Introduction to Inner Shell Spectroscopy

36b429d92ffc266d1abf718a18865c0e?s=47 Bruce Ravel
March 03, 2014

Introduction to Inner Shell Spectroscopy

This talk is an introduction to to XAS and XRF aimed at the early graduate student. My intent is to provide a gentle introduction to these sophisticated techniques and give the audience some ideas about how these X-ray techniques might be used in their own research.

36b429d92ffc266d1abf718a18865c0e?s=128

Bruce Ravel

March 03, 2014
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  1. Introduction XAS XRF Experiment Real-world problem XAS Applications Microprobe XAS

    Community Introduction to Inner Shell Spectroscopy Bruce Ravel Synchrotron Science Group, Materials Measurement Science Division Materials Measurement Laboratory National Institute of Standards and Technology & Local Contact, Beamline X23A2 National Synchrotron Light Source SUNY Stonybrook, Physics 518 13 March 2014 Introduction to Inner Shell Spectroscopy 1 / 43
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    Community Copyright This document is copyright c 2010-2014 Bruce Ravel. This work is licensed under the Creative Commons Attribution-ShareAlike License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/ or send a letter to Creative Commons, 559 Nathan Abbott Way, Stanford, California 94305, USA. You are free: to Share — to copy, distribute, and transmit the work to Remix — to adapt the work to make commercial use of the work Under the following conditions: Attribution – You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). Share Alike – If you alter, transform, or build upon this work, you may distribute the resulting work only under the same, similar or a compatible license. With the understanidng that: Waiver – Any of the above conditions can be waived if you get permission from the copyright holder. Public Domain – Where the work or any of its elements is in the public domain under applicable law, that status is in no way affected by the license. Other Rights – In no way are any of the following rights affected by the license: Your fair dealing or fair use rights, or other applicable copyright exceptions and limitations; The author’s moral rights; Rights other persons may have either in the work itself or in how the work is used, such as publicity or privacy rights. Notice – For any reuse or distribution, you must make clear to others the license terms of this work. This is a human-readable summary of the Legal Code (the full license). Introduction to Inner Shell Spectroscopy 2 / 43
  3. Introduction XAS XRF Experiment Real-world problem XAS Applications Microprobe XAS

    Community This Talk This talk is an introduction to the inner-shell spectroscopies, XAS and XRF. Outline An overview of the basic physics of inner shell spectroscopies An introduction to XAS and XRF beamline instrumentation A flavor of the sorts of science that can be accomplished with XAS and XRF using examples from my own research. My hope is that you will leave with a sense of how XAS and XRF might be applied to your research. Introduction to Inner Shell Spectroscopy 3 / 43
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    Community XAS and XRF X-ray Absorption Spectroscopy and X-Ray Fluorescence spectroscopy These are inner shell spectroscopies. Inner shell means that an x-ray interacts primarily with a deep-core electron rather than with a valence electron. Spectroscopy means that some aspect of the interaction changes as a function of photon energy. Introduction to Inner Shell Spectroscopy 4 / 43
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    Community The basic physical process in XAS and XRF X-ray in n=1 K edge n=2 L edges n=3 M edges n=4 N edges n=1 K edge n=2 L edges n=3 M edges n=4 N edges n=1 K edge n=2 L edges n=3 M edges n=4 N edges X-ray out n=1 K edge n=2 L edges n=3 M edges n=4 N edges Auger e - out 1 An incoming photon interacts with a deep-core electron. Shown here, a 1s electron is excited for a K-edge spectrum. 2 The deep-core electron is promoted to some unoccupied state above the Fermi energy, propagates away, and leaves behind a core-hole. 3 A short time later (1 or 2 femtoseconds), a higher-lying electron decays into the core-hole and emits a photon. 4 Alternately, the energy from the higher-lying electron can be used to emit an Auger electron. Introduction to Inner Shell Spectroscopy 5 / 43
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    Community Characteristic energies Each element has a characteristic set of excitation and fluorescence energies. Iron: Z=26 Edge Energy K 7112 L3 706.8 L2 719.9 L1 844.6 Line Transition Energy Strength Kα1 K-L3 6405.2 0.580 Kα2 K-L2 6392.1 0.294 Kβ1 K-M3 7059.3 0.082 Kβ3 K-M2 7059.3 0.043 Kβ5 K-M4,5 7110.0 0.001 Uranium: Z=92 Edge Energy K 115606 L3 17166 L2 20948 L1 21757 Line Transition Energy Strength Lα1 L3-M5 13614.0 0.686 Lα2 L3-M4 13438.0 0.077 Lβ2 L3-N4,5 16387.7 0.181 Lβ5 L3-O4,5 17063.2 0.038 Lβ6 L3-N1 15727.0 0.013 L L3-M1 11618.0 0.005 Introduction to Inner Shell Spectroscopy 6 / 43
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    Community A simple picture of X-ray absorption An incident x-ray of energy E is absorbed, destroying a core electron of binding energy E0 and emitting a photo-electron with kinetic energy (E − E0 ). The core state is eventually filled, ejecting a fluorescent x-ray or an Auger electron. An empty final state is required. No available state, no absorption! When the incident x-ray energy is larger than the binding energy, there is a sharp increase in absorption. For an isolated atom, µ(E) has a sharp step at the core-level binding energy and is a smooth function of energy above the edge. Introduction to Inner Shell Spectroscopy 7 / 43
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    Community X-ray absorption in condensed matter The ejected photo-electron can scatter from neighboring atoms. R has some relationship to λ and there is a phase shift associated with the scattering event. Thus the outgoing and scattered waves interfere. The scattering of the photo-electron wave function interferes with itself. µ(E) depends on the density of states with energy (E − E0 ) at the absorbing atom. This interference at the absorbing atom will vary with energy, causing the oscillations in µ(E). Introduction to Inner Shell Spectroscopy 7 / 43
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    Community XAS and Valence State As the valence increases Mn0→ Mn2+ → Mn3+ → Mn4+ the edge position shifts to higher energy. XAS is a direct measure of valence state Since each element has its own edge energy, an element’s valence can be measured even in a heterogeneous sample Since x-rays are deeply penetrating into matter, minimal sample preparation is required No assumption of symmetry or periodicity is made, so the sample can be crystalline, amorphous, thin film, in solution, surface sorbed, · · · , whatever Introduction to Inner Shell Spectroscopy 8 / 43
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    Community XAS and Local Atomic Structure The different Mn species display big differences in the fine structure beyond the edge as the valence increases (Mn0 , Mn2+ , Mn3+ , Mn4+ ). The white line and subsequent oscillations are quite different. The oscillatory portion of the spectrum can be isolated and ... ... Fourier transformed. This FT function can be interpreted to yield partial pair distribution functions of atoms about the absorber. The Mn-O distances are different for the Mn2+ , Mn3+ , and Mn4+ and clearly different from the Mn-Mn distance in Mn metal. Introduction to Inner Shell Spectroscopy 9 / 43
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    Community XAS is a direct measure of local structure Since each element has its own edge energy, an element’s local structure can be measured even in a heterogeneous sample Since x-rays are deeply penetrating into matter, minimal sample preparation is required No assumption of symmetry or periodicity is made, so the sample can be crystalline, amorphous, thin film, in solution, surface sorbed, · · · , whatever Samples can be measured in situ, which can mean cryostat or furnace high pressure cell electrochemistry cell or fuel cell peristaltic or stop-flow pump with liquid samples high field magnet etc... As a result, XAS is used in a very broad array of scientific disciplines Introduction to Inner Shell Spectroscopy 10 / 43
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    Community Fluorescence from Many Elements X-ray fluorescence is a spectroscopy in which the incident energy is fixed and the energy dependence of the secondary photons is measured. Every element with an edge below the incident energy will fluoresce. Glass with every 2nd element Ca–Ge, incident energy = 11153 eV Introduction to Inner Shell Spectroscopy 11 / 43
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    Community Fluorescence from A Sediment Sample Here are the XRF spectra with incident beams above and below the U LIII edge for sediment heavily contaminated with uranium. Combined with a standard measured under identical conditions, concentrations can be quantified. Introduction to Inner Shell Spectroscopy 12 / 43
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    Community Using the Fluorescence Spectrum for XAS We can place a region of interest (ROI) around the U Lα peak and measure its variation as a function of incident energy. In this way, we measure signal only from the absorber and reject all other photons entering the detector. Introduction to Inner Shell Spectroscopy 13 / 43
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    Community Learning About Your Sample I once performed a study to measure the bonding between Hg and catalytic DNA molecules. I was given a solution with 3 mM Hg chlorate 3 mM DNA 50 mM cacodylic acid (buffer) 100 mM NaClO4 (salt) Here is the fluorescence spectrum: A quick Wikipedia search told me that cacodylic acid is: The big peak is As Kα (∼10.5 keV), the little one is Hg Lα (∼10 keV). Introduction to Inner Shell Spectroscopy 14 / 43 B. Ravel, et al., EXAFS studies of catalytic DNA sensors for mercury contamination of water, Radiation Physics and Chemistry 78:10 (2009) pp S75-S79 DOI: 10.1016/j.radphyschem.2009.05.024
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    Community A Typical XAS Beamline CM Mono FM Hutch Fluo I 0 Slits I T I R Sample CM=Collimating Mirror FM=Focussing Mirror =X-ray Detector Monochromator: Si(111) or Si(311) or Si(220) or · · · Introduction to Inner Shell Spectroscopy 15 / 43
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    Community The HXMA Beamline at the CLS Introduction to Inner Shell Spectroscopy 16 / 43
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    Community Beamline Optics Source The source can be a bend magnet, a wiggler, or an undulator. XAS beamlines of each sort exist around the world. Collimating mirror Correct the vertical divergence of the beam and suppress harmonic content. Monochromator Use Bragg diffraction from a highly perfect crystal to select one energy (i.e. one wavelength) from the white light coming from the source. Two crystals are needed to direct the beam into the hutch. Focussing mirror Change the beam profile from a large rectangle to a small circle with minimal reduction of flux. Together these deliver a small, monochromatic, tunable beam into the hutch for use in an experiment. Introduction to Inner Shell Spectroscopy 17 / 43
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    Community Hutch Instrumentation Fluo I 0 Slits I T I R Sample Reference mirror This is the typical layout of the hutch instrumetation. Depending on the details of the experiment, the sample area might include special equipment. Furnace or cryostat Electrochemistry or fuel cell High pressure cell High field magnet Peristaltic or stop flow fluid pump etc... Introduction to Inner Shell Spectroscopy 18 / 43
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    Community Hutch Instrumentation: Transmission XAS Fluo I 0 Slits I T I R Sample Reference mirror In a transmission experiment, we measure the direct attenuation of the x-ray beam (Beer’s law). It =I0 exp(−µt) µt = ln I0 It Ion chambers are easy to use and accurate over many decades of intensity. X­ray Current amplifier High Voltage Filled with inert gas Introduction to Inner Shell Spectroscopy 18 / 43
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    Community Hutch Instrumentation: Fluorescence XAS Fluo I 0 Slits I T I R Sample Reference mirror The fluorescence detector might be an ion chamber or it might be an energy discriminating detector. If ∝µI0 µ ∝ If I0 The energy discriminating detector is useful for low concentrations or very heterogeneous samples. Introduction to Inner Shell Spectroscopy 18 / 43
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    Community Elements Measured at a Typical Hard X-Ray Beamline K-edges, measured with Si(111) monochromator K-edges, measured with Si(311) monochromator L-edges Soft x-ray beamlines exist which deliver photons in the 100 eV to 1 keV range (e.g. first row K, transition metal L, actinide N) Introduction to Inner Shell Spectroscopy 19 / 43
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    Community My backyard When I bought my house, there was a wooden deck off the dining room. I replaced this with a paving stone patio and converted the adjacent plot of ground into a vegetable garden. Introduction to Inner Shell Spectroscopy 20 / 43
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    Community Wood preservative The wood used to make the deck was treated with the wood preservative chromated copper arsentate (CCA), which is chromium-bearing analogue of copper orthoarsente, Cu3(AsO4)2·4H2O. CCA-treated wood is known to leach all three elements into surround- ing soils. I had some questions: 1 How much As is in the soil? Is it higher than elsewhere in the garden? (Use XRF) 2 What chemical species is the As in the soil? (Use XAS) Introduction to Inner Shell Spectroscopy 21 / 43 The orthoarsenate image is from Wikimedia commons and is in the public domain.
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    Community XRF spectra I took soil samples from a few centimeters below the surface from a spot adjecent to the old deck and from a spot 5 meters away and slightly uphill. Here are the XRF spectra from those two spots: There is a clear enhancement of both As and Cr in the soil adjacent to the old deck. The As is enhanced roughly two-fold. Introduction to Inner Shell Spectroscopy 22 / 43
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    Community As standards As a point of reference, here are the XAS spectra from two inorganic As standards, As3+ 2 O3 and As5+ 2 O5. Note that the edge of As5+ standard is shifted substantially to higher energy and that its white line is much enhanced. As5+ is water soluble, thus more mobile than As3+ . Also As5+ is quite toxic. Introduction to Inner Shell Spectroscopy 23 / 43
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    Community XAS from the soil samples Here are the raw µ(E) data from the two soil locations. Sure enough, the signal from the site adjacent to the old deck is enhanced by about a factor of 2. Here are the normalized data compared to standards. The As is slightly reduced, but predominantly As5+ . As in soil is well known to bind to soil particles as As5+ . Should I be worried about the produce I grow in the garden? Introduction to Inner Shell Spectroscopy 24 / 43
  28. Introduction XAS XRF Experiment Real-world problem XAS Applications Microprobe XAS

    Community XRF spectra from plant leaves Here are XRF spectra from the leaf of a squash plant growing in the soil adjacent to the old deck. Although toxic As5+ is present in the soil in elevated quantities, very little is taken up by the plants growing that soil. The squash were delicious! Introduction to Inner Shell Spectroscopy 25 / 43
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    Community XAS Examples XAS is used in an amazingly wide variety of disciplines. Here are a few examples from my work in the past few years. Economic geology Measure the rate of reduction of Au3+ chloride to metallic Au and identify an intermediate species Minerology Supporting evidence for a novel U5 /U6 mineral formed under certain hydrothermal conditions Dielectric materials BaTaO2N represents a class of materials with tunable dielectric properties XAS beamlines regularly see experiments on magnetic materials, superconductors, materials for recording media, metallo-organic compounds, metalloproteins, Earth mantel materials, extraterrestrial materials, liquids and amorphous solids, etc., etc., etc.... Introduction to Inner Shell Spectroscopy 26 / 43
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    Community Economic geology (I) One way that gold deposits form is by having Au chloride fluids rise from the deep earth, wash over cyanobacteria colonies, and reduce to metallic gold. Au3+Cl Before Exposed After We simulated this process at the beamline by exposing cyanobacteria to an Au3+ solution and “watching” the evolution of the Au XAS from Au3+ to Au0 . Questions What is the rate constant? Is there an intermediate species? Introduction to Inner Shell Spectroscopy 27 / 43 M. Lengke et el., Mechanisms of Gold Bioaccumulation by Filamentous Cyanobacteria from Gold(III)-Chloride Complex, Environ. Sci. Technol. 40(20) p. 6304-6309. (2006), DOI: 10.1021/es061040r
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    Community Economic geology (II) We see that 7 minutes after injection, the data strongly resemble the Au3+ Cl. After one week, the data resemble Au metal. Over the course of the time series, the white line ∼ 11921 shrinks while the bump ∼ 11945 grows, suggesting the reduction to Au metal. Introduction to Inner Shell Spectroscopy 28 / 43 M. Lengke et el., Mechanisms of Gold Bioaccumulation by Filamentous Cyanobacteria from Gold(III)-Chloride Complex, Environ. Sci. Technol. 40(20) p. 6304-6309. (2006), DOI: 10.1021/es061040r
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    Community Economic geology (III) We can analyze these data as a linear combination of species, including Au3+ Cl, Au metal, and Au1+ sulfide. We can plot out the contributions from these species as a function of time to get a sense of reaction rates. Introduction to Inner Shell Spectroscopy 29 / 43 M. Lengke et el., Mechanisms of Gold Bioaccumulation by Filamentous Cyanobacteria from Gold(III)-Chloride Complex, Environ. Sci. Technol. 40(20) p. 6304-6309. (2006), DOI: 10.1021/es061040r
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    Community Minerology (I) A deep understanding of the nuclear fuel cycle requires study of “exotic” pentavalent uranium minerals that can form under specific mine or storage facility conditions. One such mineral, UV(H2O)2(UVIO2)2O4(OH)+4·H2O, has recently been synthesized. XRD is an indirect measure of valence — XAS is a direct measure! Introduction to Inner Shell Spectroscopy 30 / 43 N. Belai et el., Pentavalent Uranium Oxide via Reduction of [UO2]2+ Under Hydrothermal Reaction Conditions, Inorg. Chem., 2008, 47 (21), pp 10135âĂŞ10140, DOI: 10.1021/ic801534m
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    Community Minerology (II) XAS on UV(H2O)2(UVIO2)2O4(OH)+4·H2O XANES data We see evidence of UV by the intermediate edge position between our UIV and UVI standards. EXAFS analysis The crystal structure refined from the XRD is consistent with the EXAFS data. Introduction to Inner Shell Spectroscopy 31 / 43 N. Belai et el., Pentavalent Uranium Oxide via Reduction of [UO2]2+ Under Hydrothermal Reaction Conditions, Inorg. Chem., 2008, 47 (21), pp 10135âĂŞ10140, DOI: 10.1021/ic801534m
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    Community Dielectric materials (I) Tantalum oxynitrides are a class of dielectric materials with high K which is tunable by selection of the A cation. By mixing A cations, a temperature-constant dielectric is possible. First principles DFT suggests that the different ionic radii of O and N introduce substantial disorder around the Ta atom. Introduction to Inner Shell Spectroscopy 32 / 43 B. Ravel et el., Role of local disorder in the dielectric response of BaTaO2N, Phys. Rev. B73, p. 184121 (2006), DOI: 10.1103/PhysRevB.73.184121
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    Community Dielectric materials (II) The DFT results in a rather complex coordination environment about the Ta atom — much more complex than the simple perovskite structure. With some effort, this complexity can be incorporated into the data analysis. The EXAFS data are shown to be (mostly) consistent with the DFT results. Introduction to Inner Shell Spectroscopy 33 / 43 B. Ravel et al., Role of local disorder in the dielectric response of BaTaO2N, Phys. Rev. B73, p. 184121 (2006), DOI: 10.1103/PhysRevB.73.184121
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    Community Hutch Instrumentation: Microprobe Fluo I 0 Slits I T I R Sample Reference mirror The energy discriminating detector can see all elements in a sample with edges below the incident energy. This is a Vortex 4 element silicon drift detector Introduction to Inner Shell Spectroscopy 34 / 43
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    Community Focussing optics Different types of focussing optics can be matched to the relevant length scales of different samples 1D focussing + slits A total external reflection mirror is bent to condense the x-rays vertically. Slits are used to define the horizontal extent. (> 50 µm) Kirkpatrick-Baez mirrors Short mirrors with excellent figures are used in both directions to define a small spot. (1–25 µm) Refractive optics Fresnel zone plates use refraction to define a small first order spot (< 1 µm) Introduction to Inner Shell Spectroscopy 35 / 43
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    Community X-ray Fluorescence Mapping The mapping experiment involves placing the sample on an 3-dimensional stage and in the focal spot of the beam. The sample is rastered in ˆ y and ˆ z to cover a two-dimensional area. At each point xy, the XRF spectrum is measured. Integrating the elemetal regions of interest yields maps of the elemental distributions. Introduction to Inner Shell Spectroscopy 36 / 43
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    Community Gravel Contaminated with U Gravel embedded in epoxy with a polished surface Under a UV lamp, U glows greenish. Introduction to Inner Shell Spectroscopy 37 / 43 D. Phillips et el., Env. Sci. and Tech., 2008, 42 (19), pp 7104âĂŞ7110 DOI: 10.1021/es8001579
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    Community Gravel Contaminated with U Gravel embedded in epoxy with a polished surface UV photo + superposed U map — 200 µm probe at APS 10ID. Introduction to Inner Shell Spectroscopy 37 / 43 D. Phillips et el., Env. Sci. and Tech., 2008, 42 (19), pp 7104âĂŞ7110 DOI: 10.1021/es8001579
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    Community XRF Spectra at each Position Here are a few of the XRF spectra from the marked area on the U map from the previous page. Introduction to Inner Shell Spectroscopy 38 / 43 D. Phillips et el., Env. Sci. and Tech., 2008, 42 (19), pp 7104âĂŞ7110 DOI: 10.1021/es8001579
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    Community µ-EXAFS High quality XAS data is measured with the 200 µm probe. We can see the variation in U quantity under the spot in the XAS step size. Normalizing the data, we see variability in the XANES, indicating spatial heterogeneity in U speciation. The EXAFS is of high quality and can be analyzed to uncover the different structural environments around the U at the various locations. Introduction to Inner Shell Spectroscopy 39 / 43 D. Phillips et el., Env. Sci. and Tech., 2008, 42 (19), pp 7104âĂŞ7110 DOI: 10.1021/es8001579
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    Community Arsenic Hyper-Accumulating Plant (I) An Arabadopsis mutant was plucked from arsenite contaminated medium and pressed between two pieces of kapton tape. Introduction to Inner Shell Spectroscopy 40 / 43 M. Pischke and B. Ravel, unpublished
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    Community Arsenic Hyper-Accumulating Plant (II) We measured XANES from a vein in the leaf with a 20 µm probe at APS 13BM. ∼25% As trisglutathiol and ∼75% Arsenite Introduction to Inner Shell Spectroscopy 41 / 43 M. Pischke and B. Ravel, unpublished
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    Community Where to go for more information http://xafs.org/ Introduction to Inner Shell Spectroscopy 42 / 43
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    Community Information about the software Ifeffit A suite of interactive programs for XAFS analysis, combining high-quality and well-tested XAFS analysis algorithms, tools for general data manipulation, and graphical display of data. http://cars9.uchicago.edu/ifeffit/ Athena & Artemis Graphical programs for the processing and analysis of XAFS data. http://bruceravel.github.io/demeter The Ifeffit mailing list Discussion of and related XAFS analysis programs. Also covered are general discussions of XAFS, XAFS theory, and related spectroscopies. http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ and friends are free software free as in beer and free as in speech Introduction to Inner Shell Spectroscopy 43 / 43