Dear Andrew, that functional group is a sulfoxide, and it is indeed chiral because has a lone pair on the sulfur, which is pyramidal; there is a short description here: https://en.wikipedia.org/wiki/Sulfoxide
So it is the same (R,S) chirality you would have on a tetrahedral carbon. The carbon analogue of a sulfoxide, that is a carbonyl group, is planar and therefore is not chiral; this explains why you lose the chirality. Kind regards, Paolo On 08/02/2016 15:05, Andrew Dalke 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 > > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
