More odd is the carbon stereocentre with two methyls... Generally trivalent nitrogens are not considered chiral due to inversion of the lone-pair. The two usual exceptions are when they are a bridgehead or in a tight ring (cyclopropane). This is the same in most toolkits, the InChI technical documentation provides useful examples.
InChI actually only sees one stereo centre since it strips the proton off: InChI=1S/C13H26N2/c1-4-14-8-5-12(6-9-14)15-10-7-13(15)11(2)3/h11-13H,4-10H2,1-3H3/p+1/t13-/m1/s1 It may well be chiral in this case but since it's not you should also strictly remove the other stereocentre in the para position to the nitrogen For the record just tested and ChemAxon/CDK/OpenBabel do the same. John Regards, John W May [email protected] On 19 August 2015 at 09:00, Rob Smith <[email protected]> wrote: > Dear RDKit community, > > I'm trying to use RDKit to read in Corina generated stereoisomers (from a > Mol file), assign chiral tags and stereochemistry to the structure and > output the canonical smiles string for each isomer of a given molecule (in > Python), when I do this, half the canonical smiles strings are not unique. > > When I read in the output from Corina into an Indigo instance, then use > the canonical smiles from Indigo to create an RDKit molecule, canonical > smiles strings generated from the molecule objects are all unique. > > I may be missing an option to enable RDKit to 'visualise' the chiral > centre adjacent to the protonated nitrogen, so if someone can spot where > I've made a mistake, I'd really appreciate it. I've included the output and > Python script below. If you require any further information, please let me > know. > > Many thanks, > Rob > > Output: > > RDKit Read in of Molecule > RDKit Output - CCN1CC[C@@H]([N@@H+]2CC[C@@H]2[C@H](C)C)CC1 > RDKit Output - CCN1CC[C@@H]([N@@H+]2CC[C@@H]2[C@H](C)C)CC1 > RDKit Output - CCN1CC[C@@H]([N@H+]2CC[C@@H]2[C@H](C)C)CC1 > RDKit Output - CCN1CC[C@@H]([N@H+]2CC[C@@H]2[C@H](C)C)CC1 > RDKit Output - CCN1CC[C@@H]([N@@H+]2CC[C@H]2[C@H](C)C)CC1 > RDKit Output - CCN1CC[C@@H]([N@@H+]2CC[C@H]2[C@H](C)C)CC1 > RDKit Output - CCN1CC[C@@H]([N@H+]2CC[C@H]2[C@H](C)C)CC1 > RDKit Output - CCN1CC[C@@H]([N@H+]2CC[C@H]2[C@H](C)C)CC1 > > INDIGO Read in of Molecule > RDKit Output - CC[N@]1CC[C@@H]([N@@H+]2CC[C@@H]2C(C)C)CC1 > RDKit Output - CC[N@]1CC[C@H]([N@@H+]2CC[C@@H]2C(C)C)CC1 > RDKit Output - CC[N@]1CC[C@@H]([N@H+]2CC[C@@H]2C(C)C)CC1 > RDKit Output - CC[N@]1CC[C@H]([N@H+]2CC[C@@H]2C(C)C)CC1 > RDKit Output - CC[N@]1CC[C@@H]([N@@H+]2CC[C@H]2C(C)C)CC1 > RDKit Output - CC[N@]1CC[C@H]([N@@H+]2CC[C@H]2C(C)C)CC1 > RDKit Output - CC[N@]1CC[C@@H]([N@H+]2CC[C@H]2C(C)C)CC1 > RDKit Output - CC[N@]1CC[C@H]([N@H+]2CC[C@H]2C(C)C)CC1 > > Python script : > > from rdkit import Chem > import subprocess # Used to run Corina > from indigo import * > > def runCorinaTest(inputMol): > indigo = Indigo() > > molFile = Chem.MolToMolBlock(inputMol) > > corinaCommand = "echo \'" + molFile + "\' | " > # Then Corina - generate stereoisomers... > corinaCommand = corinaCommand + "/apps/corina/corina -t n -d > canon,stergen,preserve,names,wh,flapn,msc=7,msi=128 -i t=sdf" > corinaResult = subprocess.check_output([corinaCommand], shell=True) # > Gives the stereoisomer species as an SDF string > > allMoleculeObjects = [] > allMolecules = corinaResult.split("$$$$\n") # Separate Corina output > into individual molecules > allMolecules = allMolecules[0:len(allMolecules)-1] > > print("RDKit Read in of Molecule") > > for eachMolecule in allMolecules: > eachMolecule = eachMolecule + "$$$$\n" > mol = Chem.MolFromMolBlock(eachMolecule, sanitize=True, > removeHs=True, strictParsing=False) > Chem.rdmolops.AssignAtomChiralTagsFromStructure(mol, > replaceExistingTags=True) > Chem.rdmolops.AssignStereochemistry(mol) > print("RDKit Output - " + Chem.MolToSmiles(mol, > isomericSmiles=True)) > > print("INDIGO Read in of Molecule") > for eachMolecule in allMolecules: > eachMolecule = eachMolecule + "$$$$\n" > mol = indigo.loadMolecule(eachMolecule) > # print("Indigo Output - " + mol.canonicalSmiles()) > # Use Indigo Canonical Smiles to create RDKit molecule > mol = Chem.MolFromSmiles(mol.canonicalSmiles()) > if mol is not None: > print("RDKit Output - " + Chem.MolToSmiles(mol, > isomericSmiles=True)) > > return 0 > > mol = Chem.MolFromSmiles("CC(C)C1[NH+](C2CCN(CC)CC2)CC1") > z = runCorinaTest(mol) > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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