Re: [Cdk-user] Aromaticity and amide groups

[Christoph S. <ste...@eb...>]

As I said in my other email:
We may want to impose some "stability" on atom types and then go through
subsequent rounds of atomtyping for a molecule until they stabilize.

Cheers,

Chris

On 18/05/2010 23:00, Egon Willighagen wrote:
> On Tue, May 18, 2010 at 5:51 PM, Mark Rijnbeek <ma...@eb...> wrote:
>> Marcus, a Chebi curator said he really wouldn't regard the N in case no
>> 3. as being part of an amide group.  The main features of the structure
>> are the aromatic imidazole ring and the carboxy group. Granted, the
>> carboxy group is electron-withdrawing and may tend to disrupt the
>> delocalisation of the ring electrons but nevertheless he would still
>> regard the system as aromatic.
> 
> Ah, interesting case. I think I'll agree with Marcus here. The carboxy
> group is more stable than the matching enol... but ring delocalization
> is even more favorable... tautomerism case.
> 
> Good catch. Not easy to detect though... I'll look into it.
> 
> Egon
> 
> 

-- 
Dr. Christoph Steinbeck
Head of Chemoinformatics and Metabolism
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
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