[Ifeffit] How to identify N and O atoms in the first coordinate

Frenkel, Anatoly frenkel at bnl.gov
Fri Dec 19 15:34:36 CST 2008

Dear Mengqiang,
To the best of my knowledge, in most cases Nitrogen cannot be discerned from Oxygen as a nearest neighbor since their scattering properties are similar. Thus, if you want to solve an "inverse" problem ("Which type of neighbors do I have") you cannot do it. However, if you believe you have some knowledge about the type of metal-oxygen bonding: either M=O or a M-O or a M-OH or a M-OH2 (the first one is the shortest and the strongest, the others may have similar interatomic distances but different bond strengths), you can advance somewhat.
If you have a certain number of distinct models you want to compare the data against, it can be done via a linear combination fitting, or by direct algebraic extraction of any given type of the pair contribution from the data, as described, for example here:
E. Poverenov, I. Efremenko, A. I. Frenkel, Y. Ben-David, L. J. W. Shimon, G. Leitus, J. M. L. Marin, D. Milstein. A terminal Pt(IV)-oxo complex bearing no stabilizing electron withdrawing ligands and exhibiting diverse reactivity. Nature 255, 1093-1096, 2008. 

See supplementary info to that article for specific details.


From: ifeffit-bounces at millenia.cars.aps.anl.gov on behalf of mzhu at udel.edu
Sent: Fri 12/19/2008 4:20 PM
To: ifeffit at millenia.cars.aps.anl.gov
Subject: [Ifeffit] How to identify N and O atoms in the first coordinate

Hello all,
  Merry Christmas!
  I have some samples of heavy metal sorption on bacterial biofilm. I want to figure out what elements are coordinated with the heavy metal in the first coordinate. Since the oxygen and nitrogen have similar scattering factors, how can I differetiate them? Using shell-by-shell fitting or linear combination fitting with standards? Thanks.

Best wishes,

Mengqiang Zhu

Mengqiang Zhu
Ph.D Candidate
Environmental Soil Chemistry
Department of Plant and Soil Sciences
University of Delaware
152 Townsend Hall
Newark, DE 19716
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