[Ifeffit] Question--FEFF calclulated atom coordinates and labels

[Xinyu Luo]

Hello Ming, Shelly, and Chris




I want to chime in here and add my question. If I understand it correctly, C1 refers to the two C atoms next to the N atom, and C3 is on the methyl pendant group. In this way, the eight degeneracies of [@ C1.1 @] and [@ N1.1 C1.1 @] can be satisfied. However, the remaining C atom on the ring has then to be C2, but it seems it can't generate eight degeneracy of the path (raw 5, @ N1.1 C2.1 @). I don't know how to apportion C1 and C2 in that image then...




Kind regards

Xinyu



-----Original Messages-----
From:"Kelly, Shelly D." <skelly at anl.gov>
Sent Time:2022-01-13 22:48:27 (Thursday)
To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Cc:
Subject: Re: [Ifeffit] Question--FEFF calclulated atom coordinates and labels



Hi Ming:

 

The Path-column on the paths-page shows @ symbol for the scattering atom.  A single scattering path is shown as “@ O1.1 @”  This can be understood as the photoelectron generated at the absorbing atom travels to the first occurrence of the first oxygen atom in the unit cell and then back to the adsorbing atom.  The unit cell may contain many O atoms.  Each of them are denoted by the number following the letter, i.e. O1, O2, O3.  When the unit cell is expanded to make the cluster the O1 atom may show up in the first path and then again at a longer distance in say the 4th path.  The second occurrence from the absorbing atom of the O1 atom will be denoted at O1.2.

 

Kind regards,

Shelly

 

 

From: Ifeffit <ifeffit-bounces at millenia.cars.aps.anl.gov> On Behalf Of Ming Zhang
Sent: Thursday, January 13, 2022 6:20 AM
To: ifeffit at millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Question--FEFF calclulated atom coordinates and labels

 


sorry for the trouble, I forgot to register this email.




-----原始邮件-----
发件人:"Ming Zhang" <mzhang17 at zju.edu.cn>
发送时间:2022-01-13 14:41:04 (星期四)
收件人: ifeffit at millenia.cars.aps.anl.gov
抄送:
主题: Question--FEFF calclulated atom coordinates and labels

Dear IFEFFIT members,

 

I’m practicing EXAFS fitting with some standard crystal data. I GOT SOME QUESTIONS when I imported the CIF File into the FEFF calculation.

1) I’m confused with the atom label. The VESTA GUI shows that there are C1, C2, and C3 carbons in a unit cell. However, after FEFF calculation, they become C1.1 C2.1 C3.1, so do the other atoms like nitrogen and hydrogen. Since I need to set some geometry constraints, I have to figure out the nomenclature of the atom coordinates calculated by FEFF and link those atoms to real physical images.

2) I’m also confused with the calculated degeneracy, like the path of @ C1.1 @ (I have no idea about the atom C1.1 stands for). It’s a zinc absorber placed in a tetrahedron coordinated by the N atom of imidazole. Very intuitively, the degeneracy of @ N1.1 @ (row 1) is 4, and YES IT IS. But how comes the single scattering path (row 2) of the C atom next to N become 8? Also in row 5, degeneracy of @ N1.1 C2.1 @ is 8. Notably, we only got 3 C atoms in a coordinated molecule, so even treating closely located C atoms into the same one couldn’t help explain this.

FEFF calculation

 

VESTA GUI

 

The CIF file is attached. I would appreciate it very much if you could help me out.

 

Best regards

Ming Zhang
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