Posts Tagged ‘Supramolecular chemistry’

The shortest known CF…HO hydrogen bond.

Sunday, March 24th, 2019

There is a predilection amongst chemists for collecting records; one common theme is the length of particular bonds, either the shortest or the longest. A particularly baffling type of bond is that between the very electronegative F atom and an acid hydrogen atom such as that in OH. Thus short C-N…HO hydrogen bonds are extremely common, as are C-O…HO. But F atoms in C-F bonds are largely thought to be inert to hydrogen bonding, as indicated by the use of fluorine in many pharmaceuticals as inert isosteres.[1] Here I do an up-to-date search of the CSD crystal structure database, which is now on the verge of accumulating 1 million entries, to see if any strong C-F…HO hydrogen bonding may have been recently discovered.



  1. S. Purser, P.R. Moore, S. Swallow, and V. Gouverneur, "Fluorine in medicinal chemistry", Chem. Soc. Rev., vol. 37, pp. 320-330, 2008.

π-Facial hydrogen bonds to alkenes (revisited): how close can an acidic hydrogen approach?

Saturday, April 15th, 2017

Back in the early 1990s, we first discovered the delights of searching crystal structures for unusual bonding features.[1] One of the first cases was a search for hydrogen bonds formed to the π-faces of alkenes and alkynes. In those days the CSD database of crystal structures was a lot smaller (<80,000 structures; it’s now ten times larger) and the search software less powerful. So here is an update. 



  1. H.S. Rzepa, M.H. Smith, and M.L. Webb, "A crystallographic AM1 and PM3 SCF-MO investigation of strong OH ⋯π-alkene and alkyne hydrogen bonding interactions", J. Chem. Soc., Perkin Trans. 2, pp. 703-707, 1994.

The π-π stacking of aromatic rings: what is their closest parallel approach?

Thursday, April 13th, 2017

Layer stacking in structures such as graphite is well-studied. The separation between the π-π planes is ~3.35Å, which is close to twice the estimated van der Waals (vdW) radius of carbon (1.7Å). But how much closer could such layers get, given that many other types of relatively weak interaction such as hydrogen bonding can contract the vdW distance sum by up to ~0.8Å or even more? This question was prompted by the separation calculated for the ion-pair cyclopropenium cyclopentadienide (~2.6-2.8Å).


The conformation of enols: revealed and explained.

Thursday, April 6th, 2017

Enols are simple compounds with an OH group as a substituent on a C=C double bond and with a very distinct conformational preference for the OH group. Here I take a look at this preference as revealed by crystal structures, with the theoretical explanation.


The “hydrogen bond”; its early history.

Saturday, December 31st, 2016

My holiday reading has been Derek Lowe’s excellent Chemistry Book setting out 250 milestones in chemistry, organised by year. An entry for 1920 entitled hydrogen bonding seemed worth exploring in more detail here.


How does an OH or NH group approach an aromatic ring to hydrogen bond with its π-face?

Wednesday, June 22nd, 2016

I previously used data mining of crystal structures to explore the directing influence of substituents on aromatic and heteroaromatic rings. Here I explore, quite literally, a different angle to the hydrogen bonding interactions between a benzene ring and OH or NH groups.