Determining the Structure and Defects of Manganese Oxides using X-Ray Absorption Spectroscopy

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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

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Biosignatures

• Biological indicators for the presence of life
• Stable over time
• Biologically and abiotically formed states are
  distinguishable
• Search for life on other planets

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Manganese Oxides

• Formed by various bacteria in nature- desert
  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

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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)

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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

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Experimental Setup
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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

8
Data Analysis

• Normalize raw data to edge
• Subtract background, spline

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EXAFS ?(k) plot

• K3-weighted to enhance oscillations at high k

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EXAFS Fitting

• Fit EXAFS with FEFF paths (single scattering
  model)
• Parameters radial distance (R), disorder (?2)

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EXAFS ?(k) stack plot

• Rank by defects 6.8, 8.0, 9.0 k(Å-1) trends

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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)

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• Todorokite (Layer/Tunnel)
• Birnessite (Layer)

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• Coronadite (Tunnel)
• Ramsdellite (Small Tunnel)

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Fourier Transform Plot

• Trend at 4-6Å
• Disorder caused by
• Vacancies
• Cations
• Bending

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Constrained-to-XRD fits

• Amplitude reduction? fit produced lower
  coordination numbers than predicted
• If constrained to XRD parameters before fitting
  (CN6), 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

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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

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Acknowledgements

• Special thanks to
• John Bargar and Apurva Mehta
• Ellie Schofield and Sam Webb
• Susan Schultz, Farah Rahbar, and Steve Rock
• SLAC, DOE