Technical Support Forum Index
Technical Support Forum
Access ChemAxon scientists and developers here. For registration and login issues contact website support.

Support Ticket System is replacing forum

This forum was converted into a searchable archive. You cannot add posts here any more. For support please use our new Ticket System.

Create your first ticket
Reactor: Sulfoxide chirality lost.
To watch this topic for replies  Register (enables digests) or give email address:
This topic is locked: you cannot edit posts or make replies.
Display posts from previous:   
    View previous topic :: View next topic    
Author Message
Guillermo

Joined: 06 Apr 2016
Posts: 6

View user's profile

Back to top
Link to postPosted: Wed Jul 06, 2016 9:27 pmPost subject: Reactor: Sulfoxide chirality lost. Reply with quote

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.

Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
Posts: 1163

View user's profile

Back to top
Link to postPosted: Thu Jul 07, 2016 4:07 pmPost subject: Reply with quote

Could you attach the reaction and the generated output?

Guillermo

Joined: 06 Apr 2016
Posts: 6

View user's profile

Back to top
Link to postPosted: Fri Jul 08, 2016 9:52 pmPost subject: Reply with quote

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.




 Filename: Sulfoxide-Michael-Addition-Products.mrv    Filesize: 5.7 KB    Downloaded: 218 Time(s)
 Description:  Sulfoxide products (Marvin file).

 Filename: Sufloxide-Michael-Adition-Reaction.mrv    Filesize: 6.02 KB    Downloaded: 215 Time(s)
 Description:  Marvin reaction file for Micheal Addition

 Filename: Benzophenone_Imine_Resin_with_ID-Fixed.sdf    Filesize: 1.91 KB    Downloaded: 115 Time(s)
 Description:  Resin for Micheal Addition Reaction

 Filename: Sulfoxides.sdf    Filesize: 2.2 KB    Downloaded: 124 Time(s)
 Description:  Sulfoxide (2 enantiomers)
Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
Posts: 1163

View user's profile

Back to top
Link to postPosted: Tue Jul 12, 2016 5:06 pmPost subject: Reply with quote

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

Go to start of metadata

Reaction stereo centers can be defined in two ways:

  1. as an INVRET (inversion/retention) atom property in the MOL (or RXN, RDF) form
  2. by setting atom parity using up/down-wedge bonds...

For more read this page.

Guillermo

Joined: 06 Apr 2016
Posts: 6

View user's profile

Back to top
Link to postPosted: Tue Jul 12, 2016 6:03 pmPost subject: Reply with quote

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.




 Filename: amidation-reaction.mrv    Filesize: 1.95 KB    Downloaded: 153 Time(s)
 Description:  amide products retaining the chirality of the starting amines

 Filename: amino_esters.sdf    Filesize: 3.99 KB    Downloaded: 118 Time(s)
 Description:  chrial amino esters

 Filename: acids.sdf    Filesize: 1.35 KB    Downloaded: 113 Time(s)
 Description:  carboxylic acids
Guillermo

Joined: 06 Apr 2016
Posts: 6

View user's profile

Back to top
Link to postPosted: Tue Jul 19, 2016 5:00 pmPost subject: Reply with quote

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

Thanks. Guillermo.

Zsolt
ChemAxon personnel
Joined: 11 Jan 2006
Posts: 1163

View user's profile

Back to top
Link to postPosted: Wed Jul 20, 2016 10:59 amPost subject: Reply with quote

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.




 Filename: reactant.png    Filesize: 6.99 KB    Viewed: 27345 Time(s)
 Description:  
reactant.png

 Filename: reaction1.png    Filesize: 1.56 KB    Viewed: 27345 Time(s)
 Description:  
reaction1.png

 Filename: output_reaction1.png    Filesize: 6.91 KB    Viewed: 27345 Time(s)
 Description:  
output_reaction1.png

 Filename: reaction2.png    Filesize: 2.01 KB    Viewed: 27345 Time(s)
 Description:  
reaction2.png

 Filename: output_reaction2.png    Filesize: 7 KB    Viewed: 27345 Time(s)
 Description:  
output_reaction2.png

 Filename: reaction3.png    Filesize: 3.31 KB    Viewed: 27345 Time(s)
 Description:  
reaction3.png

 Filename: output_reaction3.png    Filesize: 7.11 KB    Viewed: 27345 Time(s)
 Description:  
output_reaction3.png
This topic is locked: you cannot edit posts or make replies.
Page 1 of 1


To watch this topic for replies   Register (enables digests) or give email address  
Jump to:  
You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot vote in polls in this forum
You cannot attach files in this forum
You can download files in this forum