> -----Ursprüngliche Nachricht----- > Von: Greg Landrum [mailto:[email protected]] > Gesendet: Montag, 25. Juli 2011 20:15 > An: Wolf Ihlenfeldt > Cc: BlueObelisk-Discuss > Betreff: Re: [BlueObelisk-discuss] question: rules for absolute > stereochemistry labels of chiral phosphates > > 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.
No, I do not think that is correct. The phantom atom addition is in my understanding a synchronized process. Either you add to both atoms of the multi bond (and that would include the stereocenter) or none. Adding phantom atoms only at the outer atom of a multi bond is definitely not the correct procedure. 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 I do not have access to this paper. Can you share a PDF? > > 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
