Posts Tagged ‘model’

Experimental evidence for “hidden intermediates”? Epoxidation of ethene by peracid.

Sunday, August 25th, 2013
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The concept of a “hidden intermediate” in a reaction pathway has been promoted by Dieter Cremer[1] and much invoked on this blog. When I used this term in a recent article of ours[2], a referee tried to object, saying it was not in common use in chemistry. The term clearly has an image problem. A colleague recently sent me an article to read (thanks Chris!) about isotope effects in the epoxidation of ethene[3] and there I discovered a nice example of hidden intermediates which I share with you now.



  1. E. Kraka, and D. Cremer, "Computational Analysis of the Mechanism of Chemical Reactions in Terms of Reaction Phases: Hidden Intermediates and Hidden Transition States", Accounts of Chemical Research, vol. 43, pp. 591-601, 2010.
  2. H.S. Rzepa, and C. Wentrup, "Mechanistic Diversity in Thermal Fragmentation Reactions: A Computational Exploration of CO and CO2Extrusions from Five-Membered Rings", The Journal of Organic Chemistry, vol. 78, pp. 7565-7574, 2013.
  3. T. Koerner, H. Slebocka-Tilk, and R.S. Brown, " Experimental Investigation of the Primary and Secondary Deuterium Kinetic Isotope Effects for Epoxidation of Alkenes and Ethylene with m -Chloroperoxybenzoic Acid ", The Journal of Organic Chemistry, vol. 64, pp. 196-201, 1999.

The importance of being complete.

Monday, September 26th, 2011
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To (mis)quote Oscar Wilde again, ““To lose one methyl group may be regarded as a misfortune; to lose both looks like carelessness.” Here, I refer to the (past) tendency of molecular modellers to simplify molecular structures. Thus in 1977, quantum molecular modelling, even at the semi-empirical level, was beset by lost groups. One of my early efforts (DOI: 10.1021/ja00465a005) was selected for study because it had nothing left to lose; the mass spectrometric fragmentation of the radical cations of methane and ethane. Methyl, phenyl and other “large” groups were routinely replaced by hydrogen in order to enable the study. Cations indeed were always of interest to modellers; the relative lack of electrons almost always meant unusual or interesting structures and reactions (including this controversial species, DOI: 10.1021/ja00444a012). Inured to such functional loss, we modellers forgot that (unless in a mass spectrometer), cations have to have a counter anion. Here I explore one example of the model being complete(d).


A short history of molecular modelling: 1860-1890.

Saturday, February 5th, 2011
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In 1953, the model of the DNA molecule led to what has become regarded as the most famous scientific diagram of the 20th century. It had all started 93 years earlier in 1860, at a time when the tetravalency of carbon was only just established (by William Odling) and the concept of atoms as real entities was to remain controversial for another 45 years (for example Faraday, perhaps the most famous scientist alive in 1860 did not believe atoms were real). So the idea of constructing a molecular model from atoms as the basis for understanding chemical behaviour was perhaps bolder than we might think. It is shown below, part of a set built for August Wilhelm von Hofmann as part of the lectures he delivered at the Royal College of Chemistry in London (now Imperial College).

The original August Wilhelm von Hofmann molecular model, located in the archives at the Royal institution, London and used by Hofmann in his 1865 lecture there