1. GeoSoilEnviroCARS 09-Apr-2001 Matt Newville, GeoSoilEnviroCARS Consortium for Advanced Radiation Sources University of Chicago X-ray Absorption (XANES and EXAFS) Objective: Chemical associations, speciation, and structural information for heavy elements (Z > 20) with spatial sensitivity at the 1-10 micron scale, and few sample constraints. X-ray Microprobe Techniques: Oxidation state of selected element, Near-neighbor distances and coordination numbers Elemental abundance and correlations X-ray Fluorescence X-ray Microprobe for Environmental Sciences Fluorescence Tomography3-dimensional density and elemental abundances and correlations X-ray DiffractionCrystallographic and surface structures Steve Sutton Mark Rivers Peter Eng

2. GeoSoilEnviroCARS 09-Apr-2001 GSECARS Beamline Optics for Microprobe Undulator Beamline: High collimation allows efficient focusing, for x-ray microprobe, and x -ray diffraction (small crystals, high pressure). Very high power densities of white beam need to be absorbed by beamline optics. Bending Magnet Beamline: 2 nd -generation source, with fairly high energy x-rays (up to 100KeV) Storage Ring High Pressure Diffraction Station (Diamond-Anvil-Cell, Large Volume Press) Monochromator: LN 2 -cooled Si (111) Large Focusing Mirrors (May, 2001) Microprobe Station Tomography and diffraction Station Diffraction Station GeoSoilEnviroCARS: Sector 13 Advanced Photon Source, Argonne National Lab

3. GeoSoilEnviroCARS 09-Apr-2001 Advanced Photon Source Undulator Beamlines APS UNDULATOR A Period length: 3.30 cm Number of periods: 7 Length: 2.47 m Kmax: 2.78 (effective; at minimum gap) Minimum gap: 10.5 mm Energy Tuning Range: 2.9 - 13.0 keV (1 st harmonic) 2.9 - 45.0 keV (3 rd and 5 th harmonic) On-axis peak brilliance (at 6.5 keV): 9.6x10 18 ph/s/mrad 2 /mm 2 /0.1%bw Power (closed gap): : 6.0 kW On-axis power density (closed gap): 167 kW/mrad 2 Source Size and Divergence: Vert:  = 21  m,  ’ = 7  rad Horiz:  = 359  m,  ’ = 21  rad

4. GeoSoilEnviroCARS 09-Apr-2001 Element Specific: Elements with Z>16 can be seen at the APS, and it is usually easy to distinguish different elements. X-ray Fluorescence: Measure characteristic x-ray emission lines from de-excitation of electronic core levels for each atom. Natural Samples: samples can be in solution, liquids, amorphous solids, soils, aggregrates, plant roots, surfaces, etc. Low Concentration: concentrations down to a few ppm can be seen. Quantitative: precise and accurate elemental abundances can be made. x-ray interaction with matter well-understood. Small Spot Size: measurements can be made on samples down to a few microns in size. Combined with Other Techniques: XANES, EXAFS, XRD X-ray Fluorescence Microprobe

5. GeoSoilEnviroCARS 09-Apr-2001 X-ray Absorption Spectroscopy: Measure energy-dependence of the x-ray absorption coefficient  (E) [either log(I 0 /I) or (I f / I 0 )] of a core-level of a selected element X-ray Absorption Spectroscopy: XANES and EXAFS Element Specific: Elements with Z>20 can have EXAFS measured at the APS. EXAFS = Extended X-ray Absorption Fine-Structure XANES = X-ray Absorption Near-Edge Spectroscopy Valence Probe: XANES gives chemical state and formal valence of selected element. Natural Samples: samples can be in solution, liquids, amorphous solids, soils, aggregrates, plant roots, surfaces, etc. Low Concentration: concentrations down to 10 ppm for XANES, 100 ppm for EXAFS. Small Spot Size: XANES and EXAFS measurements can be made on samples down to ~5 microns in size. Local Structure Probe: EXAFS gives atomic species, distance, and number of near-neighbor atoms around a selected element..

6. GeoSoilEnviroCARS 09-Apr-2001 1. An x-ray of energy E is absorbed by an atom, destroying a core electron state with energy E 0 and creating a photo-electron with energy (E-E 0 ). 2. The probability of absorption  (E) depends on the overlap of the core-level and photo-electron wave-functions. Since the core-level is localized, this overlap is determined by the photo-electron wave-function at the center of the absorbing atom. For an isolated atom, this is a smooth function of energy. 3. With another atom nearby, the photo-electron can scatter from the neighbor. The interference of the outgoing and scattered waves alters the photo-electron wave- function at the absorbing atom, modulating  (E). 4. The oscillations in  (E) depend on the near-neighbor distance, species and coordination number. X-ray Absorption Fine-Structure Spectroscopy

7. GeoSoilEnviroCARS 09-Apr-2001 Beamline13-ID-C is a world-class micro-beam facility for x-ray fluorescence (XRF) and x-ray absorption spectroscopy (XAS) studies: Focusing: Horizontal and Vertical Kirkpatrick-Baez mirrors Incident Beam: Monochromatic x-rays from LN 2 cooled Si (111) Sample Stage: x-y-z stage, 0.1  m resolution Fluorescence detector: 16-element Ge detector [shown], Si(Li) detector, Lytle Detector, or Wavelength Dispersive Spectrometer at 90 o to incident beam Data Collection: Flexible software for x-y mapping, traditional XAFS scans, XAFS scans vs. sample position. Optical Microscope: (5x to 50x) with external video system GSECARS Fluorescence and XAFS Microprobe Station

8. GeoSoilEnviroCARS 09-Apr-2001 Double Focussing With Elliptical Mirrors Kirkpatrick-Baez Focusing Mirrors: Use x-ray reflection from an elliptical shaped mirror to focus the beam with a large demagnification.

9. GeoSoilEnviroCARS 09-Apr-2001 The table-top Kirkpatrick-Baez mirrors use four-point benders and flat, trapezoidal mirrors to dynamically form an ellipsis. They can focus a 300x300  m beam to 1x1  m - a flux density gain of 10 5. With a typical working distance of 100mm, and an energy-independent focal distance and spot size, they are ideal for micro-XRF and micro-EXAFS. We use Rh-coated silicon for horizontal and vertical mirrors to routinely produce 3x3  m beams for XRF, XANES, and EXAFS. Kirkpatrick-Baez Focusing Mirrors

10. GeoSoilEnviroCARS 09-Apr-2001 Solid-State Multi-Element Ge Detector for X-Ray Fluorescence detection Ge solid-state detectors have energy resolutions of ~250 eV, which separates most fluorescence lines from different elements. They allow a full XRF spectrum (or the windowed signal from several lines) to be collected in seconds: Ge detectors are limited in total count rate (to ~100KHz), so multiple elements (10 to 30) are used in parallel to make one large detector. We use a detector with 16-elements. Detection limits are at the ppm level for XRF. XANES and EXAFS measurements of dilute species (~10ppm) in heterogeneous environments can be measured. X-ray Fluorescence Detector

11. GeoSoilEnviroCARS 09-Apr-2001 Sam Traina, Chia Chen, Isao Yamakawa (Ohio State Univ.), Gordon Brown, Jeff Warner, Jeff Catalano (Stanford Univ.) Borehole samples were collected from the vadose zone under leaking waste tanks. Radioactive (~10  Ci/g Cs-137) soil sections were embedded in epoxy, and sent for synchrotron analysis to APS and SSRL during January, 2001. Cr Redox in Boreholes below Hanford Waste Tanks Cr has been found at concentrations >10,000 ppm in the vadose zone beneath the high-level nuclear waste tanks at Hanford, WA. The very alkaline solution in the tanks favors Cr 6+ in chromate (CrO 4 2- ), which is highly mobile in groundwater, acutely toxic, teratogenic, and carcinogenic. Cr 3+ is relatively immobile in groundwater, and far less toxic. Therefore, the environmental impact of Cr from tank leachates in the vadose zone is highly dependent on the chromium speciation. Determining the extent of Cr 6+  Cr 3+ reduction within the soils, and identifying possible reduction pathways (Fe- and Mn- (oxy)hydroxides, bacterial) are vital.

12. GeoSoilEnviroCARS 09-Apr-2001 micro-XRF mapping and Cr XANES were measured at GSECARS, bulk Cr XAS SSRL beamline 11-2, and Cs and Cr XANES at PNC-CAT (APS 20-ID). Elemental maps (below) show several Cr ‘hot-spots’, but also a fairly high background level. Cr correlations with Fe and Mn (the proposed abiotic reducing agents for Cr 6+ ) varied considerably between 4 different borehole samples measured. Cr XANES measurements were made on selected areas of high/low Cr, with/without Fe, and so on. Cr under Leaking Hanford Waste Tanks: XRF Maps 300 x 300  m CrBaFe These x-ray fluorescence maps of elemental concentration were made with incident x-ray beam 5x5  m, E = 7200eV (just above the Fe K-edge). The sample was scanned through this beam in 5  m steps. (~8hr collection). Each map shows the integrated fluorescence of the characteristic line (Cr and Fe K , Ba L  ).

13. GeoSoilEnviroCARS 09-Apr-2001 Hanford Cr Oxidation State Prelminary analysis of the Cr XANES from different core samples shows high variability of the Cr 6+ / Cr 3+ ratio, with fairly significant reduction of Cr 6+ to Cr 3+ and little obvious correlation with the presence of Fe. Cr EXAFS measurements are still being processed (but seem to be dominated by typical Cr 3+ -oxide) Hanford Tank Cr: Oxidation State with XANES XANES can easily distinguish Cr 6+ from Cr 3+ from the height of the pre-edge peak.

14. GeoSoilEnviroCARS 09-Apr-2001 Metal oxide dust was introduced to a forest topsoil resulting in 5000 ppm Zn and 2500 ppm Cu in the soil. Undisturbed soil samples will be taken a various times up to 5 years to follow the distribution pathways of the toxic metals.  XRF maps show the distribution of Zn, Cu, Fe and Mn near a barley root growing in the contaminated soil. Close to a Zn oxide particle, the root is strongly enriched in Zn. Andreas Scheinost, Ruben Kretzschmar (ETH Zurich) Optical microscope image of root Zn Cu Fe Mn stele cortex Mn-rich Fe-rich Zn-rich Cu-rich Metals Distribution at Root/soil Interface Arrow mark regions where Zn  -XAFS spectra were collected.

15. GeoSoilEnviroCARS 09-Apr-2001 The Zn-rich and Cu-rich areas consist of Zn oxide. The remaining areas lack a strong second shell, and show tetrahedral Zn-O coordination, suggesting that Zn dissolved from the oxide is sorbed by the root cortex and by Fe and Mn hydroxides. Zn EXAFS and Speciation at Rhizosphere

16. GeoSoilEnviroCARS 09-Apr-2001 D. Schulze (Purdue University) Manganese is an essential nutrient for plants, needed for photosynthesis and response to stress and pathogens. Reduced Mn 2+ is soluble and bio-available in soils but Mn 4+ will precipitate (along with Mn 3+ ) as insoluble Mn oxides. The redox chemistry of Mn in soil is complex, with both reduction and oxidation catalyzed by microorganisms. Spatially-resolved  -XANES is well-suited for mapping Mn oxidation state in live plant rhizospheres to understand the role of Mn redox reactions in a plant’s ability to uptake trace elements. XRF image of total Mn concentration (left) of soil traversed by a sunflower root (dashed line) showing the heterogeneous Mn and enrichment near the root. The Mn oxidation state map (right) shows both Mn 2+ and Mn 4+ in the Mn-rich sites, with a tendency for the reduction near the root. Collecting Mn fluorescence with the incident be at a few well-chosen energies around the Mn K-edge, we make 3-d (X-Y-Energy) maps that give the spatial distribution of Mn oxidation states. Oxidation state maps: Mn redox at plant roots

17. GeoSoilEnviroCARS 09-Apr-2001 John Mavrogenes, Andrew Berry (Australian National University) Cu 25 o C Cu 495 o C Fe 25 o C Fe 495 o C Understanding the metal complexes trapped in hydrothermal solutions in minerals is key to understanding the formation of ore deposits.  XRF and  XAFS are important tools for studying the chemical speciation and form of these fluid inclusions. 65  m Natural Cu and Fe-rich brine fluid inclusions in quartz from Cu ore deposits were examined at room temperature and elevated temperatures by XRF mapping and EXAFS. Initial Expectation: chalcopyrite (CuFeS 2 ) would be precipitated out of solution at low temperature, and would dissolve into solution at high temperature. We would study the dissolved solution at temperature. Cu speciation in Hydrothermal Fluid Inclusions XRF mapping showed that the initial expectation was wrong, and that a uniform solution at room temperature was becoming less uniform at temperature. This was reversible.

18. GeoSoilEnviroCARS 09-Apr-2001 John Mavrogenes, Andrew Berry (Australian National University) These results are consistent with Fulton et al [Chem Phys Lett. 330, p300 (2000)] study of Cu solutions near critical conditions: Cu 2+ solution at low temperature, and Cu 1+ associated with Cl at high temperatures. Cu speciation in Hydrothermal Fluid Inclusions XAFS measurements at low and high temperature were also very different, with a very noticeable differences in the XANES indicating a change in speciation Low temp: Cu 2+ High temp: Cu 1+ Cu 2+ O O 2.35Å 1.96Å Cl 2.09Å Cu 1+ Low temp (?) High temp (?) Preliminary fits to the EXAFS of the high temperature phase (below) is also consistent with Fulton et al: Cu 1+ with Cl (or S) at 2.09Å, and possibly some O at 1.96Å.

19. GeoSoilEnviroCARS 09-Apr-2001 A complication in measuring fluorescence and EXAFS in many natural samples is the presence of fluorescence lines from other elements near the line of interest: The resolution of a solid-state fluorescence detector (~150eV) is sometimes not good enough to resolve nearby fluorescence lines The Wavelength Dispersive Spectrometer has much better resolution (~20eV) than a solid-state detector, and a much smaller solid angle. It uses a Rowland circle, not electronics, to select energies of interest. It needs the brightness of an undulator, but complements the Ge detectors, and allows XRF and even EXAFS on systems with overlapping fluorescence lines. High Resolution X-ray Fluorescence and EXAFS

20. GeoSoilEnviroCARS 09-Apr-2001 J. McKinley, J. Zachara, S. M. Heald (PNNL) 1000 x 200  m image of the Cs L  line in biotite with a 5x5  m beam, 5  m steps and a 2s dwelltime at each point. The incident x-ray energy was 7KeV. 137 Cs cannot be wholly extracted from contaminated soils, even using harsh chemical treatments or cation exchangers. McKinley and Zachara exposed natural mica, similar to that found near PNNL, to a Cs-rich solution, embedded the mica in epoxy resin and cut cross-sections through the mica. Cs sorbs strongly to micas at selective edge sites and interlayer binding sites. Detecting the Cs L  fluorescence line is complicated by the nearby Ti K  line. The high resolution fluorescence detector can make these measurements much easier. Using the WDS for XRF Mapping: Cs on Micas

21. GeoSoilEnviroCARS 09-Apr-2001 J. McKinley, J. Zachara, S. M. Heald (PNNL) Cs L  map of muscovite cross section with WDS: 1300 x 150  m, 5  m pixels, 1 sec dwell time. Using the WDS for XRF Mapping: Cs on Micas Optical Initial Results: Cs concentrated on mica edges 67% of total Cs is located at edges Highest Cs concentration ~ 300 ppm, average Cs concentration ~ 10 ppm, detection limit ~ 1 ppm, “Non-edge” regions contain one-third of the Cs with average concentration of ~ 5 ppm. Cs-bearing interior regions appear associated with flake partings rather than interlayer lattice sites.

22. GeoSoilEnviroCARS 09-Apr-2001 John Rakovan (Miami University) Eu is the only REE showing no zonation, but it has two valence states and two ionic sizes that straddle the size of Ca 2+. Is there a partitioning of Eu based on valence state/ionic size? 011 vicinal face 001 vicinal face 011 vicinal face. Apatites have a high affinity for Rare Earth Elements (REE), and are often used to study petrogenesis. Heterogeneities in crystal surface structure during apatite growth can strongly alter REE incorporation. Most REE show sectoral zoning in apatite based on ionic size. Ions larger than Ca 2+ (La 3+ ) preferring growth along the 001 face, and those smaller than Ca 2+ (Sm 3+ ) preferring the 011 face Sector Zoning of Rare Earth Elements in Apatites

23. GeoSoilEnviroCARS 09-Apr-2001. Energy (keV) X-ray counts Since Eu has two valence states with different ionic sizes (Eu 2+ / 1.2 Å, Eu 3+ / 1.3 Å), it was suggested that there may be a valence/ionic size variation in different growth zones. The bad news: There is far too much Mn in the apatite to separate from the Eu fluorescence line with a solid state detector. Using the high resolution WDS and the microprobe, we measured the Eu XANES on several spots in the different sectors, and across a / boundary. Result: We see almost no change at all in Eu 2+ / Eu 3+ across the zone boundary: the ratio is ~17% Eu 2+ throughout the apatite. Sector Zoning of Rare Earth Elements in Apatites

24. GeoSoilEnviroCARS 09-Apr-2001 Louis Cabri (NRC Canada), Robert Gordon, Daryl Crozier (Simon Fraser), PNC-CAT 1000ppm Au in FeAsS (arsenopyrite): The understanding of the chemical and physical state of Au in arsenopyrite ore deposits is complicated by the proximity of the Au L III and As K edges and their fluorescence lines. At the Au L III -edge, As will also be excited, and fluoresce near the Au L  line. Even using the WDS, the tail of the As K  line persists down to the Au L  line, and is still comparable to it in intensity. 250x250  m image of the Au L  line in arsenopyrite with a 6x6  m beam, 5  m steps and a 2s dwell time at each point. The x-ray energy was 12KeV. Using the WDS for XANES: 1000ppm Au in FeAsS

25. GeoSoilEnviroCARS 09-Apr-2001 The tail of the As K  line is still strong at the Au L  energy, so using a Ge detector gave the Au L III edge-step as about the same size as the As K edge-step, and the Au XANES was mixed with the As EXAFS. With the WDS, the As edge was visible, but much smaller, and so the Au XANES was clearer. Louis Cabri (NRC Canada), Robert Gordon, Daryl Crozier (Simon Fraser), PNC-CAT The Au L III edge of two different natural samples of FeAsS with the WDS. Both samples had ~1000ppm of Au. We see clear evidence for metallic and oxidized Au in these ore deposits. As K-edge 11.868 KeV As K  line 10.543 KeV Au L III -edge 11.918 KeV Au L  line 9.711 KeV CANADIAN MINERALOGIST 38, pp1265-1281 (2000) Using the WDS for XANES: 1000ppm Au in FeAsS

26. GeoSoilEnviroCARS 09-Apr-2001 Surface Diffraction: Surface of Hydrated Alumina  -Al 2 O 3 is an important model system for understanding the reactivity of naturally abundant phases of Al-containing (hydr)oxides such as gibbsite or hydrous aluminosilicate clays. The Al in these phases have similar coordination chemistry. The reaction of water with the  -Al 2 O 3 (0001) has received a lot of experimental and theoretical attention. Surface diffraction measurements of the mineral-water interface is an important first step to understanding these interactions and the atomic-level reactivity of the Hydrated mineral surface. The interaction of water with natural surfaces is one of the most fundamental chemical reactions in nature. Processes such as mineral dissolution and sorption/ desorption reactions at mineral-water interfaces play major roles in weathering, contamination of groundwater, environmental restoration, and biogeochemical cycling of elements. General Purpose Diffractometer Peter Eng (CARS), Tom Trainor, Gordon Brown, Jr (Stanford Univ), Glenn Waychunas (Lawrence Berkeley Lab) [Science 288, pp1029-1033 (2000)]

27. GeoSoilEnviroCARS 09-Apr-2001 SAMPLE: single crystal wafer of (0001)  -Al 2 O 3, 0.5mm thick, 50mm in diameter, highly polished (1 Å rms roughness), and fully hydrated (see sample cell). In situ liquid cell with thin membrane mounts on diffractometer, and traps either liquid or (in this case) humid air for scattering, reflectivity, and fluorescence. This is enough to fully hydrate the surface of Al 2 O 3. Al 2 O 3 Surface Scattering: Methods Measurement Technique: Crystal Truncation Rods A surface disrupts the infinite 3D lattice that make Bragg diffraction spots, and moves diffraction intensity to lines “between the Bragg points”. The q-dependence and shape of these “rods” is sensitive to the roughness and atomic arrangement at the crystal surface. This may not appear to be a normal “microprobe” experiment, but it does require a bright and highly- collimated x-ray beam ~10 to 20  m high. And this is a very large, synthetic crystal!

28. GeoSoilEnviroCARS 09-Apr-2001 Surface Structure of Al 2 O 3 : Results Oxygen Terminated Al 2 O 3 Surface Disordered Oxygen Overlayer Hydrated Al 2 O 3 Surface Analysis of the truncation rod data shows two important results for the surface structure of hydrated (0001)  -Al 2 O 3 : The surface is oxygen-terminated, with a slight relaxation. This differs from in vacuum measurements, which show Al termination. The relaxed structure is similar to the basal plane of gibbsite  -Al(OH) 3 There is good evidence for a disordered water or hydroxyl layer

29. GeoSoilEnviroCARS 09-Apr-2001 X-ray computed microtomography (CMT) gives 3D images of the x-ray attenuation coefficient within a sample. At each angle, a 2D absorption image is collected. The angle is rotated around  in 1 o steps through 180 o, and the 3D image is reconstructed with software. Element-specific imaging can be done by acquiring tomograms with incident energies above and below an absorption edge. Fluorescence x-ray tomography is done with a pencil-beam scanned across the sample. The sample is rotated around  and translated in x. Tranmission x-rays are can be measured as well to give an overall density tomograph. data collection is relatively slow. can be complicated by self-absorption. can collect multiple fluorescense lines. X-ray Fluorescence Tomography: Overview broad x-ray beam rotation stage Sample Phosphor Microscope objective CCD camera x-rays Visible light  thin x-ray beam rotation stage Sample Fluorescence detector fluoresced x-rays  transmitted x-rays Transmission detector x translation stage

30. GeoSoilEnviroCARS 09-Apr-2001 Fluorescence detector: multi-element Ge detector Sample stage: x-y-z-  Sample mounted on silica fiber Optical microscope, KB mirrors Fluorescence Tomography: Experimental Setup

31. GeoSoilEnviroCARS 09-Apr-2001 x  The Raw fluorescence tomography data consists of elemental fluorescence (uncorrected for self-absorption) as a function of position and angle: a sinogram. This data is reconstructed as a virtual slice through the sample by a coordinate transformation of (x,  )  (x, y). The process can be repeated at different z positions to give three-dimensional information. Fluorescence Sinograms for Zn, Fe, and As collected simultaneously for a section of contaminated root (photo, right): x: 300  m in 5  m steps  : 180  in 3  steps As Fe Zn Fluorescence Tomography: Sinograms

32. GeoSoilEnviroCARS 09-Apr-2001 The role of root-borne carbonate nodules in the attenuation of contaminant metals in aquatic plants is investigated with EXAFS, SEM and X-Ray fluorescence tomography. These images of a 300  m root cross-section (Phalaris arundinacea) show Fe and Pb are uniformly distributed in the root epidermis while Zn and Mn are correlated with nodules. Arsenic is poorly correlated with the epidermis, suggesting a non-precipitation incorporation. S. Fendorf, C. Hansel (Stanford): Toxic Metal around Root-borne Carbonate Nodules Slicing the root would cause enough damage that 2D elemental maps would be compromised. photograph of root section and reconstructed slices root from fluorescent x-ray CT. 3D Distributions of Heavy Metals in Roots Such information about the distribution of elements in the interior of roots is nearly impossible to get from x-y mapping alone:

33. GeoSoilEnviroCARS 09-Apr-2001 Thanks to: Steve Sutton, Mark Rivers, Peter Eng GeoSoilEnviroCARS, University of Chicago http://cars.uchicago.edu/gsecars/ Synchrotron x-ray microprobes have wide applicability in the earth, planetary, soil and environmental sciences. X-ray Microprobe for Environmental Sciences Greatest current demand is for microbeam applications of XANES and EXAFS. Expect demand to growth areas to be fluorescence microtomography studies of fragile materials study of in-situ biogeochemical processes surface diffraction and spectroscopy high-pressure, high-temperature (extreme condition) studies