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 [email protected] ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
