1. 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

2. Biosignatures Biological indicators for the presence of life
Stable over time
Biologically and abiotically formed states are distinguishable
Search for life on other planets
Part of a bigger project in searching for extraterrestrial life, dating
In order to be used as biosignatures

3. 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
Mn oxides are very good candidates to be used as biosignatures
Picture-> words; found a lot of manganese oxides that date up to this time and therefore we know it is when the atmosphere changed
Desert varnish is a thin layer of manganese oxide, iron oxide, and clay that is deposited by bacteria living on the surface of the rock

4. 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)
Edge at about 6552 eV
Sum of sine waves w/amplitude and phase relating to backscatterer’s distance and composition

5. 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
Mn oxides formed by bacteria are often poorly crystallized, so xrd doesn’t work as well (ideal structure). Xas- explores local structure, more suited to studying the structure of mn oxides
Defective as in not pure, bacteria deposits

6. Experimental Setup Briefly talk about the setup
Monochromator gives a very small range of energies, essentially focuses the beam to a single energy
Fluorescence collected by lytle detector after going through a filter; transmission collected by ion chamber detector
Soller filters: prevent beam divergence, restrict the angles of diffraction

7. Transmission/Fluorescence
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
We collect both transmission and fluorescence measurements
Advantages and disadvantages for both

8. Data Analysis Normalize raw data to edge Subtract background, spline
Background absorption subtracted with red line
Spline with blue function

9. EXAFS χ(k) plot K3-weighted to enhance oscillations at high k
Blue curve is our k-weighted EXAFS
Red curve is the fit from FEFF paths with the single scattering Mn oxide model

10. EXAFS Fitting Fit EXAFS with FEFF paths (single scattering model)
Parameters: radial distance (R), disorder (2)
FT gives us peaks from scattering, we see many peaks, but in our case we only looked at the first two large peaks, fitting with the first Mn-O and Mn-Mn shells
FEFF paths- based on known scattering path of a photoelectron; they give the parameters for each shell

11. EXAFS χ(k) stack plot Rank by defects 6.8, 8.0, 9.0 k(Å-1) trends
Trends, especially at 6.8- more defects, lattice disorder moving down the series (broader feature)
Also seen to a lesser degree at 8.0 and 9.0
Rank by defects 6.8, 8.0, 9.0 k(Å-1) trends

12. 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)
Show pictures of structures

13. Todorokite (Layer/Tunnel)
Birnessite (Layer)

14. Ramsdellite (Small Tunnel)
Coronadite (Tunnel)
Ramsdellite (Small Tunnel)
Coronadite has Pb cation within tunnel structure
Ramsdellite known to exhibit small tunnel structure with little or no atoms in the tunnel vacancies
Notice CN of 6 for all the structures

15. Fourier Transform Plot
Trend at 4-6Å
Disorder caused by:
Vacancies
Cations
Bending
More disorder as you move down series, especially from 4-6
Caused by vacancies, cations, bending as seen in crystal structures in previous slides

16. 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
Amplitude reduction due to vacancies, extra cations
Todorokite actually decreased in disorder, while birnessite stayed the same compared to the original EXAFS fits

17. 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

18. Acknowledgements Special thanks to: John Bargar and Apurva Mehta
Ellie Schofield and Sam Webb
Susan Schultz, Farah Rahbar, and Steve Rock
SLAC, DOE
Invaluable support and guidance
Helping me with questions and teaching me how to use some programs
Organizing the SULI program, truly wonderful experience and one I will surely never forget