I assume in general you would need to add the Molecule to CDK node, but that only results in another error. Unfortunately this is a known issue for quite a long time:
and probably has something to do with the underlying CDK.
These are community nodes not developed by KNIME but PaDEL, so there is not much we at KNIME can do about it, I’m sorry.
Maybe the workaround using the Linux command line mentioned in the first forum link works for you.