S. Della Longa

The MXAN procedure: a new method for analysing the XANES spectra of metallo­proteins to obtain structural quantitative information

The first quantitative analyses are reported of the Fe K-edge polarized X-ray absorption near-edge structure (XANES) of a single crystal of the iron protein carbonmonoxy-myoglobin (MbCO) and of its cryogenic photoproduct Mb*CO. The CO-Fe-heme local structure has been determined using a novel fitting procedure, named MXAN, which is able to fit the XANES part (from the edge to about 200 eV) of experimental X-ray absorption data. This method is based on the comparison between the experimental spectrum and several theoretical spectra that are generated by changing the relevant geometrical parameters of the site around the absorbing atom. The theoretical spectra are derived in the framework of the full multiple-scattering approach. The MXAN procedure is able to recover information about the symmetry and atomic distances, and the solution is found to be independent of the starting conditions. The extracted local structure of Mb*CO includes an Fe-CO distance of 3.08 (7) A, with a tilting angle between the heme normal and the Fe-C vector of 37 (7) degrees and a bending angle between the Fe-C vector and the C-O bond of 31 (5) degrees

X-ray absorption spectroscopy: state-of-the-art analysis.

State-of-the-art techniques for analysing X-ray absorption spectra are reviewed, with an eye to biological applications. Recent attempts to perform full spectral fitting of the XANES energy region and beyond for the purpose of structural analysis have met with encouraging success. The present paper analyses the theoretical motivations behind this success and indicates routes for future improvements. The theoretical background is not entirely new, although the point of view is, and some sections and appendices present material that the Authors believe has never been published before. The aim of this paper is to provide a theoretical analysis that is as self-contained as possible.

MXAN : a new software procedure to perform geometrical fitting of experimental XANES spectra

A new software procedure, MXAN, to fit experimental XANES spectra is presented here. The method is based on the comparison between the experimental spectrum and several theoretical calculations generated by changing the relevant geometrical parameter of the site around the absorbing atom. The x-ray photoabsorption cross section is calculated using the general multiple-scattering scheme, utilizing a complex Hedin-Lunqvist energy-dependent potential to describe the exchange correlation interaction. Our method has been applied to the study of geometrical environment of the tetrahedral zinc site of the protein superoxide dismutase (SOD). The experimental Zn K-edge XANES spectrum has been fitted in the space of the first shell coordination parameters (ligand distances and angles) following the behavior of the chi-square as a function of the local distortion from the starting crystallographic structure. The recovered structure is found to be independent on the starting conditions, showing the theoretical uniqueness of the structural solution. Strengths and limitations of the application to real systems are also discussed.

The Measurement of the Polaron Size in the Metallic Phase of Cuprate Superconductors

The statistical distribution of the Cu site conformations in the CuO2 plane of Bi2Sr2CaCu2O8+y (Bi 2212) has been measured by a fast and local probe Cu K-edge extended x-ray absorption fine structure (EXAFS) as a function of temperature. The Cu site conformations are frozen at T < T* = 120 K ~ 1.4 Tc in two well-defined conformations characterized by two Cu-O(apical) bond lengths separated by 0.17 ± 0.02 A. The Cu site conformations with short bond 2.38 ± 0.02 A have a probability of 41 ± 2% at T < T*. The diffraction experiments show that the Cu site conformations exhibit a one-dimensional anharmonic modulation, with period λp = 25 A, that has been measured by electron diffraction. These data show that the modulation is anharmonic and the plane is decorated with stripes of distorted lattice characterized by the short Cu-O(apical) bonds of width W = 11 ± 1 A at T < T* that form domain walls for the stripes of width L ~ 14 ± 1 A, characterized by the long Cu-O(apical) bond. The stripes of distorted lattice run below the lines of interstitial oxygen ions in the BiO plane, playing the role of acceptors. The lattice modulation is therefore assigned to polaronic impurity states ordered in linear arrays. The measure of the width W of the stripes provides the measure of the area of the polarons Sp ~ 4a2 (a = 5.4 A) where each hole dressed by the lattice distortion spans a domain of 8 Cu sites.

Atomic and electronic structure probed by X-ray absorption spectroscopy : full multiple scattering analysis with the G4XANES package

Abstract G4XANES, a software package calculating X-ray Absorption Near Edge Structure (XANES) spectra in the frame of the one-electron full multiple scattering formalism, is presented. The G4XANES package performs one-electron K,L-XANES “ab initio” simulations on different kinds of compounds (small molecules, crystals, free clusters, metal sites in biological compounds) by using a minimal set of input data. Polarized spectra as a function of the size of the scattering cluster are calculated, allowing to extract information on both the electronic and atomic structure around the selected absorbing atom. Recently reported spin-dependent XANES spectra have been also successfully treated. A description of the package, as well as its applications for such important classes of materials as high temperature superconductors, magnetic materials and metalloproteins, are presented.

Redox-Induced Structural Dynamics of Fe-Heme Ligand in Myoglobin by X-Ray Absorption Spectroscopy

The Fe(III) --> Fe(II) reduction of the heme iron in aquomet-myoglobin, induced by x-rays at cryogenics temperatures, produces a thermally trapped nonequilibrium state in which a water molecule is still bound to the iron. Water dissociates at T > 160 K, when the protein can relax toward its new equilibrium, deoxy form. Synchrotron radiation x-ray absorption spectroscopy provides information on both the redox state and the Fe-heme structure. Owing to the development of a novel method to analyze the low-energy region of x-ray absorption spectroscopy, we obtain structural pictures of this photo-inducible, irreversible process, with 0.02-0.06-A accuracy, on the protein in solution as well as in crystal. After photo-reduction, the iron-proximal histidine bond is shortened by 0.15 A, a reinforcement that should destabilize the iron in-plane position favoring water dissociation. Moreover, we are able to get the distance of the water molecule even after dissociation from the iron, with a 0.16-A statistical error.

Relevant role of hydrogen atoms in the XANES of Pd hydride: Evidence of hydrogen induced unoccupied states

Abstract The multiple-scattering analysis of the Pd L3 XANES (X-ray absorption near edge structure) of PdH0.6 has been carried out. The multiple scattering calculations have been carried out for PdH. The results show that hydrogen atoms have a relevant scattering amplitude for the photoelectron in the XANES energy range. The hydrogen atoms within a cluster of 57 neighbor atoms around the central Pd ion give origin to the hydrogen induced spectral feature observed at ∼ 6 eV above the white line. The orbital angular momentum of the Pd partial density of states contributing to this H induced unoccupied density of states is obtained.

Fe-Heme Conformations in Ferric Myoglobin

X-ray absorption near-edge structure (XANES) spectra of ferric myoglobin from horse heart have been acquired as a function of pH (between 5.3 and 11.3). At pH = 11.3 temperature-dependent spectra (between 20 and 293 K) have been collected as well. Experimental data solve three main conformations of the Fe-heme: the first, at low pH, is related to high-spin aquomet-myoglobin (Mb+OH2). The other two, at pH 11.3, are related to hydroxymet-myoglobin (Mb+OH-), and are in thermal equilibrium, corresponding to high- and low-spin Mb+OH-. The structure of the three Fe-heme conformations has been assigned according to spin-resolved multiple scattering simulations and fitting of the XANES data. The chemical transition between Mb+OH2 and high-spin Mb+OH-, and the spin transition of Mb+OH-, are accompanied by changes of the Fe coordination sphere due to its movement toward the heme plane, coupled to an increase of the axial asymmetry.

EXPERIMENTAL EVIDENCE OF ITINERANT Cu 3d9 - OXYGEN HOLE MANY BODY CONFIGURATION IN THE HIGH-TC SUPERCONDUCTOR YBa2Cu3O~7

Cu L3 x-ray absorption near edge structure (XANES) and Cu L3 x-ray photoelectron spectroscopy (XPS) of YBa2Cu3O6.5+x are compared. The breakdown of one-electron picture of its electronic structure is reported. The data are interpreted by mixing of Cu 3d9 and of (where is a hole in the oxygen derived band, ligand hole) many body configuration in the initial state. The localization of Cu 3d9 configuration is indicated by the bare Coulomb interaction Udd~6 eV. The conductivity is assigned to the itinerant configuration. The experimental evidence that the additional oxygen x, giving higher Tc, increases the weight of the configuration is reported. The presence of holes on the oxygen atoms is confirmed by the Ols XPS spectra. The Cu3+(Cu 3d8) configuration is not observed in L3 XANES in agreement with valence band XPS giving the energy of the 3d8 excited state at about 12 eV above the ground state. An energy scheme of the many body configurations in YBa2Cu3O~7 is obtained. These experiments give experimental evidence that the high Tc superconductivity is due to pairing of holes in the oxygen valence band interacting with localized electrons at the Cu sites.

An x-ray absorption near edge structure spectroscopy study of metal coordination in Co(II)-substituted Carcinus maenas hemocyanin

High-resolution x-ray absorption near edge structure spectroscopy was used to characterize the metal sites in three different cobalt-substituted derivatives of Carcinus maenas hemocyanin (Hc), including a mononuclear cobalt, a dinuclear cobalt and a copper-cobalt hybrid derivative. Co(II) model complexes with structures exemplifying octahedral, trigonal bipyramidal, pseudo-tetrahedral, and square planar geometries were also studied. The results provide structural information about the metal binding site(s) in the Co-Hcs that extend earlier results from EPR and optical spectroscopy (Bubacco et al. 1992. Biochemistry. 31: 9294-9303). Experimental spectra were compared to those calculated for atomic clusters of idealized geometry, generated using a multiple scattering approach. The energy of the dipole forbidden 1s-->3d transition and of the absorption edge in the spectra for all cobalt Hc derivatives confirmed the cobaltous oxidation state which rules out the presence of an oxygenated site. Comparisons between data and simulations showed that the mononuclear and dinuclear Co(II) derivatives, as well as the hybrid derivative, contain four-coordinate Co(II) in distorted tetrahedral sites. Although the spectra for Co(II) in dinuclear metal sites more closely resemble the simulated spectrum for a tetrahedral complex than do spectra for the mononuclear derivative, the Co(II) sites in all derivatives are very similar. The Cu K-edge high resolution x-ray absorption near edge structure spectrum of the hybrid Cu-Co-Hc resembles that of deoxy-Hc demonstrating the presence of three-coordinate Cu(I).