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The official sources for the RDKit library
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EmbedMolecule not handling trivalent iodine properly #4034

Open jasondbiggs opened 3 years ago

jasondbiggs commented 3 years ago

Ideally this would give a T-shaped geometry around the iodine rather than trigonal pyramidal.

m=MolFromSmiles('[I](Cl)(Cl)Cl')
rdDistGeom.EmbedMolecule(m)
image

This is using the 2021.03.1 release, on MacOS.

greglandrum commented 3 years ago

You're right, and this is a bug, but it's more or less expected: we don't have code in place to handle hypervalent species.