Determining the Determining the Structure and Defects Structure and Defects of Manganese Oxides of Manganese Oxides

using X-Ray Absorption using X-Ray Absorption SpectroscopySpectroscopy

Stanley QuanStanley QuanUniversity of California, BerkeleyUniversity of California, BerkeleyStanford Synchrotron Radiation Laboratory, Stanford Synchrotron Radiation Laboratory, SLACSLACMentors: John Bargar & Apurva MehtaMentors: John Bargar & Apurva MehtaAugust 14, 2008August 14, 2008

BiosignaturesBiosignatures Biological indicators for the Biological indicators for the

presence of lifepresence of life Stable over timeStable over time Biologically and abiotically formed Biologically and abiotically formed

states are distinguishablestates are distinguishable

Search for life on other planetsSearch for life on other planets

Manganese Manganese OxidesOxides

Well-preserved deposits up to 2.22 Well-preserved deposits up to 2.22 billion years old (anoxic billion years old (anoxic oxic state oxic state atmosphere) as desert varnishatmosphere) as desert varnish

Recent studies suggest biogenic Mn Recent studies suggest biogenic Mn oxides can be distinguished from oxides can be distinguished from abiogenic Mn oxides with EPR abiogenic Mn oxides with EPR (Electron Paramagnetic Resonance)(Electron Paramagnetic Resonance)

Must refine detailed crystal structuresMust refine detailed crystal structures

Formed by various Formed by various bacteria in nature- bacteria in nature- desert varnishdesert varnish

X-ray Absorption X-ray Absorption SpectroscopySpectroscopy Photoelectric effect- threshold energyPhotoelectric effect- threshold energy

Photoelectron emitted (“edge” around 6552 eV)Photoelectron emitted (“edge” around 6552 eV) Backscattered by surrounding atomsBackscattered by surrounding atoms Interference pattern (outgoing and backscattered)Interference pattern (outgoing and backscattered)

Extended X-ray Absorption Fine Structure Extended X-ray Absorption Fine Structure (EXAFS)(EXAFS)

Comparing to XRDComparing to XRD Mn oxides formed by bacteria are Mn oxides formed by bacteria are

poorly crystallized and defectivepoorly crystallized and defective X-Ray DiffractionX-Ray Diffraction

Assumes periodicity in order to observe a Assumes periodicity in order to observe a larger rangelarger range

Complementary to XASComplementary to XAS Immediate environment around atomImmediate environment around atom Explores local structure, better suited for Explores local structure, better suited for

Mn oxidesMn oxides

Experimental SetupExperimental Setup

Transmission/Transmission/FluorescenceFluorescence

TransmissionTransmission How much of beam goes through sampleHow much of beam goes through sample Need very concentrated sample, constant Need very concentrated sample, constant

sample thickness because looking at very sample thickness because looking at very small changessmall changes

FluorescenceFluorescence Emission after photoelectron drops back Emission after photoelectron drops back

down to steady statedown to steady state Moderately dilute samples- over-absorbance Moderately dilute samples- over-absorbance

effecteffect

Data AnalysisData Analysis Normalize raw data to edgeNormalize raw data to edge Subtract background, splineSubtract background, spline

EXAFS χ(k) plotEXAFS χ(k) plot KK33-weighted to enhance oscillations -weighted to enhance oscillations

at high kat high k

EXAFS FittingEXAFS Fitting Fit EXAFS with FEFF paths (single Fit EXAFS with FEFF paths (single

scattering model)scattering model) Parameters: radial distance (R), Parameters: radial distance (R),

disorder (disorder (22) )

EXAFS χ(k) stack plot EXAFS χ(k) stack plot

Rank by defectsRank by defects 6.8, 8.0, 9.0 k(Å6.8, 8.0, 9.0 k(Å-1)-1) trends trends

Comparing EXAFS and Comparing EXAFS and XRDXRD

Todorokite and birnessite idealTodorokite and birnessite ideal Order by structureOrder by structure

Layer/Tunnel (todorokite)Layer/Tunnel (todorokite) Layered (birnessite, lithiophorite, Layered (birnessite, lithiophorite,

chalcophanite)chalcophanite) Tunnel (coronadite, cryptomelane)Tunnel (coronadite, cryptomelane) Small Tunnel (ramsdellite, pyrolusite)Small Tunnel (ramsdellite, pyrolusite)

Todorokite (Layer/Tunnel)Todorokite (Layer/Tunnel)

Birnessite (Layer)Birnessite (Layer)

Coronadite (Tunnel)Coronadite (Tunnel)

Ramsdellite (Small Tunnel)Ramsdellite (Small Tunnel)

Fourier Transform PlotFourier Transform Plot Trend at 4-6ÅTrend at 4-6Å

Disorder caused by:Disorder caused by: VacanciesVacancies CationsCations BendingBending

Constrained-to-XRD fitsConstrained-to-XRD fits Amplitude reductionAmplitude reduction fit produced lower fit produced lower

coordination numbers than predictedcoordination numbers than predicted If constrained to XRD parameters before If constrained to XRD parameters before

fitting (CN=6), fit showed progressively fitting (CN=6), fit showed progressively more added disorder when going down more added disorder when going down the series, except for todorokite and the series, except for todorokite and birnessitebirnessite Further reinforces ranking of the manganese Further reinforces ranking of the manganese

oxides according to ideal structureoxides according to ideal structure

ConclusionConclusion By looking at the EXAFS, we were able to By looking at the EXAFS, we were able to

see that some manganese oxides are more see that some manganese oxides are more defective than othersdefective than others

From XRD we learned about their From XRD we learned about their structures, but now with EXAFS we can structures, but now with EXAFS we can characterize their structures by lattice characterize their structures by lattice disorder and defectsdisorder and defects

Knowing about the structure may lead to Knowing about the structure may lead to insight about the way they are formed by insight about the way they are formed by bacteria and help us identify them if used bacteria and help us identify them if used as biosignaturesas biosignatures

AcknowledgementsAcknowledgements Special thanks to:Special thanks to:

John Bargar and Apurva MehtaJohn Bargar and Apurva Mehta Ellie Schofield and Sam WebbEllie Schofield and Sam Webb Susan Schultz, Farah Rahbar, and Steve Susan Schultz, Farah Rahbar, and Steve

RockRock SLAC, DOESLAC, DOE