A rapid, exact curved-wave theory for EXAFS calculations

Gurman, S. J.; Binsted, Norman; Ross, I. N.

doi:10.1088/0022-3719/17/1/019

Cited by 689 publications

(366 citation statements)

References 9 publications

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“…Details of the EXAFS data analysis performed using the program Viper, 23 and of the EXAFS fitting performed using the modular package DL_EXCURV, based on the EXCURV98 code, [24][25][26][27][28] are reported in the ESI.…”

Section: Experimental Synthesismentioning

confidence: 99%

Cation distribution and vacancies in nickel cobaltite

Loche

Marras

Carta

et al. 2017

Phys. Chem. Chem. Phys.

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Samples of nickel cobaltite, a mixed oxide occurring in the spinel structure which is currently extensively investigated because of its prospective application as ferromagnetic, electrocatalytic, and cost-effective energy storage material were prepared in the form of nanocrystals stabilized in a highly porous silica aerogel and as unsupported nanoparticles.Nickel cobaltite nanocrystals with average size 4 nm are successfully grown for the first time into the silica aerogel provided that a controlled oxidation of the metal precursor phases is carried out, consisting in a reduction under H2 flow followed by mild oxidation in air. The investigation of the average oxidation state of the cations and of their distribution between the sites within the spinel structure, which is commonly described assuming the Ni cations are 2 only located in the octahedral sites, has been carried out by X-ray Absorption Spectroscopy providing evidence for the first time that the unsupported nickel cobaltite sample has a Ni:Co molar ratio higher than the nominal ratio of 1:2 and a larger than expected average overall oxidation state of the cobalt and nickel cations. This is achieved retaining the spinel structure, which accommodates vacancies to counterbalance the variation in oxidation state.3

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Section: Experimental Synthesismentioning

confidence: 99%

Cation distribution and vacancies in nickel cobaltite

Loche

Marras

Carta

et al. 2017

Phys. Chem. Chem. Phys.

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“…XAS Data Analysis-Standard EXAFS analysis was performed using the EXPROG software package (developed by C. Hermes and H. F. Nolting at the European Molecular Biology Laboratory-Outstation/ Hamburg, Germany) to process the raw data and EXCURV98 (developed by N. Binsted, S. W. Cambell, S. J. Gurman, and P. Stepherson at Science and Engineering Research Council, Daresbury, UK) using exact curve wave scattering theory (19,20) to analyze the spectra. The energy range was set to 30 -650 eV above the edge.…”

Section: X-ray Absorption Spectroscopymentioning

confidence: 99%

Coordination Geometries of Metal Ions in D- or L-Captopril-inhibited Metallo-β-lactamases

Heinz

Bauer²,

Wommer

et al. 2003

Journal of Biological Chemistry

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D-and L-captopril are competitive inhibitors of metallo-␤-lactamases. For the enzymes from Bacillus cereus (BcII) and Aeromonas hydrophila (CphA), we found that the mononuclear enzymes are the favored targets for inhibition. By combining results from extended x-ray absorption fine structure, perturbed angular correlation of ␥-rays spectroscopy, and a study of metal ion binding, we derived that for Cd(II) 1 -BcII, the thiolate sulfur of D-captopril binds to the metal ion located at the site defined by three histidine ligand residues. This is also the case for the inhibited Co(II) 1 and Co(II) 2 enzymes as observed by UV-visible spectroscopy. Although the single metal ion in Cd(II) 1 -BcII is distributed between both available binding sites in both the uninhibited and the inhibited enzyme, Cd(II) 1 -CphA shows only one defined ligand geometry with the thiolate sulfur coordinating to the metal ion in the site composed of 1 Cys, 1 His, and 1 Asp. CphA shows a strong preference for D-captopril, which is also reflected in a very rigid structure of the complex as determined by perturbed angular correlation spectroscopy. For BcII and CphA, which are representatives of the metallo-␤-lactamase subclasses B1 and B2, we find two different inhibitor binding modes.Metallo-␤-lactamases confer antibiotic resistance to bacteria by catalyzing the hydrolysis of ␤-lactam antibiotics, including carbapenems. This relatively new form of resistance is spreading and thereby escaping the effective inhibitors developed to fight the better known serine-␤-lactamases. For all metallo-␤-lactamases investigated, structurally similar enzyme active sites comprising two zinc binding sites are reported. For Bacillus cereus metallo-␤-lactamase (BcII), 1 one metal-binding site contains three His (H-site); the other one contains 1 Asp, 1 Cys, and 1 His as the metal ligating residues (DCH site) as derived from x-ray crystallography (1). For CphA, 1 His from the H-site (His-116) is supposed to be replaced by an Asn (2). Various thiol-carboxylate compounds were identified as potent inhibitors (3). The active site binding of thiomandelic acid to BcII was studied by NMR spectroscopy (4), whereas the binding of 2-[5-(1-tetrazolylmethyl)thien-3-yl]-N-[2-(mercaptomethyl)-4-(phenylbutrylglycine)] to the enzyme from Pseudomonas aeruginosa (IMP-1) was characterized by x-ray crystallography (5). With both approaches, the inhibited binuclear zinc enzymes were studied. Both studies agree in a bridging role of the metal-bound sulfur of the inhibitor, whereas the carboxylate group of the inhibitors binds to an accessible amino acid, thus stabilizing the complex. Other known inhibitory compounds are 2,3-(S,S)-disubstituted succinic acids for IMP-1 (6) or moxalactam and cefoxitin for CphA (7). The latter compounds lead to irreversible inactivation of the enzyme by the hydrolyzed reaction products.The structural investigation of D-and L-captopril binding presented here is based on results obtained from enzyme kinetic and thermodynamic studies. Captopril is known as an ...

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“…Model ¢tting was carried out with EXCURV90 using curved-wave theory and ab initio phase shift [29], with the edge positions being determined from the ¢rst in£ection points of the derivative spectra. The phase shifts experienced by the photoelectron, the amplitude of the backscattering and the electron mean free path were calculated from within EX-CURV90 using spherical wave theory and a single scattering model.…”

Section: Exafs Data Analysismentioning

confidence: 99%

“…The model compounds zinc sulphide (Zn-S 4 2.35 A î ) [30], zinc formate dihydrate (Zn-O 6 2.107 A î , averaged) [31] and zinc tetraphenylporphyrin (Zn-N 4 2.037 A î , averaged) [32] were used to check the validity of the ab initio phase shifts and amplitudes for sulphur, oxygen and nitrogen backscatterers respectively, and to establish the general parameters, AFAC (proportion of absorption causing EXAFS) and VPI (allows for inelastic scattering of the photoelectron) [29]. During least-squares ¢tting it is important to avoid correlation e¡ects between those parameters which strongly a¡ect the EXAFS amplitude and between those that in£uence the frequency of the EXAFS oscillations.…”

Section: Exafs Data Analysismentioning

confidence: 99%

EXAFS study of zinc coordination in bacitracin A

Drabløs

Nicholson

Rønning

1999

Biochimica et Biophysica Acta (BBA) - Protein Structure and Mol

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Bacitracin is a dodecapeptide antibiotic produced by Bacillus sp. The antibacterial activity depends upon the peptide binding a divalent metal. Hitherto, the exact coordination of the cation has not been established. In particular the role played by the sulphur and nitrogen atoms of the thiazoline ring of bacitracin A has not been clear. Here the coordination of Zn 2 by bacitracin A has been studied using extended X-ray absorption fine structure. The experimental data are consistent with a model in which zinc is coordinated by one oxygen and three nitrogen atoms with the sulphur atom of the thiazoline ring not being directly involved in the zinc coordination. ß

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A rapid, exact curved-wave theory for EXAFS calculations

Cited by 689 publications

References 9 publications

Cation distribution and vacancies in nickel cobaltite

Cation distribution and vacancies in nickel cobaltite

Coordination Geometries of Metal Ions in D- or L-Captopril-inhibited Metallo-β-lactamases

EXAFS study of zinc coordination in bacitracin A

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