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
Biological indicators for the presence of life
Stable over time
Biologically and abiotically formed states are
distinguishable
Search for life on other planets
Manganese Oxides
Formed by various
bacteria in naturedesert varnish
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
X-ray Absorption Spectroscopy
Photoelectric effect- threshold energy
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
Mn oxides formed by bacteria are poorly
crystallized and defective
X-Ray Diffraction
Assumes periodicity in order to observe a larger
range
Complementary to XAS
Immediate environment around atom
Explores local structure, better suited for Mn oxides
Experimental Setup
Transmission/Fluorescence
Transmission
How much of beam goes through sample
Need very concentrated sample, constant sample
thickness because looking at very small changes
Fluorescence
Emission after photoelectron drops back down to
steady state
Moderately dilute samples- over-absorbance effect
Data Analysis
Normalize raw data to edge
Subtract background, spline
EXAFS χ(k) plot
K3-weighted to enhance oscillations at high k
EXAFS Fitting
Fit EXAFS with FEFF paths (single scattering
model)
Parameters: radial distance (R), disorder (2)
EXAFS χ(k) stack plot
Rank by defects
6.8, 8.0, 9.0 k(Å-1) trends
Comparing EXAFS and XRD
Todorokite and birnessite ideal
Order by structure
Layer/Tunnel (todorokite)
Layered (birnessite, lithiophorite, chalcophanite)
Tunnel (coronadite, cryptomelane)
Small Tunnel (ramsdellite, pyrolusite)
Todorokite (Layer/Tunnel)
Birnessite (Layer)
Coronadite (Tunnel)
Ramsdellite (Small Tunnel)
Fourier Transform Plot
Trend at 4-6Å
Disorder caused by:
Vacancies
Cations
Bending
Constrained-to-XRD fits
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
Further reinforces ranking of the manganese oxides
according to ideal structure
Conclusion
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
Special thanks to:
John Bargar and Apurva Mehta
Ellie Schofield and Sam Webb
Susan Schultz, Farah Rahbar, and Steve Rock
SLAC, DOE