An efficient approach to integrated MeV ion imaging.

An ionoluminescence (IL) spectral imaging system, besides the common MeV ion imaging facilities such as µ-PIXE and µ-RBS, is implemented at the Van de Graaff laboratory of Tehran. A versatile processing software is required to handle the large amount of data concurrently collected in µ-IL and common MeV ion imaging measurements through the respective methodologies. The open-source freeware PyMca, with image processing and multivariate analysis capabilities, is employed to simultaneously process common MeV ion imaging and µ-IL data. Herein, the program was adapted to support the OM_DAQ listmode data format. The appropriate performance of the µ-IL data acquisition system is confirmed through a case study. Moreover, the capabilities of the software for simultaneous analysis of µ-PIXE and µ-RBS experimental data are presented.

Towards data format standardization for X-ray absorption spectroscopy.

A working group on data format standardization for X-ray absorption spectroscopy (XAS) has recently formed under the auspices of the International X-ray Absorption Society and the XAFS Commission of the International Union of Crystallography. This group of beamline scientists and XAS practitioners has been tasked to propose data format standards to meet the needs of the world-wide XAS community. In this report, concepts for addressing three XAS data storage needs are presented: a single spectrum interchange format, a hierarchical format for multispectral X-ray experiment, and a relational database format for XAS data libraries.

Ultrahigh vacuum/high-pressure flow reactor for surface x-ray diffraction and grazing incidence small angle x-ray scattering studies close to conditions for industrial catalysis.

A versatile instrument for the in situ study of catalyst surfaces by surface x-ray diffraction and grazing incidence small angle x-ray scattering in a 13 ml flow reactor combined with reaction product analysis by mass spectrometry has been developed. The instrument bridges the so-called "pressure gap" and "materials gap" at the same time, within one experimental setup. It allows for the preparation and study of catalytically active single crystal surfaces and is also equipped with an evaporator for the deposition of thin, pure metal films, necessary for the formation of small metal particles on oxide supports. Reactions can be studied in flow mode and batch mode in a pressure range of 100-1200 mbar and temperatures up to 950 K. The setup provides a unique combination of sample preparation, characterization, and in situ experiments where the structure and reactivity of both single crystals and supported nanoparticles can be simultaneously determined.

Advanced combined application of micro-X-ray diffraction/micro-X-ray fluorescence with conventional techniques for the identification of pictorial materials from Baroque Andalusia paintings.

The process of investigating paintings includes the identification of materials to solve technical and historical art questions, to aid in the deduction of the original appearance, and in the establishment of the chemical and physical conditions for adequate restoration and conservation. In particular, we have focused on the identification of several samples taken from six famous canvases painted by Pedro Atanasio Bocanegra, who created a very special collection depicting the life of San Ignacio, which is located in the church of San Justo y Pastor of Granada, Spain. The characterization of the inorganic and organic compounds of the textiles, preparation layers, and pictorial layers have been carried out using an XRD diffractometer, SEM observations, EDX spectrometry, FT-IR spectrometry (both in reflection and transmission mode), pyrolysis/gas chromatography/mass spectrometry and synchrotron-based micro-X-ray techniques. In this work, the advantages over conventional X-ray diffraction of using combined synchrotron-based micro-X-ray diffraction and micro-X-ray fluorescence in the identification of multi-layer paintings is demonstrated.

Quantitative X-ray fluorescence analysis of an Egyptian faience pendant and comparison with PIXE.

The X-ray fluorescence (XRF) technique is a common choice in the archaeometric field for in situ investigations with portable instruments. This work shows that XRF portable systems can be used for quantitative analyses using appropriate software, obtaining a similar accuracy to that provided with other techniques such as particle-induced X-ray emission (PIXE), as shown for an Egyptian faience pendant and for two glass standards.

Synchrotron-based X-ray spectromicroscopy used for the study of an atypical micrometric pigment in 16th century paintings.

Grünewald is a famous German painter of the 16th century, whose celebrity is associated with his unique skill in handling colors. This article presents the analysis of materials used to render a metallic aspect in the Isenhein Altarpiece and the Basel's Crucifixion. Such samples are challenging objects for microanalysis due to both chemical and physical complexity. Their study by synchrotron-based X-ray microscopy techniques was made possible thanks to recent developments carried out at the ID21 beam line (European Synchrotron Radiation Facility, ESRF). A submicron X-ray fluorescence probe revealed the main presence of lead, sulfur, antimony, and calcium. The fluorescence-line interferences (in particular K-lines of sulfur with M-lines of lead, and K-lines of calcium with L-lines of antimony) were resolved with the fitting program, PyMCA. 2D-mapping highlighted the presence of micrometer grains of sulfur and antimony into a lead matrix. XANES measurements were performed at both the sulfur K-edge and the antimony L-edge to refine information from an atomic to a molecular level. Beam stability was a key point in this study to selectively probe micrometer pigment grains, dispersed in the lead matrix. They confirm that the grains are made of stibnite (antimony sulfide), a very atypical pigment. Chemical mapping of sulfides is perfectly correlated with antimony mapping and provides a clear visualization of the stibnite pigments, in addition to their identification. Besides its artistic relevancy, this work aims at illustrating developments of synchrotron X-ray microprobe methods for the chemical characterization and observation of complex and micrometer-scale materials.

Determination of the iron oxidation state in earth materials using XANES pre-edge information.

Fe K-edge XANES spectra have been measured in more than 35 Fe(II) and Fe(III)-bearing minerals. The separation between the average pre-edge centroid positions for Fe(II) and Fe(III) is 1.4 +/- 0.1 eV. Examination of calculated pre-edge features of mechanical mixtures of phases containing different proportions of Fe(II) and Fe(III) reveals that different trends of pre-edge position vs. pre-edge intensity can be observed, depending on the coordination environment. Both pre-edge parameters have been used to estimate the ferric/ferrous ratio in 12 natural minerals.

Direct and Fe(II)-mediated reduction of technetium by Fe(III)-reducing bacteria.

The dissimilatory Fe(III)-reducing bacterium Geobacter sulfurreducens reduced and precipitated Tc(VII) by two mechanisms. Washed cell suspensions coupled the oxidation of hydrogen to enzymatic reduction of Tc(VII) to Tc(IV), leading to the precipitation of TcO(2) at the periphery of the cell. An indirect, Fe(II)-mediated mechanism was also identified. Acetate, although not utilized efficiently as an electron donor for direct cell-mediated reduction of technetium, supported the reduction of Fe(III), and the Fe(II) formed was able to transfer electrons abiotically to Tc(VII). Tc(VII) reduction was comparatively inefficient via this indirect mechanism when soluble Fe(III) citrate was supplied to the cultures but was enhanced in the presence of solid Fe(III) oxide. The rate of Tc(VII) reduction was optimal, however, when Fe(III) oxide reduction was stimulated by the addition of the humic analog and electron shuttle anthaquinone-2,6-disulfonate, leading to the rapid formation of the Fe(II)-bearing mineral magnetite. Under these conditions, Tc(VII) was reduced and precipitated abiotically on the nanocrystals of biogenic magnetite as TcO(2) and was removed from solution to concentrations below the limit of detection by scintillation counting. Cultures of Fe(III)-reducing bacteria enriched from radionuclide-contaminated sediment using Fe(III) oxide as an electron acceptor in the presence of 25 microM Tc(VII) contained a single Geobacter sp. detected by 16S ribosomal DNA analysis and were also able to reduce and precipitate the radionuclide via biogenic magnetite. Fe(III) reduction was stimulated in aquifer material, resulting in the formation of Fe(II)-containing minerals that were able to reduce and precipitate Tc(VII). These results suggest that Fe(III)-reducing bacteria may play an important role in immobilizing technetium in sediments via direct and indirect mechanisms.

Does the structure of the water-oxidizing photosystem II-manganese complex at room temperature differ from its low-temperature structure? A comparative X-ray absorption study.

Detailed information on room-temperature structure and oxidation state of the Photosystem II (PS II) manganese complex is needed to put mechanistic considerations on solid grounds. Because previously this information had not been available, the tetranuclear manganese complex was investigated by X-ray absorption spectroscopy (XAS) on PS II membrane particles at 290 K. Due to methodical progress (collection of XAS spectra within 10 s or less), significant X-ray radiation damage can be avoided; room-temperature XAS investigations on the PS II in its native membrane environment become feasible. Thus, the ambiguity with respect to the mechanistic relevance of low-temperature XAS results is avoidable. At 290 K as well as at 18 K, the manganese complex in its dark-stable state (S(1)-state) seemingly is a Mn(III)(2)Mn(IV)(2) complex comprising two di-mu(2)-oxo bridged binuclear manganese units characterized by the same Mn-Mn distance of 2.71-2.72 A at both temperatures. Most likely, manganese oxidation states and the protonation state of the bridging oxides are fully temperature independent. Remarkably, at room-temperature manganese-ligand distances of 3.10 and 3.65 A are clearly discernible in the EXAFS spectra. The type of bridging assumed to result in Mn-Mn or Mn-Ca distances around 3.1 A is, possibly, temperature-dependent as suggested by distance lengthening upon cooling by 0.13 A. However, mechanistic proposals on photosynthetic water oxidation, which involve the dimer-of-dimers model [Yachandra, V. K., et al. (1993) Science 260, 675-679] are not invalidated by the presented results.

Structure and orientation of the oxygen-evolving manganese complex of green algae and higher plants investigated by X-ray absorption linear dichroism spectroscopy on oriented photosystem II membrane particles.

X-ray absorption spectroscopy at the Mn K-edge has been performed on multilayers of photosystem II-enriched fragments of the native thylakoid membrane prepared from a higher plant (spinach) and a unicellular green alga (Scenedesmus obliquus). Spectra collected for various angles between the prevailing orientation of the thylakoid membrane normal and the X-ray electric field vector contain information on the atomic structure of the tetranuclear manganese complex of photosystem II (PS II) and its orientation with respect to the membrane normal. The previously used approach for evaluation of the dichroism of extended X-ray absorption fine structure (EXAFS) spectra [George, G. N., et al. (1989) Science 243, 789-791] is modified, and the following results are obtained for PS II in its dark-stable state (S1-state): (1) structure and orientation of the PS II manganese complexes of green algae and higher plants are highly similiar or fully identical; (2) two 2.7-A vectors, which, most likely, connect the Mn nuclei of a planar Mn2(mu-O2) structure, are at an average angle of 80 degrees +/- 10 degrees with respect to the thylakoid normal; (3) the plane of the Mn2(mu-O2) structures is rather in parallel with the thylakoid plane than perpendicular. Structural models for the oxygen-evolving manganese complex and its orientation in the thylakoid membrane are discussed within the context of the presented results.

The iron ligand sphere geometry of mammalian 15-lipoxygenases.

We investigated the geometry of the iron ligand sphere of the native rabbit 15-lipoxygenase (15-LOX) by X-ray absorption spectroscopy using synchrotron radiation. The soybean LOX-1 was used as a reference compound because its iron ligand sphere is well characterized. For structural information the X-ray absorption spectra were evaluated using the Excurve Program (CCLRC Daresbury Laboratory, Warrington, U.K.). From the positions of the absorption edges and from the intensities of the 1s-3d pre-edge transition peaks a six-coordinate ferrous iron was concluded for the rabbit 15-LOX. Evaluation of the extended region of the absorption spectra suggested six nitrogen and/or oxygen atoms as direct iron ligands, and the following binding distances were determined (means+/-S.D.; estimated accuracy is +/-0.001nm for bond distances, on the basis of more than 22 X-ray absorption spectra): 0.213+/-0.001nm, 0.213+/-0. 001 nm, 0.236+/-0.001 nm, 0.293+/-0.001 nm, 0.189+/-0.001 nm and 0. 242+/-0.001. Lyophilization of the LOX altered the binding distances but did not destroy the octahedral iron ligand sphere. For construction of a structural model of the iron ligand sphere the binding distances extracted from the X-ray spectra were assigned to specific amino acids (His-360, -365, -540, -544 and the C-terminal Ile-662) by molecular modelling using the crystal coordinates of the soybean LOX-1 and of a rabbit 15-LOX-inhibitor complex.