Re: [Rdkit-discuss] reactions with benzene rings

[Ivan Tubert-B. <iva...@sc...>]

Hi Fernando,

What happens is that atoms on the left hand side of the reaction template
get deleted unless they have mapping numbers (and everything else they were
attached to that becomes unreachable from the mapped atoms is gone as
well). Atoms on the right hand side without mapping numbers are new atoms.

In other words, your reaction as written will delete the five atoms that
complete the aromatic ring (and everything connected to them), and five new
atoms will be added in their place.

The solution is either to add mapping numbers to these five atoms, or make
sure they are not matched by the SMARTS (you can use recursive smarts if
you need to ensure that c:3 is part of a 6-aromatic-carbon ring without
actually matching the atoms.)

Hope this helps,
Ivan

On Fri, Sep 23, 2022 at 2:26 PM Fernando Schimidt <sch...@gm...>
wrote:

> Hello guys!
>
> I'm trying to understand the applications of chemical reactions using
> RDKit and the SMARTS concepts. I am testing, as an example, oxidation of
> aromatic rings:
>
> rxn = AllChem.ReactionFromSmarts(
> '[#6:1]-[#8:2]-[c:3]1ccccc1>>[#8:2]-[c:3]1-cc-cc-c1')
>
>
>
> If I understand correctly, the above reaction is limited to always using
> benzene as a reagent. When I use naphthalene or anthracene as a reagent,
> the product is always simple phenol. How do I make the reaction more
> general?
>
> Thanks for any help!
>
> Best regards
>
> Fernando
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