Posts Tagged ‘Interesting chemistry’

(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?


Rate enhancement of the Diels-Alder reaction inside a cavity

Saturday, October 30th, 2010

Reactions in cavities can adopt quite different characteristics from those in solvents. Thus first example of the catalysis of the Diels-Alder reaction inside an organic scaffold was reported by Endo, Koike, Sawaki, Hayashida, Masuda, and Aoyama[1], where the reaction shown below is speeded up very greatly in the presence of a crystalline lattice of the anthracene derivative shown below.



  1. K. Endo, T. Koike, T. Sawaki, O. Hayashida, H. Masuda, and Y. Aoyama, "Catalysis by Organic Solids. Stereoselective Diels−Alder Reactions Promoted by Microporous Molecular Crystals Having an Extensive Hydrogen-Bonded Network", Journal of the American Chemical Society, vol. 119, pp. 4117-4122, 1997.

The strongest bond in the universe!

Sunday, October 24th, 2010

The rather presumptious title assumes the laws and fundamental constants of physics are the same everywhere (they may not be). With this constraint (and without yet defining what is meant by strongest), consider the three molecules: (more…)

(Almost) 100 years of Lewis structures: are they still fit for purpose?

Monday, September 27th, 2010

The molecule below was characterised in 1996 (DOI: 10.1246/cl.1996.489) and given the name tris(dithiolene)vanadium (IV). No attempt was made in the original article to give this molecule a Lewis structure using Lewis electron pair bonds. This blog will explore some of the issues that arise when this is attempted.1


Secrets of a university admissions interviewer

Sunday, September 19th, 2010

Many university chemistry departments, and mine is no exception, like to invite applicants to our courses to show them around. Part of the activities on the day is an “interview” in which the candidate is given a chance to shine. Over the years, I have evolved questions about chemistry which can form the basis of discussion, and I thought I would share one such question here. It starts by my drawing on the blackboard (yes, I really still use one!) the following molecular structure.