Reactor: Sulfoxide chirality lost.

Dear group,

I enumerated a reaction using 2 sulfoxides (enantiomers, chirality explicitly drawn in their 2D structure) and the chirality of the sulfoxides should remain unchanged in the final products.

However, Reactor is outputting the sulfoxide units with straight bonds and not with the chiral bond contained/indicated in the original sulfoxides (reactants).

To make sure this is not only a 2D display issue, I read the 2 products with Marvin Sketch, minimized the compounds to get their 3D coordinates, and the 2 compounds are shown with the same chirality (not enantiomers).

How do you keep the specified chirality in sulfoxides when using Reactor?

Thank you. -Guillermo.

Could you attach the reaction and the generated output?

Sure.  Here are all the files I use for the reaction.

Notice the 2 sulfoxides are chiral (bond between sulfur atom and phenyl group).  This chirality is lost in the products.

Let me know if you need anything else to resolve this problem.

Thanks. Guillermo.

You have to define the stereo centers in reaction to make it work. Quote from the documentation:Skip to end of metadata

I don't understand.  Reaction centers in starting materials are indeed retained WITHOUT making this chirality specific in the reaction products.

For example, here I'm attaching a simple amidation reaction between chiral amines and carboxylic acids, in the reaction scheme I am not indicating what chirality the products are to have, and the products are correctly enumerated retaining the specified chiral center in the amines.

I did the same for the sulfoxide using up/down-wedge bonds.  The reaction takes place on the opposite side of the sulfoxides where I do indicate desired chiralities using up/down-wedge bonds ON THAT SIDE OF THE COMPOUNDS.

Following the observation with the amide enumeration example I am attaching where chiral centers are retained unless specified otherwise, the specified sulfur phenyl up/down-wedge bonds SHOULD be kept the same (intact) in the products.

Why is this not working with sulfoxides if the same process does work for other compounds (i.e., chiral amines)?

Thanks. Guillermo.

Hi, any word from the information and files I provided to your post?

Thanks. Guillermo.

I have attached a few examples. They may not be the best examples for a chemistry class, but they demonstrate how chirality is handled by Reactor.

Reaction 1

A bond connected to a chiral center is modified by the reaction. The transformation does not define the chirality in reaction schema.

Result: Chirality is lost in reaction center.
Note: The chiral center which is not part of the reaction center is not modified. 

Input: reactant.png
Reaction: reaction1.png
Output: output_reaction1.png

Reaction 2

A bond connected to a chiral center is modified by the reaction. The INVRET (inversion/retention) atom property defines the chirality modification in reaction schema.

Result: Chirality is preserved in reaction center.

Input: reactant.png
Reaction: reaction2.png
Output: output_reaction2.png 

Reaction 3

The reaction does not modify bonds connected to chiral centers.

Input: reactant.png
Reaction: reaction3.png
Output: output_reaction3.png 

I hope this helps.