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

mzhu at udel.edu mzhu at udel.edu
Sat Dec 20 10:44:47 CST 2008


Hello Anatoly,
  Thanks for your reply. I agree with you. It seems impossible to solve this problem with EXAFS. 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 


---- Original message ----
>Date: Fri, 19 Dec 2008 22:43:47 -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: <ifeffit at millenia.cars.aps.anl.gov>
>
>The fact that PCA tells between known Ni-N and Ni-O complexes by adding one more component when the wrong complex is added (N to O or vice versa) does not mean that there is specific fingerprinting sensitivity to N or O. One needs to demonstrate first that all Ni-N pairs have similar distances and disorder, regardless of their chemical surrounding, and that the same is true for Ni-O. Only in that case your PCA results indeed mean that the Ni sorbed biofilm have both types of bonds.  Otherwise you cannot prove that it is Ni-N plus Ni-O vs. a situation where there are two unique types of Ni-O that have not been matched to your Ni-O standard and may thus fool you in thinking that one of them is due to Ni-N instead. Thus, before you conclude that, you should verify whether various Ni-N and Ni-O complexes have same pair properties.  From your description it appears not to be the case since you have two components (not one) for your oxygen ligands and nitrogen ligands. 
>
>Anatoly
>
>
>----- Original Message -----
>From: ifeffit-bounces at millenia.cars.aps.anl.gov <ifeffit-bounces at millenia.cars.aps.anl.gov>
>To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
>Sent: Fri Dec 19 18:39:24 2008
>Subject: Re: [Ifeffit] How to identify N and O atoms in the first coordinate
>
>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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>>Ifeffit mailing list
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>>
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