Hi Andrew,
As chiralities go, this one has turned out to be quite valuable!
https://en.wikipedia.org/wiki/Esomeprazole
Dave
On Mon, Feb 8, 2016 at 3:05 PM, Andrew Dalke <da...@dalkescientific.com>
wrote:
> Hi!
>
> Could someone explain to this non-chemist what the chirality means in
> the following?
>
> CN[S@@](=O)C1=CC=CC=C1
>
> It comes from PubChem id 12194260 at
> https://pubchem.ncbi.nlm.nih.gov/compound/12194260 .
>
> Isn't this a symmetric structure, which can't have an orientation at that
> point? Even if it can have a chirality, which sort of chirality is it? The
> list at http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html
> says:
>
> Tetrahedral is the default class for degree four
> Allene-like is the default class for degree 2
> Square-planar is another class for degree four
> Trigonal-bipyramidal is the default class for degree five
> Octahedral is the default class for degree six
>
> but says nothing about degree three. And RDKit agrees that this is degree
> 3:
>
> >>> mol = Chem.MolFromSmiles("CN[S@@](=O)C1=CC=CC=C1")
> >>> mol.GetAtomWithIdx(2).GetDegree()
> 3
>
>
> This came up while testing my algorithm to fragment a structure. I expect
> to get the same structure back.
>
> I started with:
>
> >>> Chem.CanonSmiles("CN[S@@](=O)C1=CC=CC=C1")
> 'CN[S@@](=O)c1ccccc1'
>
> The fragmentation produces:
>
> >>> Chem.CanonSmiles("C*.N*.*[S@@](=O)C1=CC=CC=C1")
> '[*]C.[*]N.[*][S@@](=O)c1ccccc1'
>
> I can manipulate this at the SMILES level to insert two closures and
> produce the reconnect-able SMILES
>
> C2.N23.[S@@]3(=O)C1=CC=CC=C1
> ^--^
> ^------^
>
> When I process that, I get a flipped chirality:
>
> >>> Chem.CanonSmiles("C2.N23.[S@@]3(=O)C1=CC=CC=C1")
> 'CN[S@](=O)c1ccccc1'
>
> I did not expect this. The Daylight SMILES spec says:
>
> The chiral order of the ring closure bond is implied by the
> lexical order that the ring closure digit appears on the
> chiral atom (not in the lexical order of the "substituent" atom).
>
> I expected the '*' of '*[S**]' and the '3' of '[S**]3' to have the same
> bond position so give the same chirality.
>
> Finally, if I replace the '[S@@]' with a '[C@@]' or '[P@@]' I lose the
> chirality:
>
> >>> Chem.CanonSmiles("CN[C@@](=O)C1=CC=CC=C1")
> 'CNC(=O)c1ccccc1'
> >>> Chem.CanonSmiles("CN[P@@](=O)C1=CC=CC=C1")
> 'CN[P](=O)c1ccccc1'
>
>
> At this point I can't tell if there's a problem with how I understand
> stereochemistry, how I understand SMILES, or how I understand RDKit.
>
>
>
> Andrew
> da...@dalkescientific.com
>
>
>
>
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