Double bond disappearance

General Discussion
1

hello. I am currently trying to obtain simulated thermodynamic properties of PFAS compounds and its possible cleaved products in different bonds.

Recently, I have drawn one of the products of a PFAS compound (N-EtFOSA; Sulfuramid). I am interested in the corresponding S-N BDE. I have drawn the products after in which the S-N would be cleaved and would like to consider the product to have an unpaired electron (i.e., radical). I initially drew the cleaved product for one of the moieties that corresponds to having the sulfur (as shown in the first picture.

product
product1920×1080 198 KB
However, after saving the file and reopening the xyz file, the double bond for the S=O disappears and they are automatically converted into single bonds. How can I preserve the double bond? I think having the double bond could be crucial for vibrational frequency measurements as the double bond would be more limited for molecular rotation compared to single bonds.

I will like to run the radical molecule through ORCA with considering multiplicity of 2 by running the double bond added moiety.

JHK

2

XYZ files do not store bond information. So Avogadro (or more correctly Open Babel) have to infer the bond orders from the positions.

Your Orca calculation will only get a set of atoms - quantum mechanics does not care about “bond orders” - only electron density.

So I can safely say that the Orca calculation will complete no matter what.

If you want to see it again, you can use the draw tool, set the bond order to 2 and click on the bond. (Generally it’s a good idea in this case to turn off automatic hydrogens.)