Rabbit ears

I want to talk about the so-called “rabbit ears”, which is one of the most enduring concepts in organic chemistry. There have been several exciting discussions related to this topic at the American Peptide Society meeting this week.

By way of background, Professors Ron Raines and Dek Woolfson published a thought-provoking paper back in 2010, in which they analyzed the pdb (protein database) and came up with a conclusion that nearby amino acid residues in proteins display n-pi* interaction. I discussed this back in 2013 (https://amphoteros.com/2013/11/27/neighbourly-ties/). According to the Raines/Woolfson analysis, the molecular orbital-based view of the amide oxygen is more adequately described not as A (below), but as B, in which there is a p-like molecular orbital perpendicular to the C-O vector. The authors stated: “Contrary to the expectations of valence shell electron pair repulsion (VSEPR) theory, the two lone pairs of divalent oxygen do not occupy equivalent orbitals that resemble rabbit ears”.

While “B” adequately explains the interaction between adjacent amides seen by Raines and Woolfson, it does not (in my view) provide grounds for saying that the good old rabbit ears concept has no merit. However, this is exactly what some people tend to conclude from their work. What might be done in defense of the poor old rabbit ears? I suppose if there were a study clearly demonstrating the 120o (or so) angle formed upon Lewis acid coordination to oxygen, it would be convincing enough. There is indeed a paper that shows that: Corey’s 1992 report in Tetrahedron Letters exemplifies the 120o B-O-C angle both in X-ray and in solution. I am somewhat relieved that the good old VSEPR model is alive and well.

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http://www.sciencedirect.com/science/article/pii/S0040403900609024

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