Hi Paolo,
Many thanks for your response. I suspected that the dihydro-imidazol ring
was involved in this behaviour.
Still can't get my head around this aromaticity behaviour, but I trust you!
It seems that the fused dihydro-imidazol is somehow "stealing" the
aromaticity of the pyridine ring... I'll try to remember that one.
Have a good WE,
Cheers,
Alexis
On Fri, 27 Nov 2020 at 18:04, Paolo Tosco <paolo.tosco.m...@gmail.com>
wrote:
> Hi Alexis,
>
> The second molecule (smiles2) is indeed aromatic, but the first (smiles1)
> is not, as the imidazole ring condensed to the pyridine is partially
> saturated.
> The smiles1a analogue where I have added a double bond is aromatic, and
> upon canonicalization it yields an aromatic SMILES as expected.
>
> Cheers,
> p.
>
> from rdkit import Chem
>
> In [2]:
>
> mol1 = Chem.MolFromSmiles("N12C=CC=CC1=NCC2")
>
> In [3]:
>
> mol1
>
> Out[3]:
> [image: image.png]
> In [4]:
>
> smiles1 = Chem.MolToSmiles(mol1)
>
> In [5]:
>
> smiles1
>
> Out[5]:
>
> 'C1=CC2=NCCN2C=C1'
>
> In [6]:
>
> mol2 = Chem.MolFromSmiles("CN=C1C=CC=CN1C")
>
> In [7]:
>
> mol2
>
> Out[7]:
> [image: image.png]
> In [8]:
>
> smiles2 = Chem.MolToSmiles(mol2)
>
> In [9]:
>
> smiles2
>
> Out[9]:
>
> 'CN=c1ccccn1C'
>
>
>
>
>
>
>
>
>
> In [10]:
>
> mol1a = Chem.MolFromSmiles("N12C=CC=CC1=NC=C2")
>
> In [11]:
>
> mol1a
>
> Out[11]:
> [image: image.png]
> In [12]:
>
> smiles1a = Chem.MolToSmiles(mol1a)
>
> In [13]:
>
> smiles1a
>
> Out[13]:
>
> 'c1ccn2ccnc2c1'
>
>
> On Fri, Nov 27, 2020 at 5:09 PM Alexis Parenty <
> alexis.parenty.h...@gmail.com> wrote:
>
>> Hi everyone,
>>
>> Why is it that when I canonicalize the following smiles_1 I get its
>> unexpected kekule form, whereas when I canonicalize a similar smiles_2, I
>> get its expected aromatic form?
>>
>> From rdkit import Chem
>> smiles1 = Chem.CanonSmiles("N12C=CC=CC1=NCC2")
>> smiles
>> ==> 'C1=CC2=NCCN2C=C1'
>>
>> smiles2 = Chem.CanonSmiles("CN=C1C=CC=CN1C")
>> smiles2
>> ==> 'CN=c1ccccn1C'
>>
>> I would like to get the aromatic form in both cases... Is there a way to
>> force the aromatic form?
>>
>> Best,
>> Alexis
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
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