Checking Molecules for Undefined Stereochemistry


As part of a database cleanup, I'm looking to identify molecules that have one or more tetrahedral atoms with 4 different substituents but no stereochemical bond markings. We aren't looking for any automatic fixing of the structures; we just want to find a way to identify those structures that require a good look.

Are there any KNIME nodes that do this?


A perhaps not so robust method would be to use standardizer (Indigo nodes) and select standardize stereo; after that compare the output smiles with the input smiles and if they differ, then you have a molecule with a chiral center.

The other method which should be more reliable (without having tested it myself): Do a smarts-search for unspecified chirality, check the Daylight Smarts manual, e.g.

Chapter 4.1 Atomic Primitives

@ chirality anticlockwise anticlockwise, default class2
@@ chirality clockwise clockwise, default class2
@<c><n> chirality chiral class <c> chirality <n> (nodefault)
@<c><n>? chiral or unspec chirality <c><n> orunspecified (no default)

Using e.g. table creator listing your smarts and CDK Smarts Query alt Indigo Substructure Matcher, alt. RDKit Substructure Filter you should be able to find your molecules.