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

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

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) 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 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

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----- Original Message ----- From: Bruce Ravel [mailto:bravel@bnl.gov] Sent: Monday, November 26, 2012 05:29 PM To: XAFS Analysis using Ifeffit 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

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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

On Monday, November 26, 2012 05:05:17 PM Dooshaye Moonshiram wrote: the

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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@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 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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