[Ifeffit] Question on Glitch in FEFF for Ru EXAFS measurements

Dooshaye Moonshiram dmoonshi at gmail.com
Mon Nov 26 17:46:06 CST 2012


Sure it might be an interesting research problem but this is a simple
symmetrical structure with 6 nitrogens bonded to it
(Tris(bipyridine)ruthenium(II)
> dichloride) . I know there is no radiation damage as I have not seen any
shift in oxidation state from scan to scan when taking XANES. Also I check
purity and right composition of my sample by doing parallel EPR
measurement. I took EXAFS on this compound as it is my standard compound
used for comparison purposes. Actually, I am interested in higher
intemediates produced by oxidizing this compound. I was not blaming Artemis
for this phenomena. I was just wondering whether you have seen in your past
experience any such extra peak possibly coming from the standard
measurement as ***the  Ru standard EXAFS integrated between the same window
has a peak at 2.5 Angstroms in FT.

Regarding my first query, basically if you upload an experimental file on
Artemis and run a Feff calculation page from the exact same XRD
coordinates, a different fit is sometimes obtained from trial to trial when
summing all paths. Also if you run FEFF on the XRD coordinates without
presence of the experimental file, I again can get a different result,which
leads me to the conclusion that this might be a glitch. My labmates and I
have obtained these problems several times. We have to close the whole
program before running another calculation. I just wanted to bring it to
your attention.

Thank you for your help,
Dooshaye

On Mon, Nov 26, 2012 at 5:33 PM, Bobrik, Michael <mbobrik at sysplan.com>wrote:

> There's no reason for anyone to assume solution XAFS and crystal XRD data
> will converge to the same results.
> Indeed, the research problem now is how/why are they different?
>
> --------------------------
> Dr. Michael A. Bobrik
>
> Sent from the BlackBerry
>
> ----- Original Message -----
> From: Bruce Ravel [mailto:bravel at bnl.gov]
> Sent: Monday, November 26, 2012 05:29 PM
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Question on Glitch in FEFF for Ru EXAFS measurements
>
>
> I'm sorry.  No part of #1 was clear to me.  I never really know how to
> respond to these Joycean descriptions.
>
> If you expect help from the people on this list you need to do a
> better job asking questions.  Some hints can be found at
> http://bruceravel.github.com/demeter/pods/help.pod.html
>
>
> As for #2, there are any number of reasons why your XAS and XRD data
> may not say the same thing.  If the XRD explained all aspects of the
> coordination geometry, why bother measuring XAS?  Or to say that
> another way, since the XAS and XRD seem to be telling you different
> stories, don't you now have a real research problem to work on?
>
> Perhaps some of the Ru has precipitated out in another form.  Perhaps
> the XRD is faulty.  Perhaps your sample suffered radiation damage and
> changed form.  Perhaps your sample wasn't what you thought it was.  My
> point is that you should at least consider challenging your experiment
> and any assumptions about your sample before presuming Feff and Artemis
> are to blame for your woes.
>
> B
>
> On Monday, November 26, 2012 05:05:17 PM Dooshaye Moonshiram wrote:
> > Dear Bruce,
> >
> > I recently collected EXAFS data on the *Tris(bipyridine)ruthenium(II)
> > dichloride Ru 2 compound-photosensitizer in solution form. In order to
> > compare EXAFS data to XRD data, I uploaded the XRD coordinates of this
> > crystal structure from cambridge database in a FEFF calculation page in
> > ARTEMIS. I ran FEFF on the x,y and z coordinates of this standard
> compound
> > in Artemis and summed all paths to compare with my experimental
> > data(collected in solution form in fluorescence mode)*
> > *I have 2 problems*
> > *1) I found a glitch when running FEFF in ARTEMIS. In order to compare
> XRD
> > coordinates to EXAFS data, I upload the XRD coordinates in a FEFF
> > calculation page, run FEFF and sum all paths.  Now*
> > *a) **f I upload the XRD coordinates in a FEFF calculation page without
> > having the EXAFS artemis file present, I get different fits compared to*
> > *b)  if I first upload the EXAFS  experimental file and then run FEFF on
> > the XRD cartesian coordinates. It seems that **the sum of all paths from
> > the FEFF calculation page tend to mimic the experimental EXAFS file which
> > has first been uploaded and is not a true presentation of how the FT
> should
> > be.*
> > *
> > *
> > *-Please let me know if this is unclear and I can send you my EXAFS file
> as
> > well as the XRD coordinates which I obtained from Cambridge structural
> > databse*
> > *
> > *
> > *2) Another problem which I have with my EXAFS data is that I have a peak
> > at 2.5 Angstrom which does not match XRD coordinates and is not present
> if
> > I run FEFF on XRD coordinates only(true comparison as  I don't add the
> the
> > experimental file in Artemis). Could this peak be due to the Ru standard
> > somehow? All measurements were done in fluorescence mode (F/Io) at 20 K
> in
> > cryostat using a germanium detector. I  simultaneously collected EXAFS
> > measurements on Ru metal standard between Iref and IT ionization
> chambers.*
> > *
> > *
> > *Thank you for your help,*
> > *Sincerely*
> > *Best Regards*
> > *Dooshaye Moonshiram*
>
>
> --
>
>  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
>
>  Homepage:    http://xafs.org/BruceRavel
>  Software:    https://github.com/bruceravel
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