January 7th, 2016
This is the third and final study deriving from my Ph.D.[1]. The first two topics dealt with the mechanism of heteroaromatic electrophilic attack using either a diazonium cation or a proton as electrophile, followed by either proton abstraction or carbon dioxide loss from the resulting Wheland intermediate. This final study inverts this sequence by starting with the proton abstraction from an indolinone by a base to create/aromatize to a indole-2-enolate intermediate, which only then is followed by electrophilic attack (by iodine). Here I explore what light quantum chemical modelling might cast on the mechanism.
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References
- B.C. Challis, and H.S. Rzepa, "Heteroaromatic hydrogen exchange reactions. Part VIII. The ionisation of 1,3-dimethylindolin-2-one", Journal of the Chemical Society, Perkin Transactions 2, pp. 1822, 1975. https://doi.org/10.1039/p29750001822
Tags: Arenium ion, Bases, diazo, Diazonium compound, Electrophile, Electrophilic aromatic substitution, Equilibrium chemistry, Fortran, Indole, light quantum chemical modelling, Metal ions in aqueous solution, Nuclear physics, Simple aromatic rings, Solutions
Posted in Historical, reaction mechanism | No Comments »
January 5th, 2016
In May 2015, the EPSRC funding council in the UK required researchers to publish the outcomes of the funded work to include an OA (open access) version of the narrative and to cite the managed research data used to support the research with a DOI (digital object identifier). I was discussing these aspects with a senior manager (research outcomes) at the EPSRC and he asked me to provide some examples from my area of chemistry; here are some.
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January 2nd, 2016
Another mechanistic study we started in 1972[1] is here 40+ years on subjected to quantum mechanical scrutiny.
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References
- B.C. Challis, and H.S. Rzepa, "Heteroaromatic hydrogen exchange reactions. Part 9. Acid catalysed decarboxylation of indole-3-carboxylic acids", Journal of the Chemical Society, Perkin Transactions 2, pp. 281, 1977. https://doi.org/10.1039/p29770000281
Tags: aqueous ethanoic acid solutions, energy, ethanoic acid solutions, free energy barrier , quantum chemical modelling
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December 24th, 2015
The BBC TV quiz series Mastermind was first broadcast in the UK in 1972, the same time I was starting to investigate the mechanism of diazocoupling to substituted indoles as part of my Ph.D. researches. The BBC program became known for the catch phrase I've started so I'll finish; here I will try to follow this precept with the project I started then.
In 1972, one measured the rates of chemical reactions to gain insights into the transition state kinetic model. To obtain more data, we used isotopes such as 2H or 3H, together with substituents such as R-t-butyl to modify the potential energy surfaces of the reactions by inducing steric effects.[1],[2] We found that the kinetics for this reaction were actually complex‡ (in part because of pH dependence) involving a Wheland intermediate (the formation of which is shown with red curly arrows above) followed by the collapse of this intermediate to the diazo-coupled product (blue arrows). Coupling to 2-methyl indole (R=X=H, R'=Me), 2-t-butyl indole (R=H, R'=t-butyl) and 4-methyl-2-t-butyl indole (R=Me, R'=t-butyl) revealed that the kinetic isotope effects induced by replacing H by D or T were "not apparent" (i.e. close to 1), the inference being that the rate constant k1 for those systems was slower than k2; the formation of the Wheland intermediate was rate determining (the rds) for the reaction. But with 2-methyl-4,6-di-t-butyl indole (R=t-butyl, R'=Me) this changed and a deuterium isotope effect of ~7 was observed. The rate determining proton removal from the Wheland intermediate k2 was now slower than k1. With 2,4,6-tri-t-butyl indole, we ended by noting that the reaction become almost too slow to observe and furthermore was accompanied by loss of a t-butyl cation as well as a proton. At this point we attempted to infer some transition state models consistent with these observations. Note that we had relatively little data with which to derive our 3D models (one needs to define a geometry using 3N-6 variables, along with its relative energy and force constants). The text and diagram of our attempt is shown below.
The main points of this argument were;
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References
- B.C. Challis, and H.S. Rzepa, "The mechanism of diazo-coupling to indoles and the effect of steric hindrance on the rate-limiting step", Journal of the Chemical Society, Perkin Transactions 2, pp. 1209, 1975. https://doi.org/10.1039/p29750001209
- H.S. Rzepa, "Hydrogen transfer reactions of Indoles", 1974. https://doi.org/10.5281/zenodo.18777
Tags: Butyl, chemical reactions, Indole, Kinetic isotope effect, Organic chemistry, Physical organic chemistry, potential energy surfaces, relative energy
Posted in Historical, Interesting chemistry, reaction mechanism | 1 Comment »
December 20th, 2015
This question was posted on the CCL (computational chemistry list) by John McKelvey. Here, I give an answer in the form of a search of the CSD (crystal structure database).
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Tags: Azobenzene, John McKelvey, search azobenzene
Posted in Chemical IT, crystal_structure_mining | 5 Comments »
December 11th, 2015
You might have noticed the occasional reference here to the upcoming centenary of the publication of Gilbert N. Lewis’ famous article entitled “The atom and the molecule“.[1] A symposium exploring his scientific impact and legacy will be held in London on March 23, 2016, exactly 70 years to the day since his death. A list of the speakers and their titles is shown below; there is no attendance fee, but you must register as per the instructions below.
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References
- G.N. Lewis, "THE ATOM AND THE MOLECULE.", Journal of the American Chemical Society, vol. 38, pp. 762-785, 1916. https://doi.org/10.1021/ja02261a002
Tags: Alan Dronsfield, Clark Landis, Durham, France, Gilbert N. Lewis, John Nicholson, Julia Contreras-Garcia, Liverpool, London, Michael Mingos, Nick Greeves, organic chemist, Oxford, Patrick Coffey, professor, Robin Hendry, Royal Society of Chemistry Historical Group, United Kingdom, United States
Posted in Interesting chemistry | 1 Comment »
December 10th, 2015
The layout of floor 2 of the chemistry department here contains a number of small rooms which function as tutorial areas. Each has a (non-interactive) whiteboard used by students and tutors for, inter-alia, thought-showering. It was in one such room that I found myself with three colleagues this monday afternoon. We soon all sensed something not quite right about the room; it slowly dawned that the whiteboard was entirely devoid of thoughts (it is normally left adorned with chemical hieroglyphics). Before we departed, one of our number crept up to the board and showered the following (the red bit only followed by a ?; thanks Willie!). The chemistry equivalent you might say of Guerrilla gardening. The product shown in blue below is for your benefit here. It is an example of a double fragmentation reaction; by an odd coincidence following on nicely from the previous post.
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November 28th, 2015
In answering tutorial problems, students often need skills in deciding how much time to spend on explaining what does not happen, as well as what does. Here I explore alternatives to the mechanism outlined in the previous post to see what computation has to say about what does (or might) not happen.
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Tags: animation, Chemical bond, condensation, Demjanov rearrangement, energy, Rearrangement reactions, Tiffeneau–Demjanov rearrangement
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November 23rd, 2015
This reaction emerged a few years ago (thanks Alan!) as a tutorial problem in organic chemistry, in which students had to devise a mechanism for the reaction and use this to predict the stereochemical outcome at the two chiral centres indicated with *. It originates in a brief report from R. B. Woodward’s group in 1973 describing a prostaglandin synthesis,[1] the stereochemical outcome being crucial. Here I take a look at this mechanism using computation.
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References
- R.B. Woodward, J. Gosteli, I. Ernest, R.J. Friary, G. Nestler, H. Raman, R. Sitrin, C. Suter, and J.K. Whitesell, "Novel synthesis of prostaglandin F2.alpha.", Journal of the American Chemical Society, vol. 95, pp. 6853-6855, 1973. https://doi.org/10.1021/ja00801a066
Tags: activation energy, animation, energy, learning tool
Posted in Interesting chemistry, reaction mechanism | 4 Comments »