Question about wedge/hash changes from implicitizing hash Hs

Hi,

We are using Jchem Java API 5.11.2.

When we process bridge_in.mol by these Java lines, it produce bridge_out.mol.  We think bridge bonds should not be hash, but should be wedge (H hash bonds go back, so bridge bonds should go forward, I think).

Can you clarify if chemaxon behavior is correct?

Thank you very much for any guidance.

Here are Java lines:

mol.addExplicitHydrogens(MoleculeGraph.OMIT_POSTCLEAN);

mol.implicitizeHydrogens(MolAtom.ALL_H & ~MolAtom.LONELY_H & ~MolAtom.ISOTOPE_H & ~MolAtom.CHARGED_H & ~MolAtom.RADICAL_H & ~MolAtom.MAPPED_H & ~MolAtom.HCONNECTED_H & ~MolAtom.CTSPECIFIC_H);

System.out.println(mol.toFormat("mol"));

Hi Andrew,

 

We've investigated the structures you've given to us and found the following:

The two structures are identical. In fact the structure in bridge_in.mol is not correct. If you clean the structure in 3D you get the attached  structure. If you open it you can see that the Hydrogen atoms and the bridge Carbon atom are in the same direction from the ring. Because of the bridge the bridgehead Carbon atoms are forced into this position.

For structures like bridge_in we consider the wedges on the Hydrogen atoms "stronger" then the ones in the ring.

Please let us know if you need any more information.

Cheers,

Peter

Thank you for the quick response.  Let me confer with chemists here who understand these things better than me .. I'll reply again shortly.

I'm sorry for the delay .. your answer went outside my chemistry comfort zone .. our chemists are happy with this answer .. thank you again for the help.

Best,

Andrew

Thank you for the notification.

Best regards,

Peter