Structural reconstruction of the catalytic center of LiPDF through multiple scattering calculation with MXAN

Abstract Peptide deformylase (PDF, EC 3.5.1.27) is essential for the normal growth of eubacterium but not for mammalians. Recently, PDF has been studied as a target for new antibiotics. In this paper, X-ray absorption spectroscopy was employed to determine the local structure around the zinc ion of PDF from Leptospira Interrogans in dry powder, because it is very difficult to obtain the crystallized sample of Li PDF. We performed X-ray absorption near edge structure (XANES) calculation and reconstructed successfully the local geometry of the active center, and the results from calculations show that a water molecule (Wat1) has moved towards the zinc ion and lies in the distance range to coordinate with the zinc ion weakly. In addition, the sensitivity of theoretical spectra to the different ligand bodies was evaluated in terms of goodness-of-fit

Quantum critical point in SmO1−xFxFeAs and oxygen vacancy induced by high fluorine dopant

The local lattice and electronic structure of the high-T(c) superconductor SmO(1-x)F(x)FeAs as a function of F-doping have been investigated by Sm L(3)-edge X-ray absorption near-edge structure and multiple-scattering calculations. Experiments performed at the L(3)-edge show that the white line (WL) is very sensitive to F-doping. In the under-doped region (x ≤ 0.12) the WL intensity increases with doping and then it suddenly starts decreasing at x = 0.15. Meanwhile, the trend of the WL linewidth versus F-doping levels is just contrary to that of the intensity. The phenomenon is almost coincident with the quantum critical point occurring in SmO(1-x)F(x)FeAs at x ≃ 0.14. In the under-doped region the increase of the intensity is related to the localization of Sm-5d states, while theoretical calculations show that both the decreasing intensity and the consequent broadening of linewidth at high F-doping are associated with the content and distribution of oxygen vacancies

Investigation of zinc-containing peptide deformylase from Leptospira interrogans by X-ray absorption near-edge spectroscopy

Peptide deformylase (PDF, EC 3.5.1.27) is essential for the normal growth of eubacterium but not for mammalians. Recently, PDF has been studied as a target for new antibiotics. Its activity is strongly dependent on the bound metal ion. The crystallographic studies did not show any significant structural difference upon various bound metal ions. In this paper, X-ray absorption spectroscopy was employed to determine the local structure around the zinc ion of PDF from Leptospira interrogans in dry powder. XANES (X-ray absorption near-edge structure) calculations were performed and the local geometry of the active center was reconstructed successfully. By comparing with the crystal structure of an enzyme-product complex, the results from calculations show that a water molecule has moved towards the zinc ion and lies in the distance range to coordinate with the zinc ion weakly

Quantitative investigation of two metallohydrolases by X-ray absorption spectroscopy near-edge spectroscopy

The last several years have witnessed a tremendous increase in biological applications using X-ray absorption spectroscopy (BioXAS), thanks to continuous advancements in synchrotron radiation (SR) sources and detector technology. However, XAS applications in many biological systems have been limited by the intrinsic limitations of the Extended X-ray Absorption Fine Structure (EXAFS) technique e.g., the lack of sensitivity to bond angles. As a consequence, the application of the X-ray absorption near-edge structure (XANES) spectroscopy changed this scenario that is now continuously changing with the introduction of the first quantitative XANES packages such as Minut XANES (MXAN). Here we present and discuss the XANES code MXAN, a novel XANES-fitting package that allows a quantitative analysis of experimental data applied to Zn K-edge spectra of two metalloproteins: Leptospira interrogans Peptide deformylase (LiPDF) and acutolysin-C, a representative of snake venom metalloproteinases (SVMPs) from Agkistrodon acutus venom. The analysis on these two metallohydrolases reveals that proteolytic activities are correlated to subtle conformation changes around the zinc ion. In particular, this quantitative study clarifies the occurrence of the LiPDF catalytic mechanism via a two-water-molecules model, whereas in the acutolysin-C we have observed a different proteolytic activity correlated to structural changes around the zinc ion induced by pH variations

Quantitative local structure determination in mica crystals: ab initio simulations of polarization XANES at the potassium K-edge.

An attempt to refine the local structure of a layered structure such as mica is made by combining angle-resolved XANES (AXANES) and single-crystal X-ray diffraction (SC-XRD) experiments. Ab initio calculations of AXANES spectra of several tri-octahedral micas have been used to further interpolate experimental data and to deduce physico/chemical effects. Structural distortions have been found highly correlated with the compositional disordering that arises from electronic interactions between anions and cations, and extend the interlayer entering deep into nearby tetrahedral and octahedral sheets. Multiple occupations at the same atomic site have been investigated in detail both in the parallel and perpendicular components of AXANES spectra. Finally, the best fit obtained, computed in the framework of the multiple-scattering theory, is presented and the limitations of the muffin-tin potential in layered systems are briefly discussed

Charge redistribution and local lattice structure of (F, Zn)-codoped LaFeAsO superconductor

To understand the abnormal behavior of the superconducting transition temperature (T-c) because of the presence of a non-magnetic Zn impurity in the (F, Zn)-codoped LaFeAsO system (Li et al 2010 New J. Phys. 12 083008), we investigated its unique electronic and local structures via x-ray absorption spectroscopy and first-principles calculations. The data obtained showed that the presence of a Zn impurity induces an electron transfer from As to Fe atoms in both the F-underdoped and -overdoped regions. Moreover, due to the lattice mismatch, the local lattice structure is finely modulated by both F and Zn impurities. Actually, in the F-underdoped region doping by Zn is associated with regular FeAs4 tetrahedra, while distorted FeAs4 tetrahedra occur in the F-overdoped region where superconductivity is significantly suppressed

Correlation between local vibrations and metal mass in AlB2-type transition-metal diborides

Lattice vibrations have been investigated in TiB2, ZrB2 and HfB2 by temperature-dependent extended X-ray absorption fine structure (EXAFS) experiments. Data clearly show that the EXAFS oscillations are characterized by an anomalous behavior of the Debye-Waller factor of the transition-metal-boron pair, which is suggested to be associated with a superposition of an optical mode corresponding to phonon vibrations induced by the B sublattice and an acoustic mode corresponding to the transition-metal (TM) sublattice. Data can be interpreted as a decoupling of the metal and boron vibrations observed in these transition-metal diborides (TMB2), a mechanism that may be responsible for the significant reduction of the superconducting transition temperature observed in these systems with respect to the parent MgB2 compound. The vibrational behavior of TM-TM bonds has also been investigated to study the occurrence of anisotropy and anomalies in the lattice vibrational behavior of TM-TM bonds

Synthesis and characterization of Zn₁₋ₓMnₓO nanowires

©2008 American Institute of Physics. The electronic version of this article is the complete one and can be found online at: http://link.aip.org/link/?APPLAB/92/162102/1DOI:10.1063/1.2905274Mn doped ZnO nanowires (NWs) were fabricated by a one-step vapor-solid process at 500°C. The doped Mn exists in the wurtzite lattice as substitutional atom without forming secondary phases. X-ray absorption near-edge structure reveals that the doped Mn atoms occupy the Zn sites, and they lead to an expansion in lattice constants. The I-V characteristic of a single Zn₁₋ₓMnₓO NW shows a typical Ohmic contact with gold electrodes. The as-received NWs could be suitable for studying spintronics in one-dimensional diluted magnetic semiconductors