Thanks, I solved my problem via this - it looks like when I was passing
things in as SMARTS it was ignoring the directive to not have implicit
hydrogens on the R-Groups. Fixing that changed the reaction definitions to
the ones like the ones you mentioned, and gave me the chirality back.
On Mon, 24 Jan 2022 at 13:17, James Wallace <jeawall...@gmail.com> wrote:
> 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?
>>> _______________________________________________
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>
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