Stereochemistry - Stereo Configurations and Geometry

Hi,

Is there a node that can identify various configuration in the stereogenic centers (AND, OR, ABS)?
Also, is there a node that can identify E or Z bond in the molecule?

Thanks,
Shiva

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The RDKit does not currently support extended stereochemistry, so “AND, OR, ABS” would not work. It could provide information about which atoms are stereogenic and, if they are defined, what the current configuration is (for this the RDKit uses “R” and “S” labels generated by an approximation to the CIP algorithm).
Information about E or Z bonds is already possible in the backend, but there’s no node for it.

I can probably do a quick version of this with a java snippet node. How would you want this information provided in the output?

Best,
-greg

Thank you for the response Greg. I would want an output where it mentions that the provided molecule has either R or S configuration (It would be great if we can retrieve the labels on atoms in a property). Also, information about E or Z bond, whether those are present as well (Similarly it would be great if we can retrieve the labels on atoms in a property). Also if possible, can we confirm through a property whether the provided molecule has hash, wedge bonds?

Thanks,
Shiva

Hi Greg,

Also do we have a node that can specify whether a given compound is a mixture of cis sterioisomers or mixture of trans isomers? Also is there a node to confirm the cis or trans assignment?

Thanks,
Shiva

Can you please let me know, if there is a node that can confirm the specified Stereocenter?

Shiva

Hi Shiva,

The attached workflow uses a Java Snippet to collect the Z, E, and unspecified double bonds for molecules. It also adds columns with counts for each type.
Stereo_info.knwf (10.1 KB)

This just handles bonds, but there’s an example I blogged about that shows how to count the number of specified and unspecified stereocenters using the java snippet:
https://www.knime.com/blog/using-custom-data-types-with-the-java-snippet-node
-greg

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I’m not sure what you mean by “confirm the specified Stereocenter”. Can you please elaborate on that?

Greg,

Thanks for the example.

What i meant from “confirming the specified Stereocenter” is that the stereocenter’s absolute configuration is known.

Can we identify presence of RS configuration and Cis-trans isomers?
Can you also please share the link of the methods defined in the RDKit jar file?

Re: cis-trans
The current RDKit implementation assigns E/Z instead of using cis/trans.

Re: methods
There is unfortunately very little documentation available for this. You kind of just have to look at the functions/classes that are defined and “guess” (or use the RDKit C++ documentation linked from rdkit.org)

Re: R/S
I will try to make some time to put together a modified version of the workflow that flags stereocenters too

Thanks Greg. Can you please let me know once the node on R/S configuration flags is done?

Shiva

Yes, I will post on this thread.
I’m quite busy at the moment, so this likely won’t happen until next week.
-greg