Rintarou,
On Tue, Feb 7, 2017 at 9:25 AM, Suzuki, Rintarou <rsuz...@affrc.go.jp>
wrote:
>
> For the second point, atoms 6 and 8 can be inverted by RDKit_2015_03_1.
>
> RDKit_2015_03_1
> ---------------------------------
> >>> mol=Chem.MolFromSmiles('C1[C@H]2[C@@H]3O[C@@H]3[C@@H]1[C@]13O[C@]21[C@
> @H]1C[C@H]3[C@@H]2O[C@@H]21')
> >>> m=Chem.AddHs(mol)
> >>> Chem.FindMolChiralCenters( copy(m), includeUnassigned=True )
>
> [(1, 'S'), (2, 'S'), (4, 'R'), (5, 'R'), (6, 'S'), (8, 'S'), (9, 'R'),
> (11, 'S'), (12, 'S'), (14, 'R')]
>
> >>> AllChem.EmbedMolecule( m, randomSeed = 256, maxAttempts = 1,
> clearConfs = False )
>
> 0
>
The older version had less strict tests when checking the "reasonableness"
of the embedded structure.
>
> >>> Chem.MolToSmiles(Chem.RemoveHs(m), isomericSmiles=True)
>
> 'C1[C@H]2[C@@H]3O[C@@H]3[C@@H]1[C@]13O[C@]21[C@@H]1C[C@H]3[C@@H]2O[C@
> @H]21'
>
> ---------------------------------
> This conformation is different from that of
> 'C1[C@H]2[C@@H]3O[C@@H]3[C@@H]1[C@@]13O[C@@]21[C@@H]1C[C@H]3[C@@H]2O[C@
> @H]21'
> in previous mail.
>
>
> It is strange at first glance that such atoms on the axis of symmetry
> have chirality.
>
Looking at the molecule in Marvin you can see that two atoms in the middle
each have four different neighbors:
[image: Inline image 1]
This causes them to be perceived by both Marvin and the RDKit as chiral
centers.
>
> But RDKit judges atoms 6 and 8 as achiral in the following two isomers
> with lower symmetry.
>
> C1[C@@H]2[C@@H]3O[C@@H]3[C@H]1C13OC21[C@@H]1C[C@H]3[C@H]2O[C@H]21
> C1[C@@H]2[C@H]3O[C@H]3[C@H]1C13OC21[C@@H]1C[C@H]3[C@@H]2O[C@@H]21
>
Here's the first of those, those two bridging atoms now have two identical
neighbors:
[image: Inline image 2]
Best,
-greg
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