Transcript Quan

Determining the Structure and
Defects of Manganese Oxides
using X-Ray Absorption
Spectroscopy
Stanley Quan
University of California, Berkeley
Stanford Synchrotron Radiation Laboratory, SLAC
Mentors: John Bargar & Apurva Mehta
August 14, 2008
Biosignatures
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Biological indicators for the presence of life
Stable over time
 Biologically and abiotically formed states are
distinguishable
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Search for life on other planets
Manganese Oxides
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Formed by various
bacteria in naturedesert varnish
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Well-preserved deposits up to 2.22 billion years
old (anoxic  oxic state atmosphere) as desert
varnish
Recent studies suggest biogenic Mn oxides can
be distinguished from abiogenic Mn oxides with
EPR (Electron Paramagnetic Resonance)
Must refine detailed crystal structures
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X-ray Absorption Spectroscopy
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Photoelectric effect- threshold energy
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Photoelectron emitted (“edge” around 6552 eV)
Backscattered by surrounding atoms
Interference pattern (outgoing and backscattered)
Extended X-ray Absorption Fine Structure (EXAFS)
Comparing to XRD
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Mn oxides formed by bacteria are poorly
crystallized and defective
X-Ray Diffraction
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Assumes periodicity in order to observe a larger
range
Complementary to XAS
Immediate environment around atom
 Explores local structure, better suited for Mn oxides
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Experimental Setup
Transmission/Fluorescence
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Transmission
How much of beam goes through sample
 Need very concentrated sample, constant sample
thickness because looking at very small changes
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Fluorescence
Emission after photoelectron drops back down to
steady state
 Moderately dilute samples- over-absorbance effect
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Data Analysis
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Normalize raw data to edge
Subtract background, spline
EXAFS χ(k) plot
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K3-weighted to enhance oscillations at high k
EXAFS Fitting
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Fit EXAFS with FEFF paths (single scattering
model)
Parameters: radial distance (R), disorder (2)
EXAFS χ(k) stack plot
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Rank by defects
6.8, 8.0, 9.0 k(Å-1) trends
Comparing EXAFS and XRD
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Todorokite and birnessite ideal
Order by structure
Layer/Tunnel (todorokite)
 Layered (birnessite, lithiophorite, chalcophanite)
 Tunnel (coronadite, cryptomelane)
 Small Tunnel (ramsdellite, pyrolusite)
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Todorokite (Layer/Tunnel)
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Birnessite (Layer)
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Coronadite (Tunnel)
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Ramsdellite (Small Tunnel)
Fourier Transform Plot
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Trend at 4-6Å
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Disorder caused by:
Vacancies
 Cations
 Bending
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Constrained-to-XRD fits
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Amplitude reduction fit produced lower
coordination numbers than predicted
If constrained to XRD parameters before fitting
(CN=6), fit showed progressively more added
disorder when going down the series, except for
todorokite and birnessite
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Further reinforces ranking of the manganese oxides
according to ideal structure
Conclusion
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By looking at the EXAFS, we were able to see
that some manganese oxides are more defective
than others
From XRD we learned about their structures,
but now with EXAFS we can characterize their
structures by lattice disorder and defects
Knowing about the structure may lead to insight
about the way they are formed by bacteria and
help us identify them if used as biosignatures
Acknowledgements
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Special thanks to:
John Bargar and Apurva Mehta
 Ellie Schofield and Sam Webb
 Susan Schultz, Farah Rahbar, and Steve Rock
 SLAC, DOE
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