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 Part of a bigger project in searching for extraterrestrial life, dating In order to be used as biosignatures

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

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

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

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

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

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

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

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

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

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

Todorokite (Layer/Tunnel) Birnessite (Layer)

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

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

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

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 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