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

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@millenia.cars.aps.anl.gov (on behalf of "Frenkel, Anatoly" ) Subject: Re: [Ifeffit] How to identify N and O atoms in the first coordinate To:

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@millenia.cars.aps.anl.gov To: XAFS Analysis using Ifeffit 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 ----

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Date: Fri, 19 Dec 2008 16:34:36 -0500 From: ifeffit-bounces@millenia.cars.aps.anl.gov (on behalf of "Frenkel, Anatoly" ) Subject: Re: [Ifeffit] How to identify N and O atoms in the first coordinate To: "XAFS Analysis using Ifeffit" ,

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

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From: ifeffit-bounces@millenia.cars.aps.anl.gov on behalf of mzhu@udel.edu Sent: Fri 12/19/2008 4:20 PM To: ifeffit@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 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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