Archive for the ‘reaction mechanism’ Category
Wednesday, June 26th, 2013
A reader asked me about the mechanism of the reaction of 2-picoline N-oxide with acetic anhydride to give 2-acetoxymethylpyridine (the Boekelheide Rearrangement[1]). He wrote ” I don’t understand why the system should prefer to go via fragmentation-recombination (… the evidence being that oxygen labelling shows scrambling) when there is an easy concerted pathway available (… a [3,3]sigmatropic shift). Furthermore, is it possible for two pathways to co-exist?” Here is how computation might enlighten us.
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References
- A. Massaro, A. Mordini, A. Mingardi, J. Klein, and D. Andreotti, "A New Sequential Intramolecular Cyclization Based on the Boekelheide Rearrangement", European Journal of Organic Chemistry, vol. 2011, pp. 271-279, 2010. https://doi.org/10.1002/ejoc.201000936
Tags:ATM, CF 3 CO, CH 3 CO, extraneous product, free energy, free energy barrier, recombination
Posted in Interesting chemistry, pericyclic, reaction mechanism | 3 Comments »
Thursday, December 20th, 2012
I have written earlier about dihydrocostunolide, and how in 1963 Corey missed spotting the electronic origins of a key step in its synthesis.[1]. A nice juxtaposition to this failed opportunity relates to Woodward’s project at around the same time to synthesize vitamin B12. The step in the synthesis that caused him to ponder is shown below.
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References
- E.J. Corey, and A.G. Hortmann, "The Total Synthesis of Dihydrocostunolide", Journal of the American Chemical Society, vol. 87, pp. 5736-5742, 1965. https://doi.org/10.1021/ja00952a037
Tags:dispersion energy, free energy, Historical, pericyclic
Posted in Interesting chemistry, pericyclic, reaction mechanism | No Comments »
Thursday, July 12th, 2012
Years ago, I was travelling from Cambridge to London on a train. I found myself sitting next to a chemist, and (as chemists do), he scribbled the following on a piece of paper. When I got to work the next day Vera (my student) was unleashed on the problem, and our thoughts were published[1]. That was then.
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References
- M.S. Baird, J.R. Al Dulayymi, H.S. Rzepa, and V. Thoss, "An unusual example of stereoelectronic control in the ring opening of 3,3-disubstituted 1,2-dichlorocyclopropenes", Journal of the Chemical Society, Chemical Communications, pp. 1323, 1992. https://doi.org/10.1039/c39920001323
Tags:Cambridge, chemist, conformational analysis, free energy, Historical, Internet era, London, pericyclic, perturbation energy, re-analysis using modern algorithms, Reaction Mechanism, Skolnik
Posted in Interesting chemistry, reaction mechanism | 1 Comment »
Monday, July 9th, 2012
Sometimes, connections between different areas of chemistry just pop out (without the help of semantic web tools, this is called serendipity). So here, I will try to join up some threads which emerge from previous posts.
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Tags:alkyne, gas phase, gas phase model, perepoxidation, Reaction Mechanism, semantic web tools
Posted in Curly arrows, reaction mechanism | 3 Comments »
Monday, May 7th, 2012
The Baeyer-Villiger rearrangement was named after its discoverers, who in 1899 described the transformation of menthone into the corresponding lactone using Caro’s acid (peroxysulfuric acid). The mechanism is described in all text books of organic chemistry as involving an alkyl migration. Here I take a look at the scheme described by Alvarez-Idaboy, Reyes and Mora-Diez[1], and which may well not yet have made it to all the text books!
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References
- J.R. Alvarez-Idaboy, L. Reyes, and N. Mora-Diez, "The mechanism of the Baeyer–Villiger rearrangement: quantum chemistry and TST study supported by experimental kinetic data", Organic & Biomolecular Chemistry, vol. 5, pp. 3682, 2007. https://doi.org/10.1039/b712608e
Tags:final product, free energy, Historical, stereoelectronic, Tutorial material, X5
Posted in reaction mechanism | 6 Comments »
Sunday, January 8th, 2012
The tetrahedral intermediate is one of those iconic species on which the foundation of reaction mechanism in organic chemistry is built. It refers to a (normally undetected and hence merely inferred) species formed initially when a nucleophilic reagent attacks a carbonyl compound. Its importance to understanding the activity of enzymes cannot be overstated. An example of this genre is shown below, in which a thiol reacts with an acyl cyanide to form the species ringed in green.
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Tags:diastereotopic, spectroscopy, tetrahedral intermediate
Posted in Interesting chemistry, reaction mechanism | 1 Comment »