> to be molecules with nonsense formal charges on aromatic atoms, which then > fail to > be Kekulized given the mismatched valence states.
OK, I have an interesting test case from Noel's python testkekulize.py script. (Sadly, my laptop wasn't set to build the python bindings and so this is currently broken.) C1=[N+]C=Nc2[nH]cnc12 vs. c1[n+]cnc2[nH]cnc12 Now, I'm not entirely sure why there's a positive charge on that nitrogen. Let's ignore that for a second — assume there's some chemical process that makes it N+.. If we're including two explicit double-bonds in that six-membered ring, plus a double bond from the imidazole ring.. that makes three double bonds = 6 pi electrons. So I'd probably mark that ring as aromatic on an exam. That suggests that a pyrridinium n+ is OK, and contributes 1 pi electron. For example, if I add an H, Daylight depict is quite happy with this as aromatic: c1[n+H]cnc2[nH]cnc12 And as you know, the two examples you gave are rejected completely by Daylight SMILES. Thoughts? -Geoff ------------------------------------------------------------------------------ Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
