[Ifeffit] Question about using a proper model

[Georges Siddiqi]

Hi,

I may as well chime in since I actually have some expertise with trying to
get XAS of organometallic compounds on silica surfaces (mainly pertaining
to quesion#1).

These are the papers I've previously published with my group for inorganic
and organometallic compounds grafted on silica surfaces:
http://www.pnas.org/content/111/32/11624
http://onlinelibrary.wiley.com/doi/10.1002/adsc.201400125/abstract
http://onlinelibrary.wiley.com/doi/10.1002/anie.201308983/abstract

the methodology we've had the most success with consists of, synthesize
inorganic/organometallic precursor, and get XRD crystal structure, then
grafting the compound onto the silica surface.  We then take XAS
measurements of both the precursor and the grafted species.  From other
characterization methods (NMR, IR) we have a good idea that the compound
hasnt changed too much upon grafting to the silica surface.

Then we take XAS measurements of both of these samples, fit the structure
of the molecular precursor to the XRD data, then use some of the parameters
of the fit of the molecular structure to fit the surface species.

So in the previously described method we went around the problem of not
knowing the structure of the species on the surface by using complementary
characterization methods in conjunction with XAS to get a good fit.

now let's say the structure on the surface starts to deviate more from the
molecular analog (ie we do a heat treatment on the surface species on
silica), then it gets trickier and I have to add more variables to the
structure, but I was usually successful in fitting the surface species by
playing around with the molecular model.

Now, in some cases (not yet published) we havent been able to crystallize
the molecular compound, and it's structure is not published.  In those
cases we had to dig through crystallographic databases to find structures
that are similar (at least first shell coordination, and distances) to the
one we have on the surface, and try to fit it.  I've usually managed to get
a reasonable fit by doing this.

but if you cant synthesize a molecular analog, and you cant find a
crystallographic structure reasonably close to what you hope to find on the
surface (based on other characterization methods), then I'd say you're out
of luck.

best of luck,
georges

On Tue, Oct 28, 2014 at 2:57 AM, pushkar shejwalkar <
pshejwalkar2004 at gmail.com> wrote:

> Dear Matt thank you very much for the comments. I will try to change the
> E0 value in athena accordingly. It appeared to me from the lecture notes
> that we need to do some saving file in artemis and then opening it in
> athena or something like that. but may be I read it all wrong.
> Thanks again
> Pushkar
>
> On Tue, Oct 28, 2014 at 10:29 AM, Matt Newville <
> newville at cars.uchicago.edu> wrote:
>
>> Pushkar,
>>
>> On Mon, Oct 27, 2014 at 7:57 PM, pushkar shejwalkar
>> <pshejwalkar2004 at gmail.com> wrote:
>> > Dear Matt,
>> >           Thank you very much for your reply. Yes it generates list of
>> XYZ
>> > cordinates. I am wondering if its ok to use such information. The
>> reason is
>> > that while converting the XYZ file into .inp file, the format is
>> different
>> > and hence I am simply typing the coordinates into it, however I am not
>> sure
>> > as to should I change nleg values, Rmax values and other mphase mfeff
>> values
>> > and all. Is it same for all the program? just changing the coordinates
>> is
>> > enough?
>>
>> Please understand that we only know as much about what you are trying
>> to as you actually tell us.
>> While we can give you advice, we cannot actually solve your problems for
>> you.
>>
>> I think that what you are trying to do is create a feff.inp file from
>> atomic coordinates generated by some other program called Spartan
>> (coincidentally, Greek-themed!).   A feff.inp has several parts to it,
>> one being a list of X, Y, Z, IPOT, where X, Y, Z are atomic
>> coordinated (to be clear -- in Angstroms) and IPOT is an integer index
>> of one of the Potentials listed elsewhere in the file.  There must be
>> between 2 and 7 IPOTs, number sequentially starting with 0.  There is
>> exactly 1 IPOT '0' -- this is the absorbing atom.  Each scattering
>> element must have its own IPOT (including any other elements that are
>> the same Z as the absorber).
>>
>> Starting with an existing feff.inp file and modifying the list of
>> atomic coordinates and, if necessary, the list of potentials,  is
>> highly recommended.   It's not that hard.
>>
>> > About lower E0 value, I read in Shelly's paper that mostly ppl do not
>> report E0 value
>>
>> People do report E0.
>>
>> > and if they and if it is >10 then there may be problem with
>> > modelling or so.
>>
>> An E0 shift > 10 (or < -10) is a warning that something may not be
>> right.  It's not necessarily wrong, but should cause you to pause and
>> try to understand such a large discrepancy between what Feff thought
>> E0 should be and what the maximum of the first derivative is.
>>
>> > one of the method to reduce such chances of high E0 is by
>> > properly aligning spectra in athena. She mention in this a method to use
>> > first artemis for getting first shell fitting using E0=0 and then coming
>> > back to the athena and using this file as reference. But I am not sure
>> how
>> > to open artemis file in athena because if I open .fpj file in athena it
>> > doesnt recognise and says that the format is not readable if you
>> continue
>> > then athena shutdown. In artemis I cannot save file as .prj. is there a
>> way
>> > around? OR IT IS JUST THAT I AM DOING IT ALL WRONG?
>>
>> Just change E0 in Athena, perhaps copying a Group first, and use that
>> chi(k) with the updated E0 as the data to fit.    Usually Feff wants
>> E0 further up the edge than the maximum of the first derivative, but
>> not always.
>>
>> --Matt
>> _______________________________________________
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>>
>
>
>
> --
> Best Regards,
> Pushkar Shejwalkar.
> Post-doctoral -Researcher,JSPS Fellow
> Hokkaido University,
> Sapporo,
> Japan
>
>
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>
>
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