Hello,
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?
Best,
Mitch
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.
https://www.ics.uci.edu/~dock/manuals/DaylightTheoryManual/theory.smarts.html
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.