So, arer you saying it's because I'm making the hydrogen part explicit?
I'll try without that and see what I get. Thanks.
On Mon, 24 Jan 2022 at 12:35, Wim Dehaen <wimdeh...@gmail.com> wrote:
> Hi,
> I think that is not expected behavior and perhaps it could be a
> consequence of a faulty reaction definition.
> using the following with a generic amide coupling:
>
> rxn =
> AllChem.ReactionFromSmarts('[C:1](=[O:2])[OH:3].[N:4]>>[C:1](=[O:2])[N:4].[OH:3]')
> reactant1 = Chem.MolFromSmiles("C[C@@H](OC1=CC(C(=O)O)=CC=C1)C1=CC=CC=C1")
> reactant2 = Chem.MolFromSmiles("NC1(CO)CC(F)(F)C1")
> prod = rxn.RunReactants((reactant1,reactant2))[0][0]
> display(prod)
>
> i get the expected product:
> [image: image.png]
>
> C[C@@H](Oc1cccc(C(=O)NC2(CO)CC(F)(F)C2)c1)c1ccccc1
>
>
> using your more specific reaction definition that includes the whole
> reactant1 structure, the reaction does not work because the amine reactant
> is defined as [NH3] in the reaction smarts, so ammonia only. if i replace
> it with an amine generic
> 'C[C@@H](Oc1cccc(C(=O)O)c1)c1ccccc1.[N:1]>>C[C@@H](Oc1cccc(C(=O)[N:1])c1)c1ccccc1'
> reaction smarts i also get the expected product that includes the stereo
> center.
> I think if your problem persists it would be good to paste a whole code
> block that outputs the undesired product.
> best wishes
> wim
>
>
> On Mon, Jan 24, 2022 at 11:31 AM James Wallace <jeawall...@gmail.com>
> wrote:
>
>> I've been trying to use the RunReactants portion of the ChemicalReaction
>> enumeration with chiral reagents, and a chiral reaction, but I don't seem
>> to get chiral products out.
>>
>> For example, using a template reaction:
>>
>> C[C@@H](Oc1cccc(C(=O)O)c1)c1ccccc1.[NH3:1]>>C[C@
>> @H](Oc1cccc(C(=O)[NH2:1])c1)c1ccccc1
>>
>> [image: image.png]
>>
>> Reactant 1: C[C@@H](OC1=CC(C(=O)O)=CC=C1)C1=CC=CC=C1
>>
>> [image: image.png]
>>
>> Reactant 2: NC1(CO)CC(F)(F)C1
>>
>> [image: image.png]
>>
>> Product: CC(Oc1cccc(C(=O)NC2(CO)CC(F)(F)C2)c1)c1ccccc1
>>
>> [image: image.png]
>>
>> Not that the methyl at the top of the drawing no longer has an R
>> indication.
>>
>> Is there anything inherent to the RunReactants function that clears
>> chirality, as it appears to be retained right up until the combination step
>> to generate the product?
>> _______________________________________________
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>> Rdkit-discuss@lists.sourceforge.net
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>>
>
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