[Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc Samples

Farquhar, Erik efarquhar at bnl.gov
Wed Nov 11 07:52:18 CST 2015

Robert and Bruce have given you excellent answers already, so I'll pile in on more specific questions. I take it you are seeing this for all Zn samples, e.g., Zn with just N/O ligands as well as mixed N/S? What if you fit data for some standard coordination complex like Zn(imid)6, which you know is a definite Zn-N6 site? Zn EXAFS is a little outside my wheel-house, but in my experience my best fits always had <6 first shell scatterers for Zn sites. I am under the impression that good fits to mixed N/S sites are challenging to fit since the Zn-N and Zn-S scattering are out of phase with each other.

Bond valence sums might come in handy as a sanity check if you are trying to justify a 4C site over 6C, although it doesn't handle geometric distortions very well (not likely to be an issue in your case). Have a look at Thorp, Inorg. Chem. 1992, 31, 1585-1588 DOI: 10.1021/ic00035a012 and Liu&Thorp, Inorg. Chem. 1993, 32, 19, 4102-4105, 10.1021/ic00071a023. Be aware that there is an error in the table in the first paper: the r0 values for Zn-O and Zn-S are transposed. Unfortunately a Zn-S r0 isn't given, but you might find one going back to the parent Brown & Altermott reference or alternatively can interpolate from Cu and Ni values. 

Just an idea,

-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov [mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of Carolyn Carr
Sent: Monday, November 9, 2015 1:24 PM
To: ifeffit at millenia.cars.aps.anl.gov
Subject: [Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc Samples


I have a general question rather than specific. I have only ever fit XAS data on metalloproteins and one feature that I see is that when fitting Zinc samples in R-space there is no local minima. For Cobalt and Nickel samples I typically get one or a few fits that are obviously significantly better in R-factor (with reasonable distances, sigma^2, etc) but for Zinc this is not the case.

I can get many good fits and Zinc likes to increase the coordination up to 8 for all data sets I have ever fit, although there is obviously no physical basis in this. This is true of not just my own proteins but Zinc samples made by collaborators, and after looking through previous group members fit tables, they had similar issues.

My understanding is that one of the benefits of fitting in R-space is that there is a local minima, whereas in k-space there are many minima. I was wondering if there was a physical basis for this feature in Zinc samples, or if perhaps my group is not aware of some experimental setup that we should be doing for Zinc that would resolve this problem.

Thank you for any help regarding this matter,

Carolyn Carr

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