Electrides (aka solvated electrons).

July 8th, 2015
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Peter Edwards has just given the 2015 Hofmann lecture here at Imperial on the topic of solvated electrons. An organic chemist knows this species as “e” and it occurs in ionic compounds known as electrides; chloride = the negative anion of a chlorine atom, hence electride = the negative anion of an electron. It struck me how very odd these molecules are and so I thought I might share here some properties I computed after the lecture for a specific electride known as GAVKIS.[1] If you really want to learn (almost) everything about these strange species, go read the wonderful review by Zurek, Edwards and Hoffmann,[2] including a lesson in the history of chemistry stretching back almost 200 years.

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References

  1. D.L. Ward, R.H. Huang, and J.L. Dye, "Structures of alkalides and electrides. I. Structure of potassium cryptand[2.2.2] electride", Acta Crystallogr C, vol. 44, pp. 1374-1376, 1988. http://dx.doi.org/10.1107/S0108270188002847
  2. E. Zurek, P.P. Edwards, and R. Hoffmann, "A Molecular Perspective on Lithium-Ammonia Solutions", Angewandte Chemie International Edition, vol. 48, pp. 8198-8232, 2009. http://dx.doi.org/10.1002/anie.200900373

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

July 1st, 2015
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Recollect this earlier post on the topic of the Baeyer-Villiger reaction. In 1999 natural abundance kinetic isotope effects were reported[1] 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.

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References

  1. D.A. Singleton, and M.J. Szymanski, " Simultaneous Determination of Intermolecular and Intramolecular 13 C and 2 H Kinetic Isotope Effects at Natural Abundance ", J. Am. Chem. Soc., vol. 121, pp. 9455-9456, 1999. http://dx.doi.org/10.1021/ja992016z

The 2015 Bradley-Mason prize for open chemistry.

June 26th, 2015
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Open principles in the sciences in general and chemistry in particular are increasingly nowadays preached from funding councils down, but it can be more of a challenge to find innovative practitioners. Part of the problem perhaps is that many of the current reward systems for scientists do not always help promote openness. Jean-Claude Bradley was a young scientist who was passionately committed to practising open chemistry, even though when he started he could not have anticipated any honours for doing so. A year ago a one day meeting at Cambridge was held to celebrate his achievements, followed up with a special issue of the Journal of Cheminformatics. Peter Murray-Rust and I both contributed and following the meeting we decided to help promote Open Chemistry via an annual award to be called the Bradley-Mason prize. This would celebrate both “JC” himself and Nick Mason, who also made outstanding contributions to the cause whilst studying at Imperial College. The prize was initially to be given to an undergraduate student at Imperial, but was also extended to postgraduate students who have promoted and showcased open chemistry in their PhD researches.

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The formation of tetrahedral intermediates.

June 12th, 2015
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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,[1] and here I discuss that.

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References

  1. A.M. Lobo, M.M. Marques, S. Prabhakar, and H.S. Rzepa, "Tetrahedral intermediates formed by nitrogen and oxygen attack of aromatic hydroxylamines on acetyl cyanide", The Journal of Organic Chemistry, vol. 52, pp. 2925-2927, 1987. http://dx.doi.org/10.1021/jo00389a050

Natural abundance kinetic isotope effects: mechanism of the Baeyer-Villiger reaction.

June 10th, 2015
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I have blogged before about the mechanism of this classical oxidation reaction. Here I further explore computed models, and whether they match the observed kinetic isotope effects (KIE) obtained using the natural-abundance method described in the previous post.

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Natural abundance kinetic isotope effects: expt. vs theory.

June 3rd, 2015
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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.[1] 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.[2] 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.[3] 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[4],[5] and improved.[6] Here I explore how measured and calculated KIE can be reconciled.

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References

  1. 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", J. Chem. Soc., Perkin Trans. 2, pp. 1209, 1975. http://dx.doi.org/10.1039/p29750001209
  2. M.J.S. Dewar, S. Olivella, and H.S. Rzepa, "Ground states of molecules. 49. MINDO/3 study of the retro-Diels-Alder reaction of cyclohexene", J. Am. Chem. Soc., vol. 100, pp. 5650-5659, 1978. http://dx.doi.org/10.1021/ja00486a013
  3. D.A. Singleton, and A.A. Thomas, "High-Precision Simultaneous Determination of Multiple Small Kinetic Isotope Effects at Natural Abundance", J. Am. Chem. Soc., vol. 117, pp. 9357-9358, 1995. http://dx.doi.org/10.1021/ja00141a030
  4. Y. Wu, R.P. Singh, and L. Deng, "Asymmetric Olefin Isomerization of Butenolides via Proton Transfer Catalysis by an Organic Molecule", J. Am. Chem. Soc., vol. 133, pp. 12458-12461, 2011. http://dx.doi.org/10.1021/ja205674x
  5. J. Chan, A.R. Lewis, M. Gilbert, M. Karwaski, and A.J. Bennet, "A direct NMR method for the measurement of competitive kinetic isotope effects", Nature Chemical Biology, vol. 6, pp. 405-407, 2010. http://dx.doi.org/10.1038/nchembio.352

Discovering chemical concepts from crystal structure statistics: The Jahn-Teller effect

May 30th, 2015
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I am on a mission to persuade my colleagues that the statistical analysis of crystal structures is a useful teaching tool.  One colleague asked for a demonstration and suggested exploring the classical Jahn-Teller effect (thanks Milo!). This is a geometrical distortion associated with certain molecular electronic configurations, of which the best example is illustrated by octahedral copper complexes which have a d9 electronic configuration. The eg level shown below is occupied by three electrons and which can therefore distort in one of two ways to eliminate the eg degeneracy by placing the odd electron into either a x2-y2 or a z2 orbital. Here I explore how this effect can be teased out of crystal structures.

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R-X≡X-R: G. N. Lewis’ 100 year old idea.

May 22nd, 2015
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As I have noted elsewhere, Gilbert N. Lewis wrote a famous paper entitled “the atom and the molecule“, the centenary of which is coming up.[1] In a short and rarely commented upon remark, he speculates about the shared electron pair structure of acetylene,  R-X≡X-R (R=H, X=C). It could, he suggests, take up three forms. H-C:::C-H and two more which I show as he drew them. The first of these would now be called a bis-carbene and the second a biradical.

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References

  1. G.N. Lewis, "THE ATOM AND THE MOLECULE.", J. Am. Chem. Soc., vol. 38, pp. 762-785, 1916. http://dx.doi.org/10.1021/ja02261a002

Impact factors, journals and blogs: a modern distortion.

May 21st, 2015
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A lunchtime conversation with a colleague had us both bemoaning the distorting influence on chemistry of bibliometrics, h-indices and journal impact factors, all very much a modern phenomenon of scientific publishing. Young academics on a promotion fast-track for example are apparently advised not to publish in a well-known journal devoted to organic chemistry because of its apparently “low” impact factor. Chris suggested that the real reason the impact factor was “low” is that this particular journal concentrates on full articles, which for a subject area such as organic chemistry can take years to assemble and hence years for others to assimilate and report their own results, and only then creating a citation for the first article. So this slow but steady evolution of citations in a long time frame apparently shows such a journal up as having less (short-term) impact than the fast-publishing notes-type variety where the impact is immediate but possibly less long-lived. That would be no reason of itself not to publish there of course!

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