Posts Tagged ‘Interesting chemistry’

What is the largest angle possible at 4-coordinate carbon – 180°?

Sunday, September 11th, 2022

Four-coordinate carbon normally adopts a tetrahedral shape, where the four angles at the carbon are all 109.47°. But how large can that angle get, and can it even get to be 180°?


Unexpected Isomerization of Oxetane-Carboxylic Acids – catalyst design.

Saturday, August 13th, 2022

Previously, a mechanism with a reasonable predicted energy was modelled for the isomerisation of an oxetane carboxylic acid to a lactone by using two further molecules of acid to transfer the proton and in the process encouraging an Sn2 reaction with inversion to open the oxetane ring.


Dioxane tetraketone – an ACS molecule of the week with a mystery.

Wednesday, June 22nd, 2022

I have long been fascinated by polymers of either carbon dioxide, or carbon monoxide, or combinations of both. One such molecule, referred to as dioxane tetraketone when it was featured on the ACS molecule-of-the-week site and also known as the anhydride of oxalic acid, or more formally 1,4-dioxane-2,3,5,6-tetraone, has been speculated upon for more than a century.[1]



  1. H. Staudinger, "Oxalylchlorid", Berichte der deutschen chemischen Gesellschaft, vol. 41, pp. 3558-3566, 1908.

Checking a conclusion we made in 1987: Tetrahedral intermediates formed by nitrogen and oxygen attack of aromatic hydroxylamines on acetyl cyanide

Saturday, June 11th, 2022

Minds (and memories) can work in wonderful ways. In 1987[1] we were looking at the properties of “stable” tetrahedral intermediates formed in carbonyl group reactions. The reaction involved adding phenylhydroxylamine to acetyl cyanide. NMR signals for two new species were detected, and we surmised one was due to N-attack on the carbonyl and one was due to O-attack, in each case to form a stable tetrahedral intermediate. To try to identify which was which, 15N labelled hydroxylamine was used and then the 15N-13C coupling constants were measured, which could either be 1-bondJ (for N-attack) or 2-bondJ (for O-attack).



  1. A.M. Lobo, M.M. Marques, S. Prabhakar, and H.S. Rzepa, "Tetrahedral intermediates formed by nitrogen and oxygen attack of aromatic hydroxylamines on acetyl cyanide", The Journal of Organic Chemistry, vol. 52, pp. 2925-2927, 1987.

(anti)aromaticity avoided: a tutorial example

Tuesday, December 7th, 2010

More inspiration from tutorials. In a lecture on organic aromaticity, the 4n+2/4n Hückel rule was introduced (in fact, neither rule appears to have actually been coined in this form by Hückel himself!). The simplest examples are respectively the cyclopropenyl cation and anion. The former has 2 π-electrons exhibiting cyclic delocalisation, and the 4n+2 (n=0) rule predicts aromaticity. Accordingly, all three C-C distances are the same (1.363Å).


Morphing an arrow-pushing tutorial into a dihydrogen bond

Thursday, December 2nd, 2010

My university tutorial yesterday covered selective reductions of functional groups in organic chemistry. My thoughts on that topic have now morphed into something rather different. Scientific research has a habit of having this sort of thing happen.


Anatomy of an arrow-pushing tutorial: reducing a carboxylic acid.

Wednesday, December 1st, 2010

Arrow pushing (why never pulling?) is a technique learnt by all students of organic chemistry (inorganic chemistry seems exempt!). The rules are easily learnt (supposedly) and it can be used across a broad spectrum of mechanism. But, as one both becomes more experienced, and in time teaches the techniques oneself as a tutor, its subtle and nuanced character starts to dawn. An example of such a mechanism is illustrated below, and in this post I attempt to tease out some of these nuances.


Gravitational fields and asymmetric synthesis

Saturday, November 20th, 2010

Our understanding of science mostly advances in small incremental and nuanced steps (which can nevertheless be controversial) but sometimes the steps can be much larger jumps into the unknown, and hence potentially more controversial as well. More accurately, it might be e.g. relatively unexplored territory for say a chemist, but more familiar stomping ground for say a physicist. Take the area of asymmetric synthesis, which synthetic chemists would like to feel they understand. But combine this with gravity, which is outside of their normal comfort zone, albeit one we presume is understood by physicists. Around 1980, one chemist took such a large jump by combining the two, in an article spectacularly entitled Asymmetric synthesis in a confined vortex; Gravitational fields and asymmetric synthesis[1]. The experiment was actually quite simple. Isophorone (a molecule with a plane of symmetry and hence achiral) was treated with hydrogen peroxide and the optical rotation measured.



  1. R.C. Dougherty, "Chemical geometrodynamics: gravitational fields can influence the course of prochiral chemical reactions", Journal of the American Chemical Society, vol. 102, pp. 380-381, 1980.

Can a cyclobutadiene and carbon dioxide co-exist in a calixarene cavity?

Friday, November 19th, 2010

On 8th August this year, I posted on a fascinating article that had just appeared in Science[1] in which the crystal structure was reported of two small molecules, 1,3-dimethyl cyclobutadiene and carbon dioxide, entrapped together inside a calixarene cavity. Other journals (e.g. Nature Chemistry[2] ran the article as a research highlight (where the purpose is not a critical analysis but more of an alerting service). A colleague, David Scheschkewitz, pointed me to the article. We both independently analyzed different aspects, and first David, and then I then submitted separate articles for publication describing what we had found. Science today published both David’s thoughts[3] and also those of another independent group, Igor Alabugin and colleagues[4]. The original authors have in turn responded [5]. My own article on the topic will appear very shortly[6]. You can see quite a hornet’s nest has been stirred up!



  1. Y. Legrand, A. van der Lee, and M. Barboiu, "Single-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix", Science, vol. 329, pp. 299-302, 2010.
  2. A. Pichon, "Structure of a strained ring", Nature Chemistry, 2010.
  3. D. Scheschkewitz, "Comment on “Single-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix”", Science, vol. 330, pp. 1047-1047, 2010.
  4. I.V. Alabugin, B. Gold, M. Shatruk, and K. Kovnir, "Comment on “Single-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix”", Science, vol. 330, pp. 1047-1047, 2010.
  5. Y. Legrand, A. van der Lee, and M. Barboiu, "Response to Comments on “Single-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix”", Science, vol. 330, pp. 1047-1047, 2010.
  6. H.S. Rzepa, "Can 1,3-dimethylcyclobutadiene and carbon dioxide co-exist inside a supramolecular cavity?", Chem. Commun., vol. 47, pp. 1851-1853, 2011.

A historical detective story: 120 year old crystals

Wednesday, November 17th, 2010

In 1890, chemists had to work hard to find out what the structures of their molecules were, given they had no access to the plethora of modern techniques we are used to in 2010. For example, how could they be sure what the structure of naphthalene was? Well, two such chemists, William Henry Armstrong (1847-1937) and his student William Palmer Wynne (1861-1950; I might note that despite working with toxic chemicals for years, both made it to the ripe old age of ~90!) set out on an epic 11-year journey to synthesize all possible mono, di, tri and tetra-substituted naphthalenes. Tabulating how many isomers they could make (we will call them AW here) would establish beyond doubt the basic connectivity of the naphthalene ring system. This was in fact very important, since many industrial dyes were based on this ring system, and patents depended on getting it correct! Amazingly, their collection of naphthalenes survives to this day. With the passage of 120 years, we can go back and check their assignments. The catalogued collection (located at Imperial College) comprises 263 specimens. Here the focus is on just one, specimen number number 22, which bears an original label of trichloronaphthalene [2:3:1] and for which was claimed a melting point of 109.5°C. What caught our attention is that a search for this compound in modern databases (Reaxys if you are interested, what used to be called Beilstein) reveals the compound to have a melting point of ~84°C. So, are alarm bells ringing? Did AW make a big error? Were many of the patented dyes not what they seemed?