Posts Tagged ‘by-product’

The dawn of organic reaction mechanism: the prequel.

Sunday, November 13th, 2011

Following on from Armstrong’s almost electronic theory of chemistry in 1887-1890, and Beckmann’s radical idea around the same time that molecules undergoing transformations might do so via a reaction mechanism involving unseen intermediates (in his case, a transient enol of a ketone) I here describe how these concepts underwent further evolution in the early 1920s. My focus is on Edith Hilda Usherwood, who was then a PhD student at Imperial College working under the supervision of Martha Whitely.1

The doctoral degree itself had only been introduced into British universities in 1919,1 and so Usherwood was very much a forerunner of the modern system of training.The academic staff and students at Imperial totalled 30, making it one of the largest research schools in UK chemistry at the time. Usherwood’s project was on tautomers, or isomers of molecules which differ only in the position of a labile hydrogen atom. The then quite novel electron-pair symbolism introduced by G. N. Lewis’ in 1916 was adopted to represent two tautomeric equilibria (the supposed mobile or tautomeric hydrogens being enclosed in […])2

  1. [H]C:::N ⇔ C::N[H]
  2. [H]C:::CH ⇔ C::CH[H]

or in our more modern representation (in which lines replace colons, and charges are used to ensure the octet rule is adhered to when possible):

  1. H-C≡N ⇔ C≡N+-H
  2. HC≡CH ⇔ :C=CH2

Modern structural techniques such as electron diffraction or microwave spectroscopies not yet existing, the problem was tackled using specific heat measurements as a function of temperature. This method suggested to Usherwood that for e.g. equilibrium 2, the concentration of iso-acetylene (we now call this vinylidene) was insignificant at ordinary temperatures, but it became appreciable between 200-300°C. Further evidence was claimed for the formation of the “unseen” vinylidene by observing ketene as a by-product of the oxidation of acetylene. This article very much set the trend of (an almost mandatory) speculation on the outcome of (nowadays much more complex) reactions by the need to formulate a reaction mechanism in which various (otherwise undetected but) plausible intermediates are involved.

Moving on some 90 years, and how might one approach such a problem nowadays? Well, I have oft argued on this blog that a good place to obtain an immediate reality check on a proposed mechanism is a calculation. It will come as no surprise that a very accurate calculation can be done on the systems shown above. For example, CCSD(T)/cc-pVTZ will yield a free energy for the equilibria with a pretty small error (< 1 kcal/mol). We use ΔG = -RT Ln K to inter-convert free energies and equilibrium constants. If we are generous and state that in order to observe an appreciable concentration of a minor species, the equilibrium constant can be no smaller than 10-3, its energy cannot be greater than 4 kcal/mol above the more abundant isomer. Our reality check will be to see if the free energy of vinylidene is indeed no more than 4 kcal/mol greater than acetylene. Well, CCSD(T)/cc-pVTZ predicts vinylidene is 41.3 kcal/mol higher @298K, reduced to 33.8 @2000K (and before you ask, these results took a total of perhaps 30 minutes to obtain).

In 1924, the concept of calculating the relative energies of two species using first principles was not even a glimmer on the horizon. The nature of mechanisms was slowly and often painfully established by recourse to experiments alone. And many of the unseen intermediates often remained just such, their existence only inferred indirectly from the models one constructed (of specify heats in Usherwood’s case). It is perhaps no great surprise that these models do not always stand the test of time. In this case, within a year of Usherwood’s publication, Partington was suggesting that the model for the specific heats of acetylene should have included allowance for polymer formation.3 The modern take, armed with the calculation I note above, might in fact side with Partington after all. As for the formation of ketene by oxidation, it is indeed known that (peracid) oxidation of an alkyne will produce ketene, but the modern mechanism (an interesting exercise in arrow pushing for a student) does not involve vinylidene intermediates.

I will add at this point that Hilda Usherwood was married to Christopher Ingold, and the pair of them subsequently published many of the seminal articles in what became known as physical organic chemistry. That legacy continues to this day with (as I noted above) the almost mandatory speculation about the mechanism of any new reaction. But it is only in the last five years or so that these speculations have started to be increasingly tested against reliably accurate computation. A new era is underway.


1 My post was inspired by reading W. H. Brock, “The case of the Poisonous Socks”, chapter 28, RSC Publishing, 2011, 978-1-84973-324-3.

2 These representations are taken from ref 1, p 225 (and including a correction of replacing C:C as drawn there by C::C). The original article apparently appeared in the proceedings of the British Association of 1924, which is not yet available online.

3 Brock, in ref 1, p226, suggests that Usherwood stood her ground on this one, and won her case by showing that Partington’s evidence for polymerization was valid for only a small part of the temperature range she had investigated. I have not managed to track down the original sources for this exchange.

Steve Jobs and chemistry: a personal recollection.

Sunday, October 9th, 2011

Steve Jobs death on October 5th 2011 was followed by a remarkable number of tributes and reflections on the impact the company he founded has had on the world. Many of these tributes summarise the effect as a visionary disruption. Here I describe from my own perspective some of the disruptions to chemistry I experienced (for another commentary, see here).

Chemical diagram, circa 1983.

The diagram above originates in 1983 just before the impact of Jobs’ vision burst upon chemistry. It was published in one of the new-generation of camera-ready journal, the objective being to reduce publication times from a typical 12-24 months down to around around three months. Camera-ready meant that the authors had to prepare a photo-ready manuscript; the role of these journals was to photograph, print and publish. The diagram above was prepared using stencils and Rotring technical pens together with Letraset lettering. The snippet above would probably take an hour or two to draft; the diagrams for an entire article were probably about 1 weeks work. Imagine how much time would be needed for a 200 page PhD thesis (some of this time was occupied by rushing out to a purchase more Letraset sheets because one had run out of say the letter r needed to represent the bromine in the above!). The diagram below was publishedin the same camera-ready journal in 1987.

Chemical diagram, circa 1987.

It was produced using Chemdraw on an Apple Macintosh computer introduced in 1984 (and which reached UK chemistry departments in 1985) and printed on an Apple laser printer. It would have taken perhaps 5 minutes to produce. More significantly, by copying and pasting (terms which need little explanation nowadays), one could re-use the diagram repeatedly as a template in a more complex scheme for little extra effort. You might argue that these two diagrams do not actually differ in quality that much (actually, the Apple-derived diagrams are of much higher quality than implied above, and the loss of quality is because the article has subsequently been scanned by the journal). But in fact the impact of Jobs’ Macintosh computer was far greater than just being able to produce nice chemical diagrams. Because it also introduced chemists to disruptive new concepts, the consequences of which are still impacting today.

The first is the idea of the re-use of digital data, as mentioned above. Once one had a diagram drawn, one could use it to almost instantly derive other properties of the molecule. For example, the molecular weight or an atom connection table. This in turn could be used to start an online search. And it was the Macintosh that really bump-started the idea of online activities.

Although chemistry had started going online around 1980 (I remember a single terminal station enabling STN express online access to chemical abstracts being introduced then, and in fact computational chemists were already online around 1974), the idea of an entire department of researchers ALL being online in their lab or office was very much the result of introducing the Macintosh in 1985. It came with a network connector at no extra cost. This in turn allowed all owners of such a computer to connect online to the (then very expensive) laser printer, and as a by-product almost, to the rest of the world! I have described some of the disruption this introduced elsewhere. By around 1987, most of our Mac users were happily going online (it has to be said that owners of IBM PCs were rarely doing so at this time). That is one of the true legacies that Jobs’ disruptive technologies introduced to us chemists.

I am going to quote Samuel Butler now, writing in 1863: “I venture to suggest that … the general development of the human race to be well and effectually completed when all men, in all places, without any loss of time, at a low rate of charge, are cognizant through their senses, of all that they desire to be cognizant of in all other places. … This is the grand annihilation of time and place which we are all striving for, and which in one small part we have been permitted to see actually realised“.

Steve Jobs made a big contribution to that general development of the human race!