Tag Archives: hydrogen bond

Good to see Charlie’s still at it

Good to see Charlie Perrin is still pumping out papers, and interesting ones to boot.  I knew him in grad school.  He’s got to be over 80.

This one —J. Am. Chem. Soc. 141, 4103 (2019) –is about something that any undergraduate organic chemist can understand (if not the techniques he used) — keto/enol tautomerism, in which the hydrogen bounces between two oxygens, so that, given N molecules in solution, N/2  have the hydrogen bound to one oxygen and N/2 have it bound to the other.

No so in what Charlie found — a compound where the hydrogen is smack dab in the middle.  Some fancy NMR techniques were used to show this.

Hydrogen bonds are extremely subtle (which is why we don’t understand water as well as we might).  Due to the small mass of the proton it isn’t appropriate to treat the proton in hydrogen bonded systems as a classical particle.  When quantum mechanics enters, aspects such as zero point motion, quantum delocalization and tunneling come into play.  These are called quantum nuclear effects (aka Ubbelohde effects).

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Was I the last to find out?

Quick ! Can you form a hydrogen bond from a carbon hybridized sp3 to an oxygen atom?

I didn’t think so, but you can. This, in spite of reading about proteins for over half a century. [ Proc. Natl. Acad. Sci. vol. 111 pp. E888 – E895 ’14 ] describes this (along with lots of references backing up the statements which follow) to such bonds forming between the transmembrane segments of membrane proteins (estimated to be 30% of all our proteins).

Whether or not they contribute to membrane stability isn’t known. Consider the alpha carbon of an amino acid. It is adjacent to a carbonyl group of an amide (electron hungry, but less so than a pure carbonyl because of resonance) and the nitrogen atom of an amide (slightly more electronegative than carbon, and probably more electron hungry because it loses part of its lone pair to resonance).

They are usually found from the alpha carbon of glycine on one helix to the carbonyl of an adjacent transmembrane helix. Glycine zippers (e.g. the G X X X G motif) have long been known in transmembrane helices. Since glycine is the smallest amino acid, having them on the same side of the helix was thought to be a way to pack adjacent helices together.

What would you consider good evidence for such a bond? Spectroscopy of model compounds with deuterium for the alpha hydrogen would be one way (it’s been done). The best evidence would be a shortened distance between the hydrogen and the carbonyl and this has been found as well.

Humbling ! !