[Ifeffit] How to distinguish whether the coordination element is heavy or light

Matt Newville newville at cars.uchicago.edu
Sun Jul 6 11:17:42 CDT 2014


Hi Zhanfei, Bruce, Scott,

Sorry for jumping in to this conversation a bit late.  Like Bruce said,
there is no magic trick for determining whether a part of the R-space
spectrum comes from one or more scatterers.  And while XAFS is sensitive to
Z, the sensitivity is weak.

Because it's XAFS School week here in Chicago, I thought I'd go through a
test of the Z dependence, and also try out a "trick" (I believe I first
heard this from Mali Balasubramanian, but I suspect others may know this
trick too) that relies on phase-corrected Fourier transforms, and is
somewhat related to Scott's description of Joe Woicik's comments.

The phase-correction "trick":    If you correct for the phase-shift, the
peak in |chi(R)| should be at the interatomic distance (ignoring subtleties
in the XAFS equation).   Turning this around, the peak in the
phase-corrected |chi(R)| will be at the interatomic distance if and only if
the phase-shift applied was correct... which means that Z is correct (to
within some uncertainty).    How well does this actually work on real data?

To work through these two related ideas,  I used ZnSe as a test case -- a
very simple structure with a well-isolated first shell, and I have some
decent data on it lying around.   This also seemed like a useful enough
category of analysis, that I thought it would be useful to better
document.  Scripts and results are at


http://xraypy.github.io/xraylarch/xafs/feffit.html#example-6-testing-exafs-sensitivity-to

(turning this into an Artemis project is left as an exercise for the
interested reader).   The results of just changing scatterer in the fits
are pretty clear, and suggest that Z +/- 2 might be a reasonable
rule-of-thumb even when refining, R and S02, at least in this case of a
well-isolated first shell.    The results might be different for lighter
backscatterers, but there are claims, especially in the  bio-XAFS
literature, that one can distinguish  N and O ligands at least in some
cases.    Still, given that the ZnSe case is so clear, it seems reasonable
to stick with the more pessimistic "Z +/- 5" rule-of-thumb, as long as the
possibility that one can do better  in certain cases (and may do much worse
in others!).

The phase-correction approach is interesting in that it asks  "is this
particular fit self-consistent?" instead of "which of these fits is
best?".  This independent of the fit quality could make it a useful
secondary check of Z and R (much like a bond valence sum can be an
independent check on the consistency of N, R, and valence).   It does not
seem highly accurate on its own --  also suggesting Z +/- 2 or 3 is about
as well as one can do without further knowledge of the scatterers.   That
might be partially related to how well one can actually determine the peak
position for chi(R) on a grid of 0.03 Ang, and partly related to the fact
that other terms in the EXAFS equation alter the phase.   In principle,
those could be accounted for -- another exercise for the interested reader.

I don't think the phase-correction "trick" would help Zhanfei -- it will
NOT work on a mixed coordination shell.  But the approaches described
might be useful and/or inspiring to others.

--Matt
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