Problem with coordination compounds and hydrogen addition

Dear All,

when trying to draw structures like Cl[Ru]1234[N]5=C(C=CC=C5)C5=[N]1C=CC=C5.O=S21CCS3(=O)CCS4(=O)CC1 |c:4,6,9,12,14,t:2,@:15,@@:18|

containing a 1,4,7-trithionane 1,4,7-trioxide ligand, MarvinSketch always adds hydrogens to my coordinating thiooxides, which is just wrong. However the bonds are drawn as normal, non-coordinating bonds, since I need the stereochemistry here. It is not doing that for the uncoordinated ligand or coordination bonds.

Any suggestions how to fix that problem?

Thanks in advance!

Hi Martinel,

I suggest to put valence property on the affected S atoms as you represent coordinate bonds with single bonds.

This can't be represented in cxsmiles, only in mrv or mol formats.

Cheers,

Peter

Thank you Peter!

I tend to always need stuff that is not available yet...

With set valence properties the structure is projected correctly. If I produce SMILES with set valence properties, the structure is even projected correctly in ChemDraw. However MarvinSketch adds either Hs or radicals when converting it back to a structure... I guess there are always drawbacks, but I can live with this solution!