Archive for the ‘reaction mechanism’ Category

Dimethyl ketal hydrolysis catalysed by hydroxide and hydronium ions

Wednesday, April 7th, 2021

In the preceding post, I looked at a computed mechanism for the hydrolysis of a ketal by water. Of course, pure water consists of three potential catalysts, water itself or [H2O], and the products of autoionisation, [OH] and [H3O+]. The latter are in much smaller concentration, equivalent to a penalty of ~11.9 kcal/mol on any free energy barrier. Here I take a look at these ion-catalysed routes to see if that penalty can be overcome.


A computational mechanism for the aqueous hydrolysis of a ketal to a ketone and alcohol.

Thursday, April 1st, 2021

The previous post was about an insecticide and made a point that the persistence of both insecticides and herbicides is an important aspect of their environmental properties. Water hydrolysis will degrade them, a typical residency time being in the order of a few days. I noted in passing a dioxepin-based herbicide[1] which contains a ketal motif and which in water can hydrolise to a ketone and alcohol. The reverse (acid catalysed) formation of a ketal is a staple of the taught organic chemistry curriculum. Here as a prelude to looking at the hydrolysis of that dioxepin, I take a look at a possible computational mechanism for the hydrolysis of 2,2-dimethoxypropane using pure water, without the help of acid or base.



  1. P. Camilleri, D. Munro, K. Weaver, D.J. Williams, H.S. Rzepa, and A.M.Z. Slawin, "Isoxazolinyldioxepins. Part 1. Structure–reactivity studies of the hydrolysis of oxazolinyldioxepin derivatives", J. Chem. Soc., Perkin Trans. 2, pp. 1265-1269, 1989.

The Stevens rearrangement: how history gives us new insights.

Friday, January 29th, 2021

In a recent post, I told the story of how in the early 1960s, Robert Woodward had encountered an unexpected stereochemical outcome to the reaction of a hexatriene, part of his grand synthesis of vitamin B12. He had constructed a model of the reaction he wanted to undertake, perhaps with the help of a physical model, concluding that the most favourable of the two he had built was not matched by the actual outcome of the reaction. He was thus driven to systematise such (Pericyclic) reactions by developing rules for them with Roald Hoffmann. This involved a classification scheme of “allowed” and “forbidden” pericyclic reactions and his original favoured model in fact corresponded to the latter type. When physical model building in the 1960s was gradually replaced by models based on quantum mechanical calculations from the 1970s onwards, the term “allowed” morphed into “a relatively low energy transition state for the reaction can be located” and very often “no transition state exists for a forbidden reaction”. The famous quote “there are no exceptions” (to this rule) was often interpreted that if a “forbidden reaction” did apparently proceed, its mechanism was NOT that of a pericyclic reaction. Inspired by all of this, I recollected a famous “exception” to the rules which is often explained by such non-pericyclic character, the Stevens rearrangement[1],[2],[3] by a 1,2-shift.



  1. T.S. Stevens, E.M. Creighton, A.B. Gordon, and M. MacNicol, "CCCCXXIII.—Degradation of quaternary ammonium salts. Part I", J. Chem. Soc., vol. 0, pp. 3193-3197, 1928.
  2. T.S. Stevens, "CCLXX.—Degradation of quaternary ammonium salts. Part II", J. Chem. Soc., vol. 0, pp. 2107-2119, 1930.
  3. T.S. Stevens, W.W. Snedden, E.T. Stiller, and T. Thomson, "CCLXXI.—Degradation of quaternary ammonium salts. Part III", J. Chem. Soc., vol. 0, pp. 2119-2125, 1930.

Is cyanogen chloride (fluoride) a source of C⩸N(+)? More mechanistic insights.

Friday, December 4th, 2020

I asked the question in my previous post. A computational mechanism revealed that AlCl3 or its dimer Al2Cl6 could catalyse a concerted 1,1-substitution reaction at the carbon of Cl-C≡N, with benzene displacing chloride which is in turn captured by the Al. Unfortunately the calculated barrier for this simple process was too high for a reaction apparently occuring at ~room temperatures. Comments on the post suggested using either a second AlCl3 or a proton to activate the carbon of the C≡N group by coordination on to nitrogen. A second suggestion was to involve di-cationic electrophiles. Here I report the result of implementing the N-coordinated model below.


Is cyanogen chloride (fluoride) a source of C⩸N(+)?

Saturday, November 28th, 2020

In 2010 I recounted the story of an organic chemistry tutorial, in which I asked the students the question “how would you synthesize 3-nitrobenzonitrile“.


The Willgerodt-Kindler reaction. Completing the Box set.

Monday, September 7th, 2020

These four posts (the box set) set out to try to define the energetics for a reasonable reaction path for the Willgerodt-Kindler reaction. The rate of this reaction corresponds approximately to a free energy barrier of ~30 kcal/mol. Any pathway found to be >10 kcal/mol at its highest point above this barrier was deemed less probable. The first three efforts at defining such pathways all gave such a result. Here I try a fourth pathway in search of the hitherto elusive appropriately low energy barrier.


The Willgerodt-Kindler Reaction: mechanistic reality check 3. A peek under the hood for transition state location.

Thursday, August 27th, 2020

The two previous surveys of the potential energy surface for this, it has to be said, rather obscure reaction led to energy barriers that were rather to high to be entirely convincing. So here is a third possibility.


The Willgerodt-Kindler Reaction: mechanistic reality check 2.

Friday, August 14th, 2020

Continuing an exploration of the mechanism of this reaction, an alternative new mechanism was suggested in 1989 (having been first submitted to the journal ten years earlier!).[1] Here the key intermediate proposed is a thiirenium cation (labelled 8 in the article) and labelled Int3 below.



  1. M. Carmack, "The willgerodt-kindler reactions. 7. The mechanisms", Journal of Heterocyclic Chemistry, vol. 26, pp. 1319-1323, 1989.

The Willgerodt-Kindler Reaction: mechanistic reality check 1.

Tuesday, July 21st, 2020

The Willgerodt reaction[1], discovered in 1887 and shown below, represents a transformation with a once famously obscure mechanism. A major step in the elucidation of that mechanism came[2] using the then new technique of 14C radio-labelling, shortly after the atom bomb projects during WWII made 14CO2 readily available to researchers. Here I am going to start the process of applying the far more recent technique of quantitative quantum mechanical modelling to see if some of the proposed mechanisms stand up to its scrutiny.



  1. C. Willgerodt, "Ueber die Einwirkung von gelbem Schwefelammonium auf Ketone und Chinone", Berichte der deutschen chemischen Gesellschaft, vol. 20, pp. 2467-2470, 1887.
  2. W.G. Dauben, J.C. Reid, P.E. Yankwich, and M. Calvin, "The Mechanism of the Willgerodt Reaction1", Journal of the American Chemical Society, vol. 72, pp. 121-124, 1950.

Curly arrows in the 21st Century. Proton-coupled electron transfers.

Wednesday, June 10th, 2020

One of the most fascinating and important articles dealing with curly arrows I have seen is that by Klein and Knizia on the topic of C-H bond activations using an iron catalyst.[1] These are so-called high spin systems with unpaired electrons and the mechanism of C-H activation involves both double headed (two electron) and fish-hook (single electron) movement. Here I focus on a specific type of reaction, the concerted proton-coupled-electron transfer or cPCET, as illustrated below. These sorts of reactions happen also to be of considerable biological importance, including e.g. the mechanism of photosynthesis and many other important transformations.



  1. J.E.M.N. Klein, and G. Knizia, "cPCET versus HAT: A Direct Theoretical Method for Distinguishing X-H Bond-Activation Mechanisms", Angewandte Chemie International Edition, vol. 57, pp. 11913-11917, 2018.