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

Thu May 1 10:06:47 CDT 2008

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 at millenia.cars.aps.anl.gov
> [mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of Frenkel,
> Anatoly
> Sent: dinsdag 29 april 2008 16:23
> To: ifeffit at 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 at millenia.cars.aps.anl.gov
> <ifeffit-bounces at millenia.cars.aps.anl.gov>
> To: ifeffit at millenia.cars.aps.anl.gov
> <ifeffit at 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
>
>
>
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-- 
 Bruce Ravel  ------------------------------------ bravel at 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/