular diffusion constants were studied by NMR spectroscopy to provide information about the solution structures of a variety of Cu(II) and Zn(II) monomeric and dimeric complexes of indomethacin (IndoH). These studies showed that monomeric Zn(II)-Indo complexes substantially dimerize in DMF-d7 and DMSO-d6 solutions at room temperature, whereas the Cu(II) and Zn(II) dinuclear complexes remain largely intact in these solutions. There is evidence of an equilibrium between monomers and dimers for the Zn(II) complexes in solution, as shown by a reduced diffusion constant and lower average radius compared to the Cu(II) dimer. Such an equilibrium between monomers and dimers for the Zn(II) complexes is also consistent with previous results obtained from XAFS analysis of DMF solutions of such complexes. The greater lability and lower thermodynamic stability of the Zn(II) dimer complex compared to the Cu(II) analogue, as determined from the NMR experiments, is likely to result in the more ready release of free Indo in the GI tract. This is consistent with the previously observed higher GI toxicities of the Zn-Indo pharmaceutical preparations compared to the Cu(II)-Indo counterparts.     

Hydration of counterions in cation exchange resins studied by X-ray absorption fine structure

X-Ray absorption fine structure has revealed that K(+) is partially desolvated when transferred into the interior of cation-exchange resin, while Rb(+) and Sr(2+) keep their first hydration structures.     

Hydrolytic protein cleavage mediated by unusual mononuclear copper(II) complexes: X-ray structures and solution studies

The crystal structures and redox and UV-vis/EPR spectroscopic properties of two new mononuclear copper(II) complexes, [Cu(HL1)Cl2] (1) and [Cu(L1)Cl] (2), prepared through the reaction between copper(II) chloride and the ligand 2-[(bis(pyridylmethyl)amino)methyl]-4-methyl-6-formylphenol (HL1) under distinct base conditions, are reported along with solution studies. Also, we demonstrate that these CuII complexes are able to cleave unactivated peptide bonds from bovine serum albumin (BSA) and the thermostable enzyme Taq DNA polymerase at micromolar concentration, under mild pH and temperature conditions. The cleavage activity seems to be specific with defined proteolytic fragments appearing after protein treatment. The location of the specific cleavage sites was tentatively assigned to solvent-accessible portions of the protein. These are two of the most active Cu(II) complexes described to date, since their cleavage activity is detected in minutes and evidence is here presented for a hydrolytic mechanism mediating protein cleavage by these complexes.     

Synthesis, characterization, and X-ray crystal structures of copper(II) and nickel(II) complexes with Schiff base

New copper(II) complexes, [Cu₂L¹L²] · ClO₄ (I) and [Ni(L³)₂] (II), where L¹ is the monoanionic form of 2-[1-(2-emthylaminoethylimino)ethyl]phenol, L² is the dianionic form of N,N′-ethylene-bis(2-hydroxyacetophenonylideneimine), L³ is the mono-anionic form of 2-(1-iminoethyl)phenol, were prepared and characterized using elemental analysis, FT-IR spectroscopy, and X-ray single-crystal diffraction. In complex I, the Cu(1) atom is coordinated by the NNO tridentate ligand L¹ and the two phenolate O atoms of L², forming a square pyramidal geometry. The Cu(2) atom in complex I is coordinated by the NNOO tetradenate ligand L², forming a square planar geometry. The Ni atom in complex II is coordinated by two phenolate O and two imine N atoms from two ligands L³, forming a square planar geometry. In the crystal structure of I, the perchlorate anions are linked to the dinuclear copper(II) complex cations through intermolecular N-H...O hydrogen bonds. In the crystal structure of II, the mononuclear nickel complex molecules are linked through intermolecular N-H...O hydrogen bonds, forming a trimer.     

New sights into the electrochemical interface provided by in situ X-ray absorption fine structure and surface X-ray scattering

Various important processes, such as electron transfer reactions, adsorption/desorption, solvation/desolvation, and formation/cleavage of chemical bonds, take place at electrolyte/electrode interfaces during electrocatalytic reactions. Those processes have been understood on the basis of changes in the surface composition, atomic arrangement, and molecular and electronic structures of the interfaces by using various in situ analysis techniques. To date, in situ analysis and observation of those interfacial processes at an ideal single-crystal surface are indispensable not only for fundamental understanding of the reaction mechanism but also for rational design of the highly efficient and durable electrocatalytic materials. Here, historical and recent progress of in situ studies on electrocatalytic reactions is briefly reviewed with a focus on two major techniques, X-ray absorption fine structure and surface X-ray scattering.