X-ray absorption spectroscopy

Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA.
Photosynthesis Research (Impact Factor: 3.5). 09/2009; 102(2-3):241-54. DOI: 10.1007/s11120-009-9473-8
Source: PubMed


This review gives a brief description of the theory and application of X-ray absorption spectroscopy, both X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS), especially, pertaining to photosynthesis. The advantages and limitations of the methods are discussed. Recent advances in extended EXAFS and polarized EXAFS using oriented membranes and single crystals are explained. Developments in theory in understanding the XANES spectra are described. The application of X-ray absorption spectroscopy to the study of the Mn(4)Ca cluster in Photosystem II is presented.

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    • "Scattering (RIXS) are routine methods in surface and solid-state investigations at third generation synchrotron radiation sources [1] [2] [3] [4]. The development of forth generation free-electron-laser (FEL) sources such as FERMI, FLASH, LCLS and XFEL opens new perspectives for single-shot XES and RIXS measurements of low-density, liquid and condensed matter [5] [6] [7] [8] [9]. "
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    ABSTRACT: We present the design and characterization of a compact and portable spectrometer realized for photon in-photon out experiments (in particular X-Ray Emission Spectroscopy, XES), in particular tailored to be used at the FERMI freeelectron- laser (FEL) at ELETTRA (Italy). The spectrometer can be installed on different end stations at variable distances from the target area both at synchrotron and FEL beamlines. Different input sections can be accommodated in order to fit the experimental requests, with/without an entrance slit and with/without an additional relay mirror. The design is compact in order to realize a portable instrument within a total footprint of less than one square meter. The instrument is based on the use of two flat-field grazing-incidence gratings and an EUV-enhanced CCD detector to cover the 25-800 eV spectral range, with spectral resolution better than 0.2%. The absolute response of the spectrometer, has been measured in the whole spectral region of operation, allowing calibrated measurements of the photon flux. The characterization on the Gas Phase beamline at ELETTRA Synchrotron as instrument for XES and some experimental data of the FEL emission taken at EIS-TIMEX beamline at FERMI, where the instrument has been used for photon beam diagnostics, are presented.
    SPIE Optical Engineering + Applications; 09/2014
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    • "XAS of arsenic in environmental samples generally uses the principles of x-ray fluorescence ; that is, incoming X-rays with energy at or higher than the binding energy of a core electron of the arsenic compound (E O ) are absorbed, ejecting a core electron and allowing another electron from the outer shells to fill the hole, emitting florescence [55]. X-ray absorption spectra are characterized by a sharp increase in absorption at specific X-ray photon energies giving rise to an absorption edge that is characteristic of the absorbing element [56]. The absorption edge corresponds to the energy required to eject a core electron; when a 1 s electron is ejected this is called a K-edge. "
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    ABSTRACT: The toxicity of arsenic greatly depends on its chemical form and oxidation state (speciation) and therefore accurate determination of arsenic speciation is a crucial step in understanding its chemistry and potential risk. High performance liquid chromatography with inductively coupled mass spectrometry (HPLC-ICP-MS) is the most common analysis used for arsenic speciation but it has two major limitations: it relies on an extraction step (usually from a solid sample) that can be incomplete or alter the arsenic compounds; and it provides no structural information, relying on matching sample peaks to standard peaks. The use of additional analytical methods in a complementary manner introduces the ability to address these disadvantages. The use of X-ray absorption spectroscopy (XAS) with HPLC-ICP-MS can be used to identify compounds not extracted for HPLC-ICP-MS and provide minimal processing steps for solid state analysis that may help preserve labile compounds such as those containing arsenic-sulfur bonds, which can degrade under chromatographic conditions. On the other hand, HPLC-ICP-MS is essential in confirming organoarsenic compounds with similar white line energies seen by using XAS, and identifying trace arsenic compounds that are too low to be detected by XAS. The complementary use of electrospray mass spectrometry (ESI-MS) with HPLC-ICP-MS provides confirmation of arsenic compounds identified during the HPLC-ICP-MS analysis, identification of unknown compounds observed during the HPLC-ICP-MS analysis and further resolves HPLC-ICP-MS by identifying co-eluting compounds. In the complementary use of HPLC-ICP-MS and ESI-MS, HPLC-ICP-MS helps to focus the ESI-MS selection of ions. Numerous studies have shown that the information obtained from HPLC-ICP-MS analysis can be greatly enhanced by complementary approaches.
    Spectrochimica Acta Part B Atomic Spectroscopy 09/2014; 99. DOI:10.1016/j.sab.2014.07.001 · 3.18 Impact Factor
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    ABSTRACT: Some of the important conclusions reached in this analysis of PCET are summarized below. The sections in which they are discussed are also cited. (1) PCET describes reactions in which there is a change in both electron and proton content between reactants and products. It originates from the influence of changes in electron content on acid-base properties and provides a molecular-level basis for energy transduction between proton transfer and electron transfer (section 1). (2) Coupled electron-proton transfer or EPT is defined as an elementary step in which electrons and protons transfer from different orbitals on the donor to different orbitals on the acceptor. There is (usually) a clear distinction between EPT and H-atom transfer (HAT) or hydride transfer, in which the transferring electrons and proton come from the same bond. Hybrid mechanisms exist in which the elementary steps are different for the reaction partners (sections 5.1 and 5.2). (3) EPT pathways such as PhO*/PhOH exchange have much in common with HAT pathways in that electronic coupling is significant, comparable to the reorganization energy with HDA ∼ λ. (4) Multiple-Site Electron-Proton Transfer (MS-EPT) is an elementary step in which an electron-proton donor transfers electrons and protons to different acceptors, or an electron-proton acceptor accepts electrons and protons from different donors. It exploits the long-range nature of electron transfer while providing for the short-range nature of proton transfer (section 5.1). (5) A variety of EPT pathways exist, creating a taxonomy based on what is transferred, e.g., le-12H+ WEPT (section 5.1). (6) PCET achieves "redox potential leveling" between sequential couples and the buildup of multiple redox equivalents, which is of importance in multielectron catalysis (section 2. 1). (7) There are many examples of PCET and pH-dependent redox behavior in metal complexes, in organic and biological molecules, in excited states, and on surfaces (section 2). (8) Changes in pH can be used to induce electron transfer through films and over long distances in molecules. Changes in pH, induced by local electron transfer, create pH gradients and a driving force for long-range proton transfer in Photosysem 11 and through other biological membranes (sections 3 and 7.2). (9) In EPT, simultaneous transfer of electrons and protons occurs on time scales short compared to the periods of coupled vibrations and solvent modes. A theory for EPT has been developed which rationalizes rate constants and activation barriers, includes temperature- and driving force (ΔG)-dependences implicitly, and explains kinetic isotope effects. The distance-dependence of EPT is dominated by the short range nature of proton transfer, with electron transfer being far less demanding (sections 4.2 and 5). (10) Changes in external pH do not affect an EPT elementary step. Solvent molecules or buffer components can act as proton donor acceptors, but individual H2O molecules are neither good bases (pKa(H3)O+) = - 1.74) nor good acids (pK(H2O) = 15.7) (section 5.5.3). (11) There are many examples of mechanisms in chemistry, in biology, on surfaces, and in the gas phase which utilize EPT (sections 6 and 7). (12) PCET and EPT play critical roles in the oxygen evolving complex (OEC) of Photosystem Il and other biological reactions by decreasing driving force and avoiding high-energy intermediates (section 7.2).
    Chemical Reviews 12/2007; 107(11):5004-64. DOI:10.1021/cr0500030 · 46.57 Impact Factor
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