Applications of in-situ X-ray Scattering Techniques

Sam Webb

SSRL Scattering Workshop

May 15, 2007

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

Beamline Setup (BL 11-3)

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

Acknowledgements

Anna Obraztsova and Greg Dick (SIO) Apurva Mehta (SSRL) Tanya Gallegos (U of M) Funding:

NSF-CRAEMS DOE-BER DOE-BES

R/V Knorr, Black Sea, 2003