The R/S naming system for stereocenters relies on the Cahn–Ingold–Prelog priority rules to rank the four substituents of a stereocenter; the R or S name is then attributed depending on the spatial orientation of the ranked substituents. While this is mostly used for asymmetric carbon atoms, it holds true of other stereocenters with four substituents.

However, nitrogen and phosphorus atoms can also act as stereocenters if the inversion of their configuration is blocked (e.g. because they're in a cyclic molecule) or slowed enough (e.g. because of bulky substituents). Apparently, these stereocenters are also labelled in R/S fashion. Examples I found include Tröger's base:

Tröger's base

(above is the (5S,11S)-enantiomer, below is the (5R,11R)-enantiomer), and DIPAMP:


Having said that, I can't find any reference as to how the R/S naming scheme is applied to these tetrahedral stereocenters which don't have four substituents, but a lone electron pair and three substituents instead. I assume that the same scheme can be followed if one considers the lone pair as the lowest-ranked substituent, but I can't find any canonical reference as to that.

So, how are such stereocenters named? What authoritative reference can I find on this topic?

  • $\begingroup$ Note that it need not be "non-carbon".. Carbanions are chiral as well, but I don't think they're ever needed to be named $\endgroup$ – ManishEarth May 18 '12 at 13:16
  • $\begingroup$ Now I wonder what the rules are for an ionic organic compound (Eg a carbanion with an ionic bond with $\ce{K+}$ ) $\endgroup$ – ManishEarth May 18 '12 at 17:28

but I can't find any canonical reference as to that.

Look harder ;-)

It seems to be that the lone pair has lowest priority.

OK, I can't find any authoritative reference to that (I don't have access to the original paper), but I've got plenty of others:

Alright, IUPAC says:

Except for hydrogen, ligancy, if not already four, is made up to four by adding "phantom atoms" which have atomic number zero (0) and are thus always last in order of preference.

This has various uses but perhaps the most interesting is where nitrogen occurs in a rigid skeleton, as for example in a-isosparteine (14); here the phantom atom can be placed where the nitrogen lone pair of electrons is; then N-i appears as shown alongside the formula, and the chiraiity (R) is the consequence; the same applies to N-i6. Phantom atoms are similarly used when assigning chirality symbols to chiral sulfoxides (see example to Rule E—4.9).

When ligancy is less than four, we obviously have some lone pairs hanging around (except in Hydrogen--which has been excluded, and some other cases like carbocations--which are planar anyway)

So the lone pair becomes a "phantom atom" and has 0 priority.

Now I wonder what happens to these rules if you have two lone pairs, one of them muonic ;-)

Check the first revision of this post for my original, non-authoritative references

  • $\begingroup$ "Phantom atoms are similarly used when assigning chirality symbols to chiral sulfoxides" - one particularly famous example is the proton pump inhibitor (S)-omeprazole (esomeprazole, Nexium), whose only chiral center is the sulfoxide sulfur. So, for chiral centers that are pyramidal, turn the lone pair away from you and check for the clockwise/anticlockwise order from the other three pendants. $\endgroup$ – user95 May 25 '12 at 12:24

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.