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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