Henry Rzepa's Blog Chemistry with a twist

March 24, 2019

The shortest known CF…HO hydrogen bond.

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. http://dx.doi.org/10.1039/B610213C

January 3, 2019

Dispersion-induced triplet aromatisation?

There is emerging interest in cyclic conjugated molecules that happen to have triplet spin states and which might be expected to follow a 4n rule for aromaticity.[1] The simplest such system would be the triplet state of cyclobutadiene, for which a non or anti-aromatic singlet state is always found to be lower in energy. Here I explore some crystal structures containing this motif for possible insights.



  1. A. Kostenko, B. Tumanskii, Y. Kobayashi, M. Nakamoto, A. Sekiguchi, and Y. Apeloig, "Spectroscopic Observation of the Triplet Diradical State of a Cyclobutadiene", Angewandte Chemie International Edition, vol. 56, pp. 10183-10187, 2017. http://dx.doi.org/10.1002/anie.201705228

December 17, 2017

Ammonide: an alkalide formed from ammonia and resembling an electride.

Alkalides are anionic alkali compounds containing e.g. sodide (Na), kalide (K), rubidide (Rb) or caeside (Cs). Around 90 examples can be found in the Cambridge structure database (see DOI: 10.14469/hpc/3453  for the search query and results). So what about the ammonium analogue, ammonide (NH4)? A quick search of Scifinder drew a blank! So here I take a look at this intriguingly simple little molecule.


October 24, 2017

Elongating an N-B single bond is much easier than stretching a C-C single bond.

An N-B single bond is iso-electronic to a C-C single bond, as per below. So here is a simple question: what form does the distribution of the lengths of these two bonds take, as obtained from crystal structures? 


May 29, 2017

CH⋅⋅⋅π Interactions between methyl and carbonyl groups in proteins: a small molecule check.

Filed under: crystal_structure_mining — Tags: , , , , — Henry Rzepa @ 6:31 pm

Derek Lowe highlights a recent article[1] postulating CH⋅⋅⋅π interactions in proteins. Here I report a quick check using the small molecule crystal structure database (CSD).



  1. F.A. Perras, D. Marion, J. Boisbouvier, D.L. Bryce, and M.J. Plevin, "Observation of CH⋅⋅⋅π Interactions between Methyl and Carbonyl Groups in Proteins", Angewandte Chemie International Edition, vol. 56, pp. 7564-7567, 2017. http://dx.doi.org/10.1002/anie.201702626

May 6, 2017

How does carbon dioxide coordinate to a metal?

Mention carbon dioxide (CO2) to most chemists and its properties as a metal ligand are not the first aspect that springs to mind. Here thought I might take a look at how it might act as such.


April 17, 2017

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

Filed under: crystal_structure_mining — Tags: , , , , — Henry Rzepa @ 8:13 am

Following on from my re-investigation of close hydrogen bonding contacts to the π-face of alkenes, here now is an updated scan for H-bonds to alkynes. The search query (dataDOI: 10.14469/hpc/2478) is similar to the previous one:


April 15, 2017

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

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. http://dx.doi.org/10.1039/P29940000703

April 13, 2017

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

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).


April 6, 2017

The conformation of enols: revealed and explained.

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.


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