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Reaction enumeration with aromaticity [message #1305] Tue, 01 June 2021 18:19 Go to next message
mattiafelice.palermo is currently offline  mattiafelice.palermo
Messages: 3
Registered: June 2021
Junior Member
Hello everyone,

I'm trying to create a reaction where a quinone-containing molecule (non aromatic) is reduced to hydroquinone (aromatic).

The input reaction I wrote is:
/forum/index.php?t=getfile&id=327&private=0

In the input reaction, the carbon bonds of the product rings and "sidegrop" are automatically converted to delocalized by Datawarrior.

These are the reactants:
/forum/index.php?t=getfile&id=326&private=0

When I try to run the reaction, Datawarrior outputs a list of empty products:

/forum/index.php?t=getfile&id=325&private=0

I am probably doing some very basic mistake, but I cannot figure out what I'm doing wrong... Can anybody point out what should I do to obtain the list of products?

Thank you very much for your help and let me know if you need any additional information!

Mattia
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  • Attachment: reactants.png
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  • Attachment: reaction.png
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Re: Reaction enumeration with aromaticity [message #1306 is a reply to message #1305] Wed, 02 June 2021 00:38 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 431
Registered: June 2014
Senior Member
Hi Mattia,

this was indeed a tricky one. I have checked and finally found that the problem was caused by the valence check after doing the substructure search of the generic in the real reactant. The check determines, whether all atoms in the real reactant have enough free valence needed for the reaction. For that it determines the delta between generic product and reactant atoms. Here was the problem: for the atoms with mapping numbers 4 and 9 it found the product atom valences to be +1 higher than their respective reactant valence. Since the real reactant valence atoms at the corresponding position had already the maximum valence of 4, they were sorted out after the substructure match. Calculating free valences with delocalized bonds is a tricky matter. It gets even worse, if multiple bond orders are allowed.

I have fixed this issue and deployed an update of DataWarrior. The dev patch is downloadable from the small print links on the download page after clicking the 'read and understood' checkbox. Some general tips: typically query features are only needed on the reactant side; delocalized bonds may be avoided by using the 'aromatic' query feature for bonds or atoms. A drawn double bond also matches a delocalized bond (in the reactor context). Thus, the following picture is equivalent to your generic reaction.

/forum/index.php?t=getfile&id=328&private=0

Hope, this solves it. Otherwise please let me know.

Thomas
  • Attachment: reaction.png
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[Updated on: Wed, 02 June 2021 00:42]

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Re: Reaction enumeration with aromaticity [message #1307 is a reply to message #1306] Wed, 02 June 2021 23:22 Go to previous messageGo to next message
mattiafelice.palermo is currently offline  mattiafelice.palermo
Messages: 3
Registered: June 2021
Junior Member
Hi Thomas,

thank you so much for your prompt fix and for the in-depth explanation. I apologize for the late reply, today in Italy it's national holiday!

I have updated to the development version and tried the equivalent reaction you have shown in the picture (double bond+aromatic flag), and it works as expected Smile

Unfortunately, trying to do the same with the delocalized bond version still outputs an empty product. Perhaps I'm doing something wrong? I am attaching the rxn file in case it can be of use. Let me know if I can provide any additional information to reproduce the error.

Anyways, even though for me it is more intuitive to work with the delocalized representation, of course the double bond + aromatic flag will definitely do!

Thank you very much for your help and for the wonderful free software!!

Mattia

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Re: Reaction enumeration with aromaticity [message #1308 is a reply to message #1307] Thu, 03 June 2021 09:33 Go to previous message
mattiafelice.palermo is currently offline  mattiafelice.palermo
Messages: 3
Registered: June 2021
Junior Member
Hi Thomas,

I apologize for double posting. I would like to add that while on my home pc (Core i7 4790k, 8 GB RAM, Ubuntu 20.04 kernel 5.8) I did not experience any issue with the dev version, on my work workstation (Threadripper 3995 wx, 64 GB RAM, Ubuntu 20.04 kernel 5.4), I get an error when switching from the "Generic Reaction" to "Reactants" tab in the Enumerate Combinatorial Library dialog window:

/forum/index.php?t=getfile&id=331&private=0

The error starts appearing only after I draw some specific generic reactant formulas e.g. cyclohexane does not trigger the error, cyclohexene does, butane does not trigger the error, methylethylamine does. Let me know if you need any further information.

Many thanks!

Mattia

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