On Sat, Jul 23, 2011 at 10:50 PM, Wolf Ihlenfeldt <[email protected]> wrote: > > Ghost atoms for stereo resolution are only added starting after the first > expanded shell, when a multi-bond to a new ligand is traversed, i.e. the > first time in the 2nd sphere. Adding ghost atoms directly to the stereo > center when going to the first ligand sphere does not make sense because it > disrupts the neighbor count, and implicitly the complete tree structure and > the assumed virtual geometry, of the stereo center. Single vs. double-bonded > ligands can still be implicitly prioritized via the atoms bonded to the > ligand in the 2nd sphere (at least when you work with hydrogen-complete > structures, which is what the R/S algorithm requires anyway).
The more I think about this, the less sense it makes to me. For the purposes of determining the priority of the atoms bonded to the stereo center, one does not have to attach any ghost atoms to the stereo center itself (though that would be done to determine that center's priority), they are attached to the neighboring atoms that are multiply bonded to it. In the case of the phosphate compounds I was asking about, this manifests as a ghost P attached to the doubly bonded O. The 1966 CIP paper clearly show this symmetric arrangement of ghost atoms in the text of section 2.2 This is clearly a special case, so this logic may not apply, but I would definitely like to see a published explanation. Anyone have one? -greg ------------------------------------------------------------------------------ Storage Efficiency Calculator This modeling tool is based on patent-pending intellectual property that has been used successfully in hundreds of IBM storage optimization engage- ments, worldwide. Store less, Store more with what you own, Move data to the right place. Try It Now! http://www.accelacomm.com/jaw/sfnl/114/51427378/ _______________________________________________ Blueobelisk-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
