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
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>
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