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

[mzhu at udel.edu]

Hello Anatoly,
  Thanks for your reply.

  I could not do it as the literature you mentioned since I do not have detailed structural information as they do. I am wondering if the following method can be justified to indentify nitrogen atoms:

  1) EXAFS data of 7 nickel oxygen-coordinated organic and inorganic complexes in which nickel only coordinates to oxygen atoms from carboxyl group, phosphoryl group and water molecules.

  2) Fourier back transformation of the peak from 1-2 aus. in R+ delta-R space. This R range must cover the scattering peaks from both nitrogen and oxygen. Then chi 
functions of these complexes are obtained.

  3) A principal component anlaysis (PCA) was performed over the oxygen-coordinated dataset of the chi functions obtained in the step (2). PCA analysis indicated two major components based on the IND values.

  4)Then chi functions of two nitrogen-coordinated nickel complexes was obtained using the same method as step 2). It is certain that nitrogen atoms are coordinated to the 
nickel in the first shell in addition to oxygen atoms.

  5) A target transformaiton of the chi function of two nitrogen-coordinated nickel complexes using oxygen-coordianted dataset resulted in the SPOIL values close to 5. 
Addition of one of the two complexes to the group of nickel complexes in PCA, PCA resulted in 3 components. These indicate that they have different coordination environment to the oxygen-coordinated nickel complexes. It is expected because they have nitrogen in the first shell.

  6) A target transformation conducted on a sample of nickel-sorbed biofilm (back fourier transformed chi function in 1-2 aus.) resulted in the value close to 5. It means that the sample can not be represented by the nickel organic group, either.
  
   Since the first shell only can have two types of atoms, oxgen and nitrogen. If the nickel sorbed on biofilm can not be represented by the nickel oxygen-coordinated organic group which only has oxygen in the frist shell, it must have nitrogen atoms in the first shell. Also, linear square fitting of the Ni_biofilm with the nitrogen-coordinated complexes resulted in the better goodness than other oxygen-coordinated complexes. Thus, the nitrogen must exist in the first shell of Ni_biofilm sample.

   Do you think this method is reasonable?        

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 
http://ag.udel.edu/soilchem/zhu.html 


---- Original message ----
>Date: Fri, 19 Dec 2008 16:34:36 -0500
>From: ifeffit-bounces at millenia.cars.aps.anl.gov (on behalf of "Frenkel, Anatoly" <frenkel at bnl.gov>)
>Subject: Re: [Ifeffit] How to identify N and O atoms in the first coordinate  
>To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>, <ifeffit at millenia.cars.aps.anl.gov>
>
>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.
>Regards,
>Anatoly
> 
>
>________________________________
>
>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
>http://ag.udel.edu/soilchem/zhu.html
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