I have been working on simulating for the K-edge XANES spectra of methylcobalamin (MeCbl) and cyanocobalamin (CNCbl). The only change in the two materials is one bond (the upper axial bond in an octahedral coordination at the Cobalt site) from CH3 to CN. The molecule consists of about 180 atoms in total. We, however, use a truncated (50 atom) structure and more recently, an extended (90 atom) structure. But neither of them seem to predict the relative changes in peak positions and edge chemical shifts accurately. 

As a quick summary:

Experimental XANES spectra show:

1. CNCbl has a 1 eV blue-shifted absorption edge as compared to MeCbl. 

2. The shoulder peak in CNCbl (about 6-7 eV lower than the main-peak) is much stronger (than MeCbl) and comparable in intensity to the main (strongest) peak.

We use Gaussian to identify the optimized structure and then feed it to FEFF 8.4 to simulate for the XANES. When we do the simulations we note -

1. CNCbl has an approx. 0.1-0.2 eV red-shifted absorption edge as compared to MeCbl. 

2. The shoulder peak intensity is comparable to the main peak intensity in CNCbl. However, in comparing with MeCbl, the shoulder peak intensity is still lower.

Incidentally, we see the exact same problem repeat with hydroxocobalamin OHCbl as we see with CNCbl as well ! (I do not present that here, since I assume the origin of the problem is same).

I thought, maybe truncation is affecting the the optimized geometry when we perform DFT and hence increased the cluster size to about 90 atoms but noticed no significant change. (We did this quite sometime back just with MeCbl to actually justify the use of a truncated structure. But now we are not sure where the error is).

Now I wonder if I am performing the FEFF accurately and not missing something here. 

I attach the input feff files for the truncated and the more elongated structures of both MeCbl and CNCbl. I also attach the (ATHENA deglitched, merged and normalized) experimental XAFS for MeCbl and CNCbl. 

Any help in identifying the issue is greatly appreciated ! (Sorry for the long email).

Thanks,

Ganesh Subramanian

Post Doctoral Research Scholar,

Spence Group,

Arizona State University