Copper K-edge Research Articles

XRD and EXAFS studies of azomethynic copper metallochelates as models of blue copper proteins

The structure of two biomimetic copper complexes bis[4-benzylaldimino-3-methyl-1-phenyl-5-thio (seleno)pyrazolato]copper(II)—36 32N6X2Cu (where X=S, Se) have been studied and X-ray patterns of these compounds have been prepared using the Rietveld refinement technique. Both complexes crystallized in a monoclinic lattice, space group-C2/c(15). The unit-cell parameters are a=28.917(3) Å; b=7.000(2) Å; c=17.550(4) Å; β=106.869(1) (1) for C36H32CuN6S2 and a=29.126(6) Å; b=7.042(4) Å; c=17.228(2) Å; β=105.587(2) for C36H32CuN6Se2. Analysis of the copper and selenium K-edge X-ray absorption spectra (EXAFS) of these complexes show that a copper atom is in pseudo-tetrahedric ligand environment N2X2 with typical Cu–N bonds (R=2.00–2.01 Å) and significantly different Cu–S and Cu–Se bonds (R=2.27 Å and R=2.41 Å, respectively) because of different sulfur and selenium ion radii. © 2004 International Centre for Diffraction Data.

Inter- and Intra-octarepeat Cu(II) Site Geometries in the Prion Protein: IMPLICATIONS IN Cu(II) BINDING COOPERATIVITY AND Cu(II)-MEDIATED ASSEMBLIES

Cu(II) binding to the alpha prion protein (alphaPrP) can be both intramolecular and intermolecular. X-ray absorption spectroscopy at the copper K-edge has been used to explore the site geometry under each binding mode using both insoluble polymeric Cu(II).alphaBoPrP-(24-242) (bovine PrP) complexes and soluble Cu(II) complexes of peptides containing one, two, and four copies of the octarepeat. Analysis of the extended region of the spectra using a multiple scattering approach revealed two types of sites differing in the number of His residues in the first coordination shell of Cu(II). Peptides containing one and two-octarepeat copies in sub-stoichiometric Cu(II) complexes showed the direct binding of a single His in accord with crystallographic intra-repeat geometry. Alternatively, the polymeric Cu(II).alphaBoPrP-(24-242) complex and Cu(II) in its soluble complex with a four-octarepeat peptide at half-site-occupancy showed Cu(II) directly bound to two His residues, consistent with an inter-repeat binding mode. Increasing the Cu(II) site occupancy from 0.5 to 0.75 in the peptide containing four octarepeats resulted in spectral features that are intermediate to those of the inter- and intra-repeat modes. The transition from His-Cu-His (inter-repeat) to Cu-His (intra-repeat) on increasing Cu(II) saturation offers a structural basis for the positive cooperativity of the cation binding process and explains the capacity of alphaPrP to participate in Cu(II)-mediated intermolecular interactions.

X-RAY ABSORPTION SPECTROSCOPIC STUDY OF CU-GLYPHOSATE ADSORBED BY MICROCRYSTALLINE GIBBSITE

Glyphosate [N-(phosphonomethyl)glycine] is a broad-spectrum herbicide that is used widely in agriculture, forestry, and urban settings. It is one of the most heavily applied pesticides in the US, with an annual use greater than 12 million kg. When added to soil glyphosate is readily sorbed, losing both its efficacy as an herbicide and its potential for translocation. Despite such tenacious binding to soil colloids, the adsorbent surface offers little protection from biodegradation because the glyphosate decomposes so rapidly, with a half-life as short as several days. Attempts to elucidate the sorption mechanism of glyphosate, thereby providing a mechanistic explanation for this biolability, have thus far been unsuccessful. Therefore, the goal of this research was to derive the architecture of an important model system, the Cu-glyphosate-gibbsite surface complex, in which Cu serves as a probe of the local bonding environment and gibbsite serves as a representative soil mineral adsorbent. Copper K-edge extended X-ray absorption fine structure (EXAFS) spectra of Cu-glyphosate complexes in aqueous solution at pH 5.5 revealed Cu complexation by the phosphonate moiety. Introduction of microcrystalline gibbsite resulted in the loss of P from the coordination sphere of Cu and the formation of a ternary complex through chemisorption of the phosphonate group to the oxide surface. The EXAFS spectra of Cu in the Cu-glyphosate-gibbsite surface complex matched spectra for Cu-glycine and Cu-methylglycine complexes in aqueous solution, thereby providing evidence for Cu complexation by the carboxyl O and amine N. Despite the chemisorption of glyphosate to oxide surfaces via the phosphonate group, the distal end of the glyphosate molecule extends into aqueous solution where it may be biodegraded rapidly.

EXAFS study of chromated copper arsenate timber preservative in wood

Copper and arsenic K-edge X-ray absorption fine structure spectroscopy (EXAFS) of pine wood (Pinus radiata) treated with chromated copper arsenate (CCA) timber preservative have been measured. Refinement of the data is consistent with arsenate anions bound to chromium and copper ions isolated from other heavy elements, regardless of depth into the wood. This constitutes the first substantive analysis of CCA's fixation products and has a number of implications for models of fixation.

The structural role of the copper-coordinating and surface-exposed histidine residue in the blue copper protein azurin

Copper K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy and 15N NMR relaxation studies were performed on samples of a variant azurin in which the surface-exposed histidine ligand of the copper atom (His117) has been replaced by glycine. The experiments were performed to probe the structure of the active site and the protein dynamics. The cavity in the protein structure created by the His → Gly replacement could be filled by external ligands, which can either restore the spectroscopic properties of the original type-1 copper site or create a new type-2 copper site. The binding of external ligands occurs only when the copper atom is in its oxidised state. In the reduced form, the binding is abolished. From the EXAFS experiments, it is concluded that for the oxidised type-1 copper sites the protein plus external ligand (L) provide an NSS∗L donor set deriving from His46, Cys112, Met121 and the external ligand. The type-2 copper site features an S(N/O)3 donor set in which the S-donor derives from Cys112, one N-donor from His46 and the remaining two N or O donors from one or more external ligands. Upon reduction of the type-1 as well as the type-2 site, the external ligand drops out of the copper site and the coordination reduces to 3-fold with an SS∗N donor set deriving from His46, Cys112 and Met121. The Cu-Sδ(Met) distance is reduced from about 3.2 to 2.3 Å. Analysis of the NMR data shows that the hydrophobic patch around His117 has gained fluxionality when compared to wild-type azurin, which may explain why the His117Gly variant is able to accommodate a variety of external ligands of different sizes and with different chelating properties. On the other hand, the structure and dynamics of the β-sandwich, which comprises the main body of the protein, is only slightly affected by the mutation. The unusually high reduction potential of the His117Gly azurin is discussed in light of the present results.

Ex situ and in situ X-ray absorption spectroscopy: On the kinetics of precipitation formation in (Mg 1− xCu x)O

Motivated by an ex situ TEM-investigation on the internal reduction of (Mg 1− x Cu x )O [1], we have performed a XAS analysis on the precipitation formation in (Mg 1− x Cu x )O after exposing the specimen to a o 2 = 6×10 −12 for several hours. As the reduction rate is slow, a detailed characterisation of the reaction path was elaborated for absorption measurements on quenched samples. In addition, a series of spectra was recorded applying the in situ XAS technique at the copper K-edge. The changes e.g. in the XANES region correspond well to those observed on the quenched specimens.

The structure of amorphous copper sulfide precipitates: An X-ray absorption study

X-ray absorption (XAS) and X-ray photoelectron spectroscopy (XPS) analysis of copper sulfide precipitated from aqueous solution at ambient temperatures reveals the existence of a metastable primitive structure that ages to a structure with the characteristics of amorphous covellite; XAS provides direct structural information on the structure of these amorphous copper sulfides. Extended X-ray absorption fine structure (EXAFS) analysis of the primitive structure demonstrates the presence of disulfide (S 2-groups) and a Cu S interaction of 2.8Å: the latter is not found in covellite. Copper K-edge X-ray absorption near-edge structure (XANES) indicates the dominance of 3- over 4-coordinate Cu in the primitive phase, while Cu L 3-edge spectra reveal only Cu(I) to be present in all precipitates formed. XPS data confirm the presence of only Cu(I) and reveal that three types of S are present. Upon ageing, the primitive structure transforms to one with the characteristics of covellite, and this transformation involves the reordering of the S 2- and Cu 3S CuS 3-layers. Development of the primitive phase from either a wurtzite-like structure or planar Cu 3S CuS 3-layers is possible, with the structural evolution driven by the antipathy of Cu(II) for tetrahedral coordination and anomalous electron densities in the metastable structures.

SELENOETHER COMPLEXES OF COPPER(II) ‐ SYNTHESIS, SPECTROSCOPY AND STRUCTURES

Abstract The red-brown copper(II) diselenoether complexes, [Cu (L-L)2][BF4]2 (L-L = MeSeCH2CH2SeMe, MeSeCH2CH2CH2SeMe or PhSeCH2CH2SePh) have been prepared from copper(II) fluoroborate and the ligands in anhydrous dichloromethane. Some new dithioether analogues are also described. The reaction of MeSeCH2CH2SeMe and copper(II) fluoroborate in ethanol led to an unstable dark green substance which appeared to contain both copper(I) and copper(II) and was formulated [Cu(MeSeCH2CH2SeMe)2] [BF4]x. The complexes were characterised by analysis, UV-visible and e.p.r. spectroscopy, and magnetic measurements, and cyclic voltammetry has been used to probe the Cu (II)/Cu(I) redox couples. The complexes are too unstable in solution to obtain crystals for an X-ray study, but structural data has been obtained for both the Cu(II) and Cu(I) complexes by copper K-edge EXAFS studies. Ditelluroethers reduce copper(II) salts to copper(I) complexes.

Presence of a copper(I)-thiolate regulatory domain in the copper-activated transcription factor Amt1.

The Amt1 transcription factor from Candida glabrata is activated by the formation of a tetracopper-thiolate cluster. Recombinant Amt1 (residues 1-110) is isolated as a Cu,ZnAmt1 complex. Previous mapping studies [Farrell et al. (1996) Biochemistry 35, 1571-1580] revealed that the Zn(II) site is enfolded by an independent, N-terminal domain consisting of residues 1-40. One prediction from the mapping study is that the tetracopper cluster is enfolded by residues 41-110. A truncated Amt1 peptide consisting of residues 37-110 was expressed and isolated as a CuAmt1 complex with 4 mol equiv of Cu(I) bound. The bound Cu(I) ions in the truncated Amt1 complex were spectroscopically similar to Cu(I) ions bound in the 110-mer Amt1 molecule in the energies and intensities of the ultraviolet S-->Cu charge transfer transitions and luminescence. Copper K-edge extended X-ray absorption fine structure spectroscopy (EXAFS) of the truncated CuAmt1 complex revealed the same 2.26 A mean Cu-S bond distance as in the Cu,ZnAmt1 complex. A diagnostic feature of the polycopper-thiolate cluster in Cu,-ZnAmtl1 is the short 2.7 A Cu-Cu distance determined by Cu K-edge EXAFS. The truncated CuAmt1 complex had the same short 2.7 A Cu-Cu distance. The truncated CuAmt1 complex bound DNA specifically and with high affinity consistent with residues 41-110 being an independent domain stabilized by the tetracopper cluster. Thus, Amt1 consists of three independent and contiguous domains, an N-terminal Zn module (residues 1-40), an adjacent Cu regulatory domain (residues 41-110), and a C-terminal transcriptional activation domain. Cu(I) activation of Amt1 appears to consist of conversion of the 70-residue Cu regulatory domain from an inactive conformer to a structure containing the tetracopper cluster.

Polarized XAS spectroscopy of HTSC thin films

We discuss some details of polarized XAS spectroscopy of HTSC films. To illustrate the possibilities of the method, an analysis of the influence of He + irradiation on electronic and local structures both for hole-type YBa 2Cu 8O 7− x (YBCO) and electron-type Nd 1.85Ce 0.15CuO 4 (NCCO) HTSC is presented. Copper K-edge polarized EXAFS and XANES data indicate that He + ion irradiation induces radiative defects that are situated in the chains (CuONd(Ce) for NCCO and Cu(1)O(1), Cu(1)O(4)Cu(2) for YBCO) rather than in the CuO 2 (2D) plane. The data obtained point out the essential role of the ordering in the chains for 2D plane coupling both for hole-type and electron-type high temperature superconductors.

Radiative defects structure in HTSC thin films: polarized XAS study

Copper K-edge polarized EXAFS and XANES data of YBa2Cu3O6.9 and Nd1.85Ce0.15CuO4 films indicate that He+ ion irradiation induces the radiative defects that are situated in the chains: (CuONd(Ce) for Nd1.85Ce0.15CuO4 and Cu(1)O(1), Cu(1)O(4)Cu(2) for YBa2Cu3O6.9), rather than in the CuO2 (2D) plane. Static disorder with the typical displacement from primary plane site up to 0.1Åfor the O(2) environments was observed for Nd1.85Ce0.15CuO4. In addition the oxygen deficiency in O(1) sites and the disorder of apical O(4) sites were obtained for YBa2Cu3O7−x. At the same time we have not found any local changes in-plane structure after irradiation for both compounds. The data obtained point out the essential role of the ordering in the chains for 2D plane coupling both for hole-type and electron-type high temperature superconductors.

Studies on the pre-edge region of the X-ray absorption spectra of copper(I) oxide and the diamminecopper(I) ion

The distinctive pre-edge feature in the X-ray absorption spectra of copper(I) oxide and the diamminecopper(I) ion at the copper K-edge has been studied using synchrotron radiation. The relative intensities of these features, which are characteristic of copper(I) compounds, have been measured via the peak areas. The intensity of the oxide peak, with regard to the diammine and other two-coordinate copper environments, is anomalous, being reduced by ca. 60%. This is attributed to the macromolecular nature of the oxide, and the formation of intense excitons. Effects due to the small degree of non-stoichiometry may play and additional part in modifying pre-edge intensity by influencing the exciton lifetime.

An EXAFS Investigation on Copper(I-II) Related Nasicon-Type Phosphates

An extended X-ray absorption fine structure study at the copper K-edge of Nasicon-type phosphates with formulas Cu1M2(PO4)3 (M = Ti, Zr), A1-xCuIxZr2(PO4)3 (0 < x ≤ 1, A = Na; x = 0.5, A = H) and CuII0.5M2(PO4)3 (M = Ti, Zr) is reported. For Cu1Zr2(PO4)3, H0.5CuI0.5Zr2(PO4)3, and Na1-xCuIxZr2(PO4)3 (0 <: x ≤ 1) copper pairs have been evidenced (Cu1-Cu1 = 2.40 Å) in the M1 site of the Nasicon structure. In contrast, for the copper(II) phosphates, the Cu2+ ions are surrounded by four oxygen atoms at about 1.95 Å. Copper distribution in these various materials is discussed in relation to structural parameters.

Planar oxygen-centered lattice instabilities in Tl-based high- temperature superconductors

Analysis of the copper K-edge X-ray absorption finestructure on Tl 2Ba 2CuO 6, Tl 2Ba 2CaCu 2O 8, and Tl 2Ba 1.2Sr 0.8 CuO 6 indicates that the copper-equatorial oxygen local structure changes in the vicinity of the superconducting transition. These data also show that the radial distribution function for these bonds is complex with several oxygen positions relative to the copper, indicating that the local structure of the CuO 2 planes differs significantly from the average crystal structure. These results suggest the presence of polarons in these planes, whose structure changes across the superconducting transition, and are thus coupled to the hole pairing states.

Liquid-phase Cu(acac)2/ZnEt2 syngas conversion catalysts: investigations by copper and zinc K-edge EXAFS

Cu K-edge EXAFS studies on syngas conversion catalysts, generated by the reaction of Cu(acac)2(acac = acetylacetonato) with ZnEt2 at room temp., reveal the presence small Cu metal particles (ca. 10–25 A) in solution; Zn K-edge studies suggest the formation of oligomeric Zn species with oxygen present in the first coordination sphere.

X-ray absorption spectroscopy of cuprous-thiolate clusters in proteins and model systems

Cuprous-thiolate multimetallic clusters exist in a range of different biological molecules for which no structural information exists from X-ray crystallography. Spectroscopic tools such as X-ray absorption spectroscopy have provided the major structural insights into this family of biological molecules. Recent nuclear magnetic resonance data on silver-substituted metallothionein, thought to be analogous with the copper proteins, have suggested the presence of digonal coordination. In order to test this in the copper case, we have examined a series of structurally characterized cuprous-thiolate model compounds, containing different proportions of digonal and trigonal copper sites, using copper K-edge X-ray absorption spectroscopy. The edge spectra, which have been previously used as a probe for the average copper coordination environment in proteins, show little variation between the models, indicating that these are not useful as a probe of coordination environment in the case of cuprous-thiolate clusters (as opposed to isolated metal sites). We show that systematic trends in the average Cu-S bond length from EXAFS curve-fitting analysis can be used to obtain an estimate of the fraction of digonal and trigonal copper sites. This correlation is applied to a series of different proteins containing cuprous-thiolate clusters which are found to contain significant fractions of digonal copper.more » 41 refs., 7 figs., 3 tabs.« less

151 Eu Mössbauer spectroscopy and EXAFS investigation of the metal environment and oxygen deficiency in the compound Eu 1.3 Sr 1.7Cu 2O 6−δ

The incorporation of strontium and the variation of oxygen content in compounds of the type Eu 2SrCu 2O 6 can alter the cationic oxidation states and influence the conductivity of the materials. The value of δ in the semiconducting compound Eu 1.3Sr 1.7Cu 2O 6−δ has been estimated by thermogravimetric analysis as 0.35. 151Eu Mössbauer spectroscopy shows that europium is present as Eu 3+. Europium L III-edge and copper K-edge EXAFS are consistent with the ordered anionic vacancies creating a one-dimensional tunnelled oxygen sublattice and with the partial occupation by strontium of some of the lanthanide sites.

Multinuclearity of aqueous copper and zinc bisulfide complexes: An EXAFS investigation

Copper and zinc bisulfide complexes in NaHS solutions were investigated by Extended X-ray Absorption Fine-Structure spectroscopy (EXAFS). A goal was to investigate the possibility that bisulfide complexes are multinuclear. Copper and zinc K-edge absorption spectra were recorded in fluorescence mode at room temperature and at 80 K. Lowering temperature improved signal to noise ratios, but did not significantly change measured metal-sulfur distances or coordination numbers. In equilibrium with S-absent assemblages in the Cu-S system, dissolved copper consisted of colorless Cu(I) species having Cu-S interatomic distances of 2.30-2.33 Å (coord. no. 3 ± 1 ). Second shell Cu atoms were present at 2.72-2.75 Å ( coord. no. 1.1). The presence of second shell Cu atoms, which was confirmed by duplicate experiments using different starting materials, demonstrates that the predominant complexes in these solutions are multinuclear. The Cu-Cu distance is shorter than in most known Cu-S cluster complexes and Cu-S minerals, but is in good agreement with known Cu-Cu distances in Cu 4(RS) 2− 6 clusters. In equilibrium with a CuS + S assemblage, shorter Cu-S distances and no evidence of an ordered second shell were observed. In these polysulfide-rich solutions, different Cu complexes apparently predominate. Solutions saturated with sphalerite or amorphous ZnS precipitate yielded Zn-S and Zn-Zn distances similar to those in solid sphalerite, although the Zn-Zn coordination number was lower and second shell S was also present. In the Zn case, but not the Cu case, it is possible that the species being characterized by EXAFS were <200 Å particles not in reversible equilibrium with the solution phase. EXAFS is a promising tool for determining molecular structures of complexes of geochemical interest, but at present its application is limited to solutions containing somewhat more than 1 mM of the target element.

In situ x-ray absorption spectroscopy study of underpotential deposition of copper on platinum (100)

X-Ray absorption spectroscopy (XAS) spectra have been recorded for the electrochemical adsorption of Cu on Pt(100) in the fluorescence detection mode at grazing incidence, with polarization parallel to the surface. During data collection, the Pt(100) surface was under potentiostatic control in a 10 −4 M Cu 2+ electrolytic solution, in order to maintain a monolayer coverage. The near-edge structure of the copper K-edge resembles that of Cu +. The Fourier transform of the EXAFS spectra shows a first peak at 0.15 nm, and a broad unresolved peak with maximum at 0.30 and a shoulder at 0.37 nm. The first single peak is associated with oxygen neighbours at 0.197 nm. The unresolved peak is built up from contributions of copper first and second neighbours. The distance of first copper neighbours is 0.309 nm, and that of second copper neighbours is 0.393 nm, equal to the substrate lattice parameter (0.3929 nm). This suggests that a first copper adlayer of half monolayer density is in registry with the platinum unreconstructed (100) surface net. A second copper adlayer of the same density lies over the first adlayer, at a distance of 0.135 nm. The copper atoms in this second layer are in the fourfold geometry with respect to the underlying copper half-monolayer. These layers form a c(2x2) periodicity on the Pt (100) substrate. The copper—oxygen distance is about half the second copper—copper distance. The sharing of oxygen between the two copper adlayers is unclear.

A study of the chemical shift of the x-ray absorption K-edge of copper in some Cu(II) systems

We have recorded X-ray absorption K-edge spectra of Cu in some copper (II) compounds (NH 4) 2SO 4·CuSO 4·6H 2O, CuCl 2·2H 2O, CuSO 4·5H 2O,CuO, Cu(OH) 2, La 2CuO 4, CuWO 4 and CuCO 3·Cu(OH) 2, including pure copper metal using a Cauchois-type bent-crystal X-ray spectrograph. We have also measured the X-ray absorption chemical shift, Δ E, in each of the above Cu(II) compounds and have correlated the chemical-shift, Δ E, with its two governing factors the effective charge, q, and the bond length, R, on the basis of the least-squares regression analysis. The same correlation has been used to determine the bond lengths in some other Cu(II) compounds. The values of the bond length so obtained agree fairly well with those of their crystallographic values.