Archive for the ‘Interesting chemistry’ Category

Derek Lowe asks “What’s a Journal For?” – Knowledge graphs?

Friday, October 21st, 2022

What’s a Journal For? This debate has been raging ever since preprint servers were introduced as far back as 1991! Indeed, during my recent submission of a journal article, one of the questions asked was whether the article was already deposited in such a preprint server (in a positive sense, and not one excluding further submission progress). Since my previous comment on this theme was made more than three years ago, I thought I might update it.


Nitroaryls- A less-toxic alternative reagent for ozonolysis: modelling the final step to form carbonyls.

Saturday, October 8th, 2022

Sometimes you come across a reaction which is so simple in concept that you wonder why it took so long to be accomplished in practice. In this case, replacing toxic ozone O3 as used to fragment an alkene into two carbonyl compounds (“ozonolysis”) by a relatively non-toxic simple nitro-group based reagent, ArNO2 in which the central atom of ozone is substituted by an N-aryl group. As reported by Derek Lowe, two groups have published[1], [2] details of such a reaction (Ar = 4-cyano or 3-CF3,5-NO2). But there are (at least) two tricks; the first is to use photo-excitation using purple LEDs (390nm light) to activate the nitro group. The second is to establish the best aryl substituents to use for achieving maximum yields of the carbonyl compounds and the best conditions for achieving the cyclo-reversion reaction, shown below as TS1. That step requires heating the cyclo-adduct up to ~80° in (aqueous) acetonitrile for anywhere between 1-48 hours. Here I take a computational look at that last step, the premise being that if such a model is available for this mechanism, it could in principle be used to optimise the conditions for the process.



  1. D.E. Wise, E.S. Gogarnoiu, A.D. Duke, J.M. Paolillo, T.L. Vacala, W.A. Hussain, and M. Parasram, "Photoinduced Oxygen Transfer Using Nitroarenes for the Anaerobic Cleavage of Alkenes", Journal of the American Chemical Society, vol. 144, pp. 15437-15442, 2022.
  2. A. Ruffoni, C. Hampton, M. Simonetti, and D. Leonori, "Photoexcited nitroarenes for the oxidative cleavage of alkenes", Nature, vol. 610, pp. 81-86, 2022.

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.