Posts Tagged ‘Dan Singleton’

Kinetic isotope effect models as a function of ring substituent for indole-3-carboxylic acids and indolin-2-ones.

Wednesday, January 20th, 2016

The original strategic objective of my PhD researches in 1972-74 was to explore how primary kinetic hydrogen isotope effects might be influenced by the underlying structures of the transition states involved. Earlier posts dealt with how one can construct quantum-chemical models of these transition states that fit the known properties of the reactions. Now, one can reverse the strategy by computing the expected variation with structure to see if anything interesting might emerge, and then if it does, open up the prospect of further exploration by experiment. Here I will use the base-catalysed enolisation of 1,3-dimethylindolin-2-ones and the decarboxylation of 3-indole carboxylates to explore this aspect.


Reproducibility in science: calculated kinetic isotope effects for cyclopropyl carbinyl radical.

Saturday, July 11th, 2015

Previously on the kinetic isotope effects for the Baeyer-Villiger reaction, I was discussing whether a realistic computed model could be constructed for the mechanism. The measured KIE or kinetic isotope effects (along with the approximate rate of the reaction) were to be our reality check. I had used ΔΔG energy differences and then HRR (harmonic rate ratios) to compute[cite]10.5281/zenodo.19272[/cite] the KIE, and Dan Singleton asked if I had included heavy atom tunnelling corrections in the calculation, which I had not. His group has shown these are not negligible for low-barrier reactions such as ring opening of cyclopropyl carbinyl radical.[cite]10.1021/ja1055593[/cite] As a prelude to configuring his suggested programs for computing tunnelling (GAUSSRATE and POLYRATE), it was important I learnt how to reproduce his KIE values.[cite]10.1021/ja1055593[/cite] Hence the title of this post. Now, read on.


Reproducibility in science: calculated kinetic isotope effects for the Baeyer-Villiger reaction.

Wednesday, July 1st, 2015

Recollect this earlier post on the topic of the Baeyer-Villiger reaction. In 1999 natural abundance kinetic isotope effects were reported[cite]10.1021/ja992016z[/cite] and I set out to calculate the values predicted for a particular model constructed using Quantum mechanics. This comparison of measurement and calculation is nowadays a standard verification of both experiment and theory. When the two disagree either the computational model is wrong or incomplete, or the remoter possibility that there is something not understood about the experiment.


The formation of tetrahedral intermediates.

Friday, June 12th, 2015

In the preceding post, I discussed the reaction between mCPBA (meta-chloroperbenzoic acid) and cyclohexanone, resulting in Baeyer-Villiger oxidation via a tetrahedral intermediate (TI). Dan Singleton, in whose group the original KIE (kinetic isotope measurements) were made, has kindly pointed out on this blog that his was a mixed-phase reaction, and that mechanistic comparison with homogenous solutions may not be justified. An intriguing aspect of the (solution) mechanism would be whether the TI forms quickly and/or reversibly and what the position of any equilibrium between it and the starting ketone is. This reminded me of work we did some years ago,[cite]10.1021/jo00389a050[/cite] and here I discuss that.


Natural abundance kinetic isotope effects: expt. vs theory.

Wednesday, June 3rd, 2015

My PhD thesis involved determining kinetic isotope effects (KIE) for aromatic electrophilic substitution reactions in an effort to learn more about the nature of the transition states involved.[cite]10.1039/p29750001209[/cite] I learnt relatively little, mostly because a transition state geometry is defined by 3N-6 variables (N = number of atoms) and its force constants by even more and you get only one or two measured KIE per reaction; a rather under-defined problem in terms of data! So I decided to spend a PostDoc learning how to invert the problem by computing the anticipated isotope effects using quantum mechanics and then comparing the predictions with measured KIE.[cite]10.1021/ja00486a013[/cite] Although such computation allows access to ALL possible isotope effects, the problem is still under-defined because of the lack of measured KIE to compare the predictions with. In 1995 Dan Singleton and Allen Thomas reported an elegant strategy to this very problem by proposing a remarkably simple method for obtaining KIE using natural isotopic abundances.[cite]10.1021/ja00141a030[/cite] It allows isotope effects to be measured for all the positions in one of the reactant molecules by running the reaction close to completion and then recovering unreacted reactant and measuring the changes in its isotope abundances using NMR. The method has since been widely applied[cite]10.1021/ja109686[/cite],[cite]10.1021/ja205674x[/cite] and improved.[cite]10.1038/nchembio.352[/cite] Here I explore how measured and calculated KIE can be reconciled.