missing support for NHC-carbenes which are trivalent

[nbehrnd]

Avogadro version: 1.100.0-7-gac3f38f:

• Avogadrolibs: 1.100-0-55-g11334699
• Qt: 5.12.2

Desktop version:

• OS: Windows
• Version 10, 64bit
• Compiler (if you built from source)

Describe the bug
The import of a .mol file about an NHC carbene complex into Avogadro initially displays the molecular backbone. However -- contrary to expectation -- the automatic adjustment of the hydrogens equally adds hydrogen atoms to the trivalent NHC carbene carbons despite they 1) are labeled as trivalent in the .mol file read, and 2) they already bind to three non-H atoms.

This is observed with both syntaxies, i.e. regardless if there is a 3 in the tenth column of the atom block (v2000 format), or the equivalent VAL=3 in the v3000 format.

To Reproduce
Steps to reproduce the behavior:

1. With Biovia Draw (version 24.1.0.1870), the structure is sketched. To define carbons in question as trivalent NHC carbene, highlight them. A subsequent right-click opens a new menu Atom Property with an entry Valence... to select (III).
2. Export the structure by File -> Save as in the .mol format
3. Now in Avogadro, access structure file with File -> Open
4. Add the missing hydrogens with Ctrl + Alt + H, or Build -> Hydrogens -> Adjust Hydrogens

Expected behavior
Ideally, the adjustment of hydrogens does not hydrogens NHC-carbene carbons, let alone if all three valences already are engaged with three non-H atoms.

Screenshots

Structure as defined in BioVia Draw:

Import of e.g., the .mol (v2000) after the automatic adjustment of hydrogens:

Additional context

2025-02-25_NHC_carbene.zip

[nbehrnd]

If Avogadro's addition of hydrogen atoms relies on openbabel, the issue might relate to the one filed for openbabel (reported here).

[ghutchis]

No, we handle MDL files internally and don't have support for the VAL component. Shouldn't be too hard to fix with the example file.