Synchrotron Techniques in Environmental Sciences

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Synchrotron Techniques in Environmental Sciences
Matt Newville, Steve Sutton, Mark Rivers, Peter
Eng Consortium for Advanced Radiation
Sources University of Chicago (DOE and NSF
support)
Synchrotron x-ray techniques
x-ray diffraction
crystallographic structure, phase identification,
and surface structures
x-ray imaging tomography
3-dimensional densities, elemental abundances
elemental abundance and correlations
x-ray fluorescence
x-ray absorption spectroscopy (XANES and EXAFS)
oxidation state of selected element,
near-neighbor distances and coordination numbers
2
X-ray Applications for Geo/Environmental Sciences
G. E. Brown, Jr. and N. Sturchio identified these
important issues in low-temperature geochemistry
and environmental science From An Overview of
Synchrotron Applications in Low Temperature
Geochemistry and Environmental Science. Reviews
of Mineralogy Geochemistry (vol 49, 2002)

• In-situ studies, e.g. in the presence of
• water, water vapor, biota, are critical.
• Molecular-level speciation of trace
• environmental contaminants are
• necessary for understanding their
• behavior.
• Complex natural systems and model
• systems must be studied in parallel.
• Complementary characterization and
• modeling methods are necessary.
• The nature of solid/water interface and
• sorbed species must be known.
• Molecular mechanisms of bio- and
• phyto-remediation must be understood.

Synchrotron x-ray techniques are powerful tools
for addressing these issues.
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What is a Synchrotron? A very bright x-ray source
Advanced Photon Source, Argonne National Lab,
Argonne Illinois
7 GeV electron storage ring producing
high-brilliance x-ray beams. 40 experimental
stations running simultaneously, with a wide
range of applications. 1 of 4 US DOE run x-ray
sources operated as User Facilities (easy
access). Many similar machines throughout the
world.
Electrons accelerated to 7GeV emit hard x-rays (1
to 100 keV).
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Synchrotron a very bright x-ray source
Advanced Photon Source, Argonne National Lab,
Argonne Illinois
7 GeV electron storage ring producing
high-brilliance x-ray beams. 40 experimental
stations running simultaneously, with a wide
range of applications. 1 of 4 US DOE run x-ray
sources operated as User Facilities (easy
access). Many similar machines throughout the
world.
GSECARS 1 of 7 stations doing Environmental
Science at the APS
5
X-ray Properties of Synchrotrons
x-ray brilliance for conventional laboratory and
synchrotrons brilliance of monochromatic
x-rays per second, per area, per solid angle
how many monochromatic x-rays in a beam of
light? Synchrotron x-rays have a broad energy
spectrum white light, and are collimated in
space. They can be focused to a few microns
(sometimes smaller) or as large as several
millimeters in size. x-rays are mostly
non-destructive.
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Typical Experimental Station (x-ray microprobe)
Sample Stage x-y-z stage, 1mm resolution
Incident Beam LN2 cooled Si (111) mono
CCD Camera Bruker area detector
Fluorescence detectors 16-element Ge detector
with DXP electronics Si-drift detector (shown)
Lytle Ion Chamber Bent Laue Analyzer Wavelength
Dispersive Spectrometer
Optical Microscope 5x to 50x objective with
external video system
Focusing Kirkpatrick-Baez mirrors Rh-coated Si,
typically using 2x3mm spot sizes, at 50mm from
end of mirrors.
Entrance Slits typically 250mm X 250mm ,
accepting 30 of undulator beam
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X-ray Diffraction and Scattering
X-ray Diffraction / Scattering Determine the
crystallographic phases in a sample, study
surface and interface structures
Quantitative very precise / accurate
determination of crystalline phases
Small Spot Size x-ray beam sizes of a few
microns make very small phases visible.
Several modes available using synchrotron
radiation
Single Crystal Diffraction (precise atomic
positions) Powder diffraction (phase
identification, unit cell
refinement) Small / Wide Angle Scattering
(nanometer-scale structure) Surface / Interface
studies (surface structure)
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X-ray Absorption Tomography
X-ray Tomography x-ray absorption radiography
collected at different angles to look in the
interior of objects
High Resolution micron-scale 3D volumes can be
made of millimeter sized objects.
See inside sample without actually slicing
precious or sensitive objects, one can make any
virtual slice desired.
Sample
Visible light
x-rays
x-rays
CCD camera
Get beautiful images can quickly aide
understanding of system.
w
Phosphor
Microscope objective
rotation stage
Get full 3d volume can be put into mathematical
models of fluid flow, pore volume connectivity,
etc.
Can get elemental specificity by going
above/below an absorption edge works for
elements at wt level.
Eocene age fossil
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X-ray Fluorescence and Microprobe
X-ray Fluorescence characteristic x-ray emission
lines from de-excitation of electronic core
levels for each atom.
Element Specific All elements with Zgt14 are
visible. It is usually easy to distinguish
different elements.
Quantitative precise and accurate elemental
abundances can be made.
Low Concentration concentrations down to ppm
level can be seen.
Natural Samples samples can be in solution,
liquids, amorphous solids, soils, plant roots,
surfaces, etc.
Small Spot Size measurements can be made on
samples down to a few microns in size.
Combined with Other Techniques XRD, XANES, EXAFS
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X-ray Absorption Spectroscopy XANES and EXAFS
X-ray Absorption Spectroscopy energy-dependence
x-ray absorption coefficient m(E) for a
core-level electron of an element
Element Specific Elements with Zgt14 can have
EXAFS measured
Valence Probe XANES is sensitive to chemical
state and formal valence of selected element.
Local Structure Probe EXAFS gives atomic
species, inter-atomic distance, and number of
near-neighbor atoms around a selected element..
Low Concentration 10 ppm for XANES, 100 ppm
for EXAFS.
Natural Samples samples can be in solution,
liquids, amorphous solids, soils, plant roots,
surfaces, etc.
Small Spot Size XANES and EXAFS measurements can
be made on samples down to 5 microns in size.
XANES X-ray Absorption Near-Edge Spectroscopy
EXAFS Extended X-ray Absorption Fine-Structure
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XANES Oxidation State and Coordination Chemistry
X-ray Absorption Near-Edge Spectroscopy (XANES)
gives a direct measurement of chemical state and
valence state of an element..
For atoms with partially filled d orbitals, the
amount of p-d hybridization dramatically changes
when the local coordination goes from octahedral
to tetrahedral. This gives dramatic changes in
XANES, including pre-edge peaks, which are due to
unfilled d orbitals that can be filled by an s-gtp
transition only with orbital hybridization.
This depends strongly on coordination chemistry
and formal oxidation state.
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Strontium Paleothermometer in Coral XRF
Nicola Allison, Adrian Finch (Univ of Brighton,
Univ of Hertfordshire, UK)
The abundance of Sr in aragonite (CaCO3) formed
by corals is used to estimate of seawater
temperature and composition at formation time.
Sr/Ca T XRF MAPS of a section of the
coral were made at 5mm resolution. Sr and Ca
fluorescence (and other trace elements) were
measured simultaneously at each pixel with a
multi-element solid-state detector. The Sr and
Ca maps show incomplete correlation and
substantial variations in Sr/Ca on length
scales consistent with a diurnal growth cycle.
Ca
Sr
200mm
300mm
Sr XAFS was measured at a spot with high Sr --
above the solubility limit of Sr in aragonite.
SEM images of Night growth (Left) and Daytime
growth (Right)
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Strontium Paleothermometer in Coral EXAFS
Nicola Allison, Adrian Finch (Univ of Brighton,
Univ of Hertfordshire, UK)
Since the Sr concentration was above its
solubility limit (1) in aragonite, it was not
known if Sr would precipitate out into
strontianite (SrCO3 a structural analog of
aragonite), or remain in the aragonite
phase. First shell EXAFS is same for both
strontianite and aragonite 9 Sr-O bonds at
2.5A, 6 Sr-C at 3.0A. Second shell EXAFS
clearly shows Sr-Ca (not Sr-Sr) dominating, as
shown at left by contrast to SrCO3 data, and by
comparison to simulated EXAFS spectrum of Sr
substituted into aragonite. The coral traps Sr
in thermodynamically-unfavorable aragonite
structure, even at super-saturated concentrations.
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Metal Uptake in Ni Hyperaccumulating Plants
D. Sparks, D. McNear, E. Peltier , U. of Delaware
How is Ni taken up, transported, and stored in
the hyperaccumulating species Alyssum murale
(mustard family)? Can we improve our basic
understanding of phytoremediation, and hopefully
optimize it? Samples were grown both
hydroponically and in Ni enriched soils.
Fluorescence Tomography
focused x-ray beam
Sample
Transmission detector
fluoresced x-rays
w
Alyssum murale
x
Fluorescence tomography allows us to measure
metal distribution in the interior of plant
material without physically slicing the plant.
rotation and translation stages
fluorescence detector
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X-ray Tomography Results for Alyssum Murale
D. Sparks, D. McNear, E. Peltier, et al., U. of
Delaware
Leaf Ni is in epidermal cells and veins but not
in mesophyll cell. Zn is in the veins and
exterior walls. Stem Ni is in epidermis, pith
and other ground tissues. The phloem side of
vascular bundles has little Ni, the xylem is
enriched in Ni. Zn is at the interface of the
epidermis and vascular system. Root Ni, Zn, and
Fe are all present on root exterior in dried
roots, and seen in the interior of wet roots.
Virtual slices through alyssum murale grown in
Ni-enriched soil
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Surface Scattering, the hematite surface
P. Eng, S. Ghose (U. Chicago), T. Trainor (U
Alaska, Fairbanks)
Surface x-ray diffraction 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 crystal
truncation rods is sensitive to the roughness and
atomic arrangement at the crystal surface.
Sample single crystal wafer of (1-102) a-Fe2O3,
0.5mm thick, fully hydrated, clean, and then with
100mM Pb sorbed on the surface.
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Surface Structure of Fe2O3 CTR Results
P. Eng, S. Ghose (U. Chicago), T. Trainor (U
Alaska, Fairbanks)
CTR data for hydrated (1 -1 0 2) Fe2O3 surface
with two structural models
Bulk termination
Missing Fe termination
The bulk termination gives a poor fit, and
removing one Fe from the termination gives a much
better match to the measurement.
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Surface Structure of (1-102)Fe2O3 with 100mM Pb
P. Eng, S. Ghose (U. Chicago), T. Trainor (U
Alaska, Fairbanks)
Pb(II) sorption isotherms on the hematite (1-102)
surface
Facet-specific adsorption curves can be
measured. CTR data gives the structure of the
ordered adsorption complexes and fractional
site occupancy Such experimental adsorption
isotherms give facet-specific binding energies
that can be compared to calculations.
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X-ray Applications for Geo/Environmental Sciences
G. E. Brown, Jr. and N. Sturchio identified these
important issues in low-temperature geochemistry
and environmental science From An Overview of
Synchrotron Applications in Low Temperature
Geochemistry and Environmental Science. Reviews
of Mineralogy Geochemistry (vol 49, 2002)

• In-situ studies, e.g. in the presence of
• water, water vapor, biota, are critical.
• Molecular-level speciation of trace
• environmental contaminants are
• necessary for understanding their
• behavior.
• Complex natural systems and model
• systems must be studied in parallel.
• Complementary characterization and
• modeling methods are necessary.
• The nature of solid/water interface and
• sorbed species must be known.
• Molecular mechanisms of bio- and
• phyto-remediation must be understood.

Synchrotron x-ray techniques are powerful tools
for addressing these issues.