[Ifeffit] Fwd: Re: why ss_2 is negative?
Bruce Ravel
bravel at anl.gov
Sat Feb 24 09:09:00 CST 2007
On Friday 23 February 2007 21:41, hw26 at njit.edu wrote:
> Yes, I am modeling the uranyl ligand and two equatorial ligands, one of
> which is hypothesized as U-F (from BF4 anion), and the other as U-O (from
> hydration),because in the uranyl nitrate standard sloution(without
> MOEMIMBF4), there is only one peak that represents the U-O equatorial
> ligand, but with the MOEMIMBF4, the equatorial peak is split to two peaks.
> So I guess the other equatorial U-F formed.
Hao,
A few more comments:
1. It is well advised for anyone starting to look at uranyl compounds
with XAS to read Shelly's various publications on that topic.
Geochem. Cosmo. Acta, 66(22) 3875-3891, (2002) is particularly
useful. Google scholar can help you locate more of her papers.
2. I am the first to admit that Artemis and Ifeffit are difficult
tools for the beginning exafs practitioner. These tools try to
provide a usable face to a difficult problem. Ifeffit was written
with enough flexibility and power to allow the so-called experts
to do the analysis they want to do. That means that Artemis has
enough freedom to allow the unsuspecting user to do ill-advised
things.
You really need to think about what each of the parameters means.
For example, just because Artemis allows you to float e0 freely
for each path does not mean that doing so is a good idea. There
are situations where it is a very good idea to have more than one
e0 parameter in your fit, but I suspect that yours is not one of
them. Consequently, you should consider constraining all your
paths to have the same e0.
What do I mean by "constrain"? Well, on the Guess,Def,Set page,
you can define a single e0 parameter as a guess parameter, then
use that parameter on each of the path pages. In that way, you
will have one floating parameter in your fit that is used to
describe the e0 of all your parameters.
Similarly, you should think hard about the numbers of each kind of
path. A uranyl moiety is unlikely to have more or less than 2
uranyl ligands. The uranyl bond is very strong, consequently it
is energetically unfavorable in a uranyl for those two bonds to be
over- or under-filled. Consequently, you can consider setting the
number of yl oxygens to 2. Furthermore, the equatorial plane is
likely to have between 4 and 6 oxygens, so you should think of
ways to constrain the total number of equatorial oxygens to be
something reasonable. Since the coordination number is highly
correlated with sigma^2 in a statistical sense, thinking well
about coordination number should help address your original
question.
3. Scott has made a very nice Artemis tutorial which can be found at
http://cars9.uchicago.edu/iffwiki/HoraeSoftware#contrib
It comes in the form of a series of Artemis projects. Newcomers
benefit by working through his tutorial before trying to analyse
their own data with Artemis.
4. The Ifeffit web site, my home page, and especialy http://xafs.org
are all filled with useful information for the XAS novice. If you
haven't already looked through the resources on those sites, you
really should budget some time to do so.
HTH,
B
--
Bruce Ravel ---------------------------------------------- bravel at anl.gov
Molecular Environmental Science Group, Building 203, Room E-165
MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007
Argonne National Laboratory phone and voice mail: (1) 630 252 5033
Argonne IL 60439, USA fax: (1) 630 252 9793
My homepage: http://cars9.uchicago.edu/~ravel
EXAFS software: http://cars9.uchicago.edu/~ravel/software/
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