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Overview
Why in situ? Experimental Design
Beamlines Sample prep Analysis
Reactions with x-ray scattering Example(s)
Why Should I Do Scattering When I Have EXAFS Data?
EXAFS = Local StructureWAXS = Long-Range Structure
2 4 6 8 10 12 14
-10
0
10
20
30
40
k3 (k
)
k (Å-1)
TriclinicBirnessite
Hexagonal Birnessite
-MnO2
10 5 1
0.0
0.5
1.0
2
Inte
nsi
ty (
Arb
. U
nits
)
D (Å)
Triclinic Birnessite
Hexagonal Birnessite
-MnO2
Why In-situ
Traditional powder diffraction experiments require dry, fine powders as samples
For many biological and environmental samples: Drying = artifact
Dehydration, exposure to air Powder = artifact
Other thoughts to consider… Sample throughput Sample textures Timing/Reactions
Experimental Design
Does my sample need to be wet? Transmission vs. reflection Tradeoffs due to backgrounds of sample holder
and water
High resolution vs. low Soller slits vs. analyzer vs. area detector
Data range Exposure to beam? Exposure to air?
Diffractometer (SSRL BL 2-1)
incident beamsample
detector
collimating slits
scattered x-rays
analyzer
Powder Scattering Experiment Monochromatic Sample contains all crystal
orientations Detector and sample
angles unchanged
X-ray source (Synchrotron)
Mono
Slits
Sample
Detector
Beamstop
Diffractometer (SSRL 11-3)
Tight spaces in hutch Samples:
Flat plate transmission
Reflection (half of area detector)
Capillary
BL software (Blu-Ice) 5-10 MB per picture
Diffractometer (SSRL 11-3)
Tight spaces in hutch Samples:
Flat plate transmission
Reflection (half of area detector)
Capillary
BL software (Blu-Ice) 5-10 MB per picture
Sample Preparation (Flat plate) Keep sample hydrated to avoid artifacts!
Change in oxidation state/mineralogy Collapse of hydrated structures
Use transmission geometry Why? - Better subtraction of background
scattering (water, windows) Window material important
Lexan is a good material for background removal (WAXS)
Water peaks in similar places as silica
bottom plate
top plate
lexanwindows sample
shim spacer
Optimize sample thickness depending on and sample composition. Sample should absorb ~ 20‑50% of incident beam. One “” is about max.
Other sample holders – goniometer head – sample distance ~ 37 mm (11-3, 7-2)
What if I have a powder for transmission? Flat plate is poor for dry
samples Particles are not generally
stable and settle – even out of beam!
Need a better support – tape!
Kapton not ideal Scotch Magic tape (translucent)
0.5 1.0 1.5 2.0 2.5 3.00
2000
4000
6000
8000
10000
Scotch
Kapton
Cou
nts
Q (A-1)
Data Analysis
CCD to diffractogram (2D to 1D) Geometry corrections Background subtraction
Windows, capillary, tape Water Other interferences (cotton, etc)
Integration of Powder Pattern What Can it Tell?
Peak Positions: Phase identification Lattice symmetry
Peak Shape & Width: Crystallite size Textures (preferential
orientation, multiple phases, etc.)
Peak Intensity: Crystal structure
FIT2D http://www.esrf.fr/
computing/scientific/FIT2D/
Theta Dependent Effects Absorption
Samples absorb the incident and transmitted beams
Volume effect 1/cos dependence
Compton Scattering Highest at large
Abs = (t / cos exp(-t/cos )
Measure sample absorption at the beamline!
In order to get proper removal of background (windows, water) these corrections must be made. Critical for thicker samples!
t cos
t
Background Subtraction
Background in experiments consists of lexan windows and water
0 20 40 60 80 100 1200.0
0.1
0.2
0.3
0.4
0.5
0.6
Raw Data Lexan Water
Inte
nsity
2 @ 10 keV
GUI for removal of background and thickness corrections
Designed for use with Fit-2D output (chi files)
RDSUB
http://www-ssrl.stanford.edu/~swebb/xrdbs.htm
Reactions Mineral-solution reactions
Time scale of minutes to hours Redox reactions Cation exchange Colloid transport
Sample prep = miniaturized “columns” (i.e., particles packed in a capillary) Lexan capillary
Better background (no overlap with water like silica) Doesn’t break!
Particle size and porosity Clogging
Flow rate Stalling of pump
Reaction Flow Setup (not to scale)
120 mL Syringe pump
Tubing
Gasketed capillary holder
Incident beam
Scattered Beam
SampleCotton
Flow collection system
Future Improvements…
Peristaltic pump vs. syringe pump Better flow and ability to change reactant solutions
Development of better column packing materials Gas impermeable tubing
Improve anaerobic conditions Injection loop
Easy loading of capillary Fraction collector
Analysis of post-reaction fluids Fluorescence detector
Monitor elemental changes in sample if reactions lead to deposition / removal of compounds
Examples
Mn biomineral structures Compare 2-1 and 11-3 data quality
Real time biogenic Mn oxidation Area detectors in reactions
MnOxide reactions with metals Area detectors in reactions
Sulfide mineral oxidation Wet-dry artifacts for air sensitive minerals Air exposure
Mn Oxide Biomineral Structure
BL 11-3 2 minute exposure
360 degrees are better than 1!
BL 2-1 Sum of 4 to 5 scans, ~8
hours total
14 10 2 1
Rb
Cs
K
Na
Ba
Sr
Ca
Mg
Inte
nsity
D(A)
Tradeoff between noise-resolution-time
Biogenic Mn Oxidation Mn oxidation in seawater
progresses through symmetry changes in oxide structure
Due to the effect of Ca present in interlayers Triclinic Hexagonal
a
b
aa*
Manganese in-situ Oxidation Mn(II)
Mn(IV)
Spores
Spores
Mn(IV)Oxide
Scan No. (~20 min between scan)
Q (
nm-1)
1d 2d
Triclinic peaks
10
20
30
40
50
Q
Manganese oxide reaction with metals
Q (A-1)
Time (h)
Co(II)
Mn(IV)
Co(II) reacts with pre-formed biogenic oxides to oxidize to Co(III). Mn-oxides are reduced
No evidence of new Co(III) minerals
Decrease in (001) amplitude
Biogenic MnOxides + Co(II)
001 peak broadens with reaction and shifts to larger d-spacings
Changes follow pseudo-first order reaction kinetics Slow and fast steps of Co(III) incorporation
0 10 20 30 40 50 60
0.55
0.60
0.65
0.70
0.75
0.80
0.85 th-1
= 1.27th-2
= 15.16
(001
) F
WH
M
Time (h)
0 10 20 30 40 50
0 10 20 30 40 50 608.53
8.54
8.55
8.56
8.57
8.58
8.59
8.60
8.61
(001
) P
ositi
on
Time (h)
Wet-Dry Artifacts Measurements of
anaerobic, dried sample lead to formation of peaks with different texture 1 2 3 4 5
2000
3000
Paste Dry
Cou
nts
Q (A-1)
FeS dried FeS paste, anaerobic
Fe-Sulfide oxidation reactions
FeSO2 O2
~1.2 mm from end
1 2 3 4 5
Cou
nts
Q (A-1) Time (h)
0
2
4
6
8
10
t=0 t=7 t=8 t=9 t=10
2-line Ferrihydrite
Mackinawite