Re: [Ifeffit] Using the amplitude reduction factor as alinearcombination fitting parameter

Christophe, If you are not familiar with the work of Shelly Kelly, particularly S.D. Kelly, et al, "X-ray absorption fine-structure determination of pH dependent U-bacterial cell wall interactions", Geochem. Cosmo. Acta, 66(22) 3875-3891, Nov 2002. and E.J. O'Loughlin, et al "Reduction of uranium(VI) by mixed iron(II)/iron(III) hydroxide (green rust): formation of UO2 nanoparticles," Environ. Sci. Technol., 37, 721-727, Feb. 2003. you should check them out. You will find her approach to analysis of exafs of U speciation to be very helpful. B On Wednesday 30 April 2008 02:45:14 Bruggeman Christophe wrote:

XAFS fitting is sometimes a "puzzling world", but here's some more clarification :-)

I indeed collected a series of spectra on FeS2, with varying conditions such as equilibration time and geochemical parameters. The general outlook of all these spectra are relatively similar, but some clear differences can be noticed from both the XANES and EXAFS patterns and the FTs. More precisely, based on these differences the samples can be "categorised" from "more oxidised U" to "more reduced U", but no pure end member is present anywhere in the samples. So, a first PCA was performed on the samples themselves, taking the "most oxidised" and "most reduced" as end member, and trying if the other samples could be reproduced as a linear combination of these two end members. This proved to be possible.

Now for standards: I collected some scans of U standards, but it is very difficult to have a standard which represents a pure end member in the FeS2 samples. For example, my guess is that the "reduced U" resembles uraninite, but given the fact that with such heterogeneous reduction on FeS2 surface, it is more likely that UO2 nanocolloids are formed, a crystalline uraninite standard can not be used as pure end member.

Therefore, what I would like to do, is reproduce the FTs and EXAFS spectra, starting from U standards, but adapting them (e.g. playing with Debye-Waller factors), so that I would get a pure end member for the FeS2 samples, then fix the parameters, and use the amplitude reduction factor as a sort of linear combination fitting parameter to get an idea of the amount of this pure end member in my samples.

Hopefully, this sheds some more light on the matter, Thanks already for your interest,

Christophe

-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Frenkel, Anatoly Sent: dinsdag 29 april 2008 16:23 To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Using the amplitude reduction factor as alinearcombination fitting parameter

There are a few points in your description that puzzle me. Have you collected not one but a series of spectra where some external condition (e.g., temperature, concentration, time, pH etc) were varied? If not, PCA cannot be used if only one spectrum was collected containing a mixture of two species. Such spectrum would have only one component, of course - itself. Next, assuming you did use PCA for a series of spectra, without having XANES and/or EXAFS data of test compounds how were you able to deconvolute abstract components that PCA generates into the two species that have meening of XANES or EXAFS data? Without test compounds such deconvolution is not possible unless you used not PCA but a linear combination fit of some sort... And, finally, if you used test compounds that could be reliably reproduced by your 2 principal components, why do you need to do anything else? They are your two species.

Please clarify.

Anatoly

----- Original Message ----- From: ifeffit-bounces@millenia.cars.aps.anl.gov To: ifeffit@millenia.cars.aps.anl.gov Sent: Tue Apr 29 03:06:28 2008 Subject: [Ifeffit] Using the amplitude reduction factor as a linearcombination fitting parameter

I have recently collected EXAFS spectra of uranium on a FeS2 surface. Using principal component analysis of the XANES and k3-weighted EXAFS spectra, I have found that there are two uranium species which compose the spectra. As a first tentative guess, I believe these two uranium species are uraninite (UO2(c)) and a uranyl species. I would like now to fit the fourier transform functions (real parts and magnitudes) using the theoretical paths and path degeneracies created by feff, and use the amplitude reduction factor S02 as a fitting parameter to derive the relative amounts of the two uranium species in my samples.

Normally, this S02 is taken as a constant (between 0.7 and 1.0), and the path degeneracies are fitted. So normally, S02 is not really a fitting parameter (some papers derive it even with theoretical functions). However, given the fact that S02 and N are completely correlated, I think it is justified to use this approach.

Can someone comment on this?

Many thanks in advance,

Christophe

SCK*CEN Disclaimer

http://www.sckcen.be/emaildisclaimer.html

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/