Density functional theory calculations of UO2 oxidation: evolution of UO(2+x), U4O(9-y), U3O7, and U3O8.

Formation of hyperstoichiometric uranium dioxide, UO2+x, derived from the fluorite structure was investigated by means of density functional theory (DFT) calculations. Oxidation was modeled by adding oxygen atoms to UO2 fluorite supercells. For each compound ab initio molecular dynamics simulations were performed to allow the ions to optimize their local geometry. A similar approach was used for studying the reduction of U3O8. In agreement with the experimental phase diagram we identify stable line compounds at the U4O9-y and U3O7 stoichiometries. Although the transition from fluorite to the layered U3O8 structure occurs at U3O7 (UO2.333) or U3O7.333 (UO2.444), our calculated low temperature phase diagram indicates that the fluorite derived compounds are favored up to UO2.5, that is, as long as the charge-compensation for adding oxygen atoms occurs via formation of U(5+) ions, after which the U3O8-y phase becomes more stable. The most stable fluorite UO2+x phases at low temperature (0 K) are based on ordering of split quad-interstitial oxygen clusters. Most existing crystallographic models of U4O9 and U3O7, however, apply the cuboctahedral cluster. To better understand these discrepancies, the new structural models are analyzed in terms of existing neutron diffraction data. DFT calculations were also performed on the experimental cuboctahedral based U4O9-y structure, which enable comparisons between the properties of this phase with the quad-interstitial ones in detail.

Stability and migration of large oxygen clusters in UO(2+x): density functional theory calculations.

Using ab initio molecular dynamics simulations and nudged elastic band calculations we examine the finite temperature stability, transition pathways, and migration mechanisms of large oxygen clusters in UO(2+x). Here we specifically consider the recently proposed split quad-interstitial and cuboctahedral oxygen clusters. It is shown that isolated cuboctahedral clusters may transform into more stable configurations that are closely linked to the split quad-interstitial. The split quad-interstitial is stable with respect to single interstitials occupying the empty octahedral holes of the UO(2) lattice. In order to better understand discrepancies between theory and experiments, the simulated atomic pair distribution functions for the split quad-interstitial structures are analyzed with respect to the distribution function for U(4)O(9) previously obtained from neutron diffraction data. Our nudged elastic band calculations suggest that the split quad-interstitial may migrate by translating one of its constituent di-interstitial clusters via a barrier that is lower than the corresponding barrier for individual interstitials, but higher than the barrier for the most stable di-interstitial cluster.

The Axial Oxygen Atom and Superconductivity in YBa2Cu3O7.

Changes in the copper K-edge x-ray absorption spectrum of YBa(2)Cu(3)O(7) across the critical temperature indicate that, accompanying the superconducting transition, the mean square relative displacement of some fraction of the Cu2-O4 bonds becomes smaller or more harmonic (or both), that there may be a slight increase in the associated Cul-O4 distance, and that electronic states involving these atom pairs become more atomic-like. If there is an association between the superconductivity and this lattice instability, then the bridging axial oxygen is of central importnce in determining the high tranition temperature of YBa(2)Cu(3)O(7). Because this structural perturbation will affect the dynamic polrizability of the copper oxygen sublattice, it is consistent with an excitonic pairing mhanism in these materials.

Axial oxygen-centered lattice instabilities and high-temperature superconductivity.

Copper K-edge x-ray absorption data indicate that an axial oxygen-centered lattice instability accompanying the 93 K superconducting transition in YBa(2)Cu(3)O(7) is of a pseudo-(anti)ferroelectric type, in that it appears to involve the softening of a double potential well into a structure in which the difference between the two copper-oxygen distances and the barrier height have both decreased. This softer structure is present only at temperatures within a fluctuation region around the transition. A similar process involving the analogous axial oxygen atom also accompanies the superconducting transition in T1Ba(2)Ca(3)Cu(4)O(11), where the superconducting transition temperature T(c) is ~120 K. The mean square relative displacement of this oxygen atom in YBa(2)Cu(3)O(7) is also specifically affected by a reduction in the oxygen content and by the substitution of cobalt for copper, providing further evidence for the sensitivity of the displacement to additional factors that also influence the superconductivity. On the basis of the implied coupling of this ionic motion to the superconductivity, a scenario for high-temperature superconductivity is presented in which both phonon and electronic (charge transfer) channels are synergistically involved.

High-Temperature XAS Study of Fe2SiO4 Liquid: Reduced Coordination of Ferrous Iron.

X-ray absorption spectroscopy (XAS) of Fe(2+) in Fe(2)SiO(4) liquid at 1575 kelvin and 10(-4) gigapascal (1 bar) shows that the Fe(2+) -O bond length is 1.98 +/- 0.02 angstroms compared with approximately 2.22 angstroms in crystalline Fe(2)SiO(4) (fayalite) at the melting point (1478 kelvin), which indicates a decrease in average Fe(2+) coordination number from six in fayalite to four in the liquid. Anharmonicity in the liquid was accounted for using a data analysis procedure. This reduction in coordination number is similar to that observed on the melting of certain ionic salts. These results are used to develop a model of the medium-range structural environment of Fe(2+) in olivine-composition melts, which helps explain some of the properties of Fe(2)SiO(4) liquid, including density, viscosity, and the partitioning of iron and nickel between silicate melts and crystalline olivines. Some of the implications of this model for silicate melts in the Earth's crust and mantle are discussed.

Human nucleotide excision repair protein XPA: extended X-ray absorption fine-structure evidence for a metal-binding domain.

The ubiquitous, multi-enzyme, nucleotide excision repair (NER) pathway is responsible for correcting a wide range of chemically and structurally distinct DNA lesions in the eukaryotic genome. Human XPA, a 31 kDa, zinc-associated protein, is thought to play a major NER role in the recognition of damaged DNA and the recruitment of other proteins, including RPA, ERCC1, and TFIIH, to repair the damage. Sequence analyses and genetic evidence suggest that zinc is associated with a C4-type motif, C105-X2-C108-X17-C126-X2-C129, located in the minimal DNA binding region of XPA (M98-F219). The zinc-associated motif is essential for damaged DNA recognition. Extended X-ray absorption fine structure (EXAFS) spectra collected on the zinc associated minimal DNA-binding domain of XPA (ZnXPA-MBD) show directly, for the first time, that the zinc is coordinated to the sulfur atoms of four cysteine residues with an average Zn-S bond length of 2.34+/-0.01 A. XPA-MBD was also expressed in minimal medium supplemented with cobalt nitrate to yield a blue-colored protein that was primarily (>95%) cobalt associated (CoXPA-MBD). EXAFS spectra collected on CoXPA-MBD show that the cobalt is also coordinated to the sulfur atoms of four cysteine residues with an average Co-S bond length of 2.33+/-0.02 A.

Local structure fluctuations as a signature of an inhomogeneous ground state in high-Tc superconductors.

In-plane polarized Cu K-edge XAFS on La2CuO4.1 is presented, which indicates a radial in-plane Cu-O distribution function that is not a single Gaussian. Fits to the isolated Cu-O XAFS signal show the presence of a two-site radial distribution function, similar to that found in other La-based cuprate superconductors at temperatures below the temperature associated with the pseudogap appearance, T*. The appearance of the two-site distribution is interpreted as evidence of a non-homogeneous ground state, preceding the superconducting transition. Similar results found in other copper-oxide superconductors indicate that this non-homogeneous ground state is a general feature of these materials.

Fluorine-19 chemical shifts as probes of the structure and reactivity of the iron-molybdenum cofactor of nitrogenase.

The reaction of the iron-molybdenum cofactor with thiolate and the redox behavior of the iron-molybdenum cofactor-thiolate complex have been studied by 19F NMR using p-CF3C6H4S- as the reporter ligand. These experiments give results different from those produced by other methods which have been performed near 4 K rather than at ambient temperature. Specifically, these data show that the iron-molybdenum cofactor-thiolate complex is not the product of an irreversible reaction. Rather, the complex is in dynamic equilibrium with the free iron-molybdenum cofactor and free thiolate. Models of the reactions of nitrogenase may need to take this temperature-dependent difference into account because the lability of the iron-molybdenum thiolate bond means its making and breaking could be involved in substrate binding or reduction. The 19F NMR results reported here also show that the S = 3/2 state of the iron-molybdenum cofactor-thiolate complex can be easily and reversibly oxidized by one electron. However, electron exchange between the oxidized and reduced states of the complex is quite slow at approximately 1 mM. Based on low temperature spectroscopic studies, the oxidized iron-molybdenum cofactor-thiolate complex was expected to be diamagnetic. Isotropically shifted NMR spectra of the oxidized cofactor samples at 240-320 K, however, indicate at least partial population of a paramagnetic state, possibly with S = 1.

Selenol binds to iron in nitrogenase iron-molybdenum cofactor: an extended x-ray absorption fine structure study.

The biological N2-fixation reaction is catalyzed by the enzyme nitrogenase. The metal cluster active site of this enzyme, the iron-molybdenum cofactor (FeMoco), can be studied either while bound within the MoFe protein component of nitrogenase or after it has been extracted into N-methylformamide. The two species are similar but not identical. For example, the addition of thiophenol or selenophenol to isolated FeMoco causes its rather broad S = 3/2 electron paramagnetic resonance signal to sharpen and more closely approach the signal exhibited by protein-bound FeMoco. The nature of this thiol/selenol binding site has been investigated by using Se-K edge extended x-ray absorption fine structure (EXAFS) to study selenophenol ligated to FeMoco, and the results are reported here. EXAFS data analysis at the ligand Se-K edge was performed with a set of software, GNXAS, that provides for direct calculation of the theoretical EXAFS signals and least-squares fits to the experimental data. Data analysis results show definitively that the selenol (and by inference thiol) binds to Fe at a distance of 2.4 A. In contrast, unacceptable fits are obtained with either Mo or S as the liganded atom (instead of Fe). These results provide quantitative details about an exchangeable thiol/selenol binding site on FeMoco in its isolated, solution state and establish an Fe atom as the site of this reaction. Furthermore, the utility of ligand-based EXAFS as a probe of coordination in polynuclear metal clusters is demonstrated.

Cyanide and methylisocyanide binding to the isolated iron-molybdenum cofactor of nitrogenase.

19F NMR and x-ray absorption experiments have been performed with both the isolated FeMo cofactor and the MoFe protein of nitrogenase in search of direct evidence for substrate or inhibitor binding. Using 19F NMR as a probe and p-CF3C6H4S- as the receptor ligand, the data show that the nitrogenase inhibitors CN- and CH3NC bind to the isolated FeMo cofactor-RFS- complex in N-methylformamide with a finite formation constant. Their binding increases the electronic relaxation time of the complex and increases the life-time of the FeMo cofactor-p-CF3C6H4S- bond, Parallel molybdenum K edge and extended x-ray absorption fine structure experiments show that CH3NC does not bind to molybdenum. Although CO and N3- both relieve CN- and CH3NC inhibition of electron flow through nitrogenase, unlike the latter, they do not appear to bind to isolated FeMo cofactor. In experiments with the dithionite-reduced MoFe protein, we did not detect any changes in the molybdenum K edge or extended x-ray absorption fine structure spectra upon addition of CO, N2, C2H2, NaCN, CH3NC, or azide demonstrating that either these substrates and inhibitors do not bind to molybdenum or that the FeMo cofactor site of nitrogenase is inaccessible to substrate binding except under turnover conditions.