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

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@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 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@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