[Ifeffit] (no subject)

[Matthew Marcus]

Wback in the 70s and 80s, Powers, et. al. claimed to observe a Cu-Fe distance of 3.75A, seeing it in both the Cu and Fe edges.  However, a bit of Googling shows that
this result is in some doubt.  I once saw a Cr-Cr distance of 6 or 7A in a Cr-bis(arene) complex at 8K.  Sometimes, the contributions from the light atoms just smear out
because the distances form a near-continuous distribution way out there, leaving a heavier scatterer like Fe visible.  This can be simulated if you have a big enough cluster
size.  You may run into a limit on the number of paths, though, since there will be a huge number of them.  I would guess that you would only see the Fe-Fe at low temps.
I suspect that with something as floppy and as asymmetric as a protein, the MS paths won't contribute because you won't get a huge number of them piling up at one distance,
nor will you get focusing except for some nearby ligands such as carbonyls (Fe-C-O).  When you do the simulation, don't forget to add in some reasonable MSRD.
    mam
----- Original Message ----- 
  From: Frenkel, Anatoly 
  To: ifeffit at millenia.cars.aps.anl.gov 
  Sent: Wednesday, March 11, 2009 4:49 PM
  Subject: Re: [Ifeffit] (no subject)


  I would like to be proven wrong but my feeling is, without even knowing anything about this particular system, that one cannot observe Fe-Fe pair at that distance in such complex case. 
  However, to approach it more rigorously, the first step would be to examine the relative "importance" factors of different paths in the output of FEFF. If Fe-Fe path is well isolated in distance and importance from others (in reality, it probably is not the case) it can be done, otherwise - not. 

  Anatoly




------------------------------------------------------------------------------
  From: ifeffit-bounces at millenia.cars.aps.anl.gov <ifeffit-bounces at millenia.cars.aps.anl.gov> 
  To: ifeffit at millenia.cars.aps.anl.gov <ifeffit at millenia.cars.aps.anl.gov> 
  Sent: Wed Mar 11 09:40:31 2009
  Subject: [Ifeffit] (no subject) 


  Hi all,

  I measured Fe(II) edge EXAFS data for my protein that has two iron sites (Fe-Fe distance ~5A). My question is how to fit the model with the data? Can I discard the contribution of multiple scattering effects to the fitting? One most important information that I want to obtain is on the Fe-Fe distance. Is it enough to conclude from the raw data FT that the Fe-Fe  distance in my protein sample has been changed in comparison to the Fe-Fe distance in the model (created with Feff using the crystal structure coordinates)? I try fitting using arthemis but got bad and weird results. is there any manual or step-by step guide that I can learn how to fit model of two metal sites to my data? 

  Anther question that I have how can I get to the past discussions in the forum- is there any database for questions and answers that I can learn on the analysis of EXAFS data? 

  Any help will be appreciated,

  MJacob





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