Paragraph 2.2. in the 1966 article is "Valnce-Bond Conventions: Multiple-Bond Unsaturation and Aromaticity". It contains several conventions of which convention (b) is the one applying here: "(b) Contibutions by d orbitals to bonds of quadriligant atoms are neglected."
Later we can find: "Convention (b) excludes double-bonded structures of e.g., sulphoxides and sulphinates." Clearly this also applies to phosphorus compounds. Best regards, Jean Le mardi 26 juillet 2011 à 00:21 +0200, Wolf-D. Ihlenfeldt a écrit : > > > -----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 ------------------------------------------------------------------------------ Magic Quadrant for Content-Aware Data Loss Prevention Research study explores the data loss prevention market. Includes in-depth analysis on the changes within the DLP market, and the criteria used to evaluate the strengths and weaknesses of these DLP solutions. http://www.accelacomm.com/jaw/sfnl/114/51385063/ _______________________________________________ Blueobelisk-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
