I recently followed this bloggers trail; link1 → link2 to arrive at this delightful short commentary on atom-atom bonds in crystals by Jack Dunitz. Here he discusses that age-old question (to chemists), what is a bond? Even almost 100 years after Gilbert Lewis’ famous analysis, we continue to ponder this question. Indeed, quite a debate on this topic broke out in a recent post here. My eye was caught by one example in Jack’s article: “The close stacking of planar anions, as occurs in salts of croconic acid …far from producing a lowering of the crystal energy, this stacking interaction in itself leads to an increase by several thousand kJ mol−1 arising from Coulombic repulsion between the doubly negatively charged anions” I thought I might explore this point a bit further in this post.
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 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. 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. Hence the title of this post. Now, read on.
- Rzepa, Henry S.., "KINISOT. A basic program to calculate kinetic isotope effects using normal coordinate analysis of transition state and reactants.", 2015. http://dx.doi.org/10.5281/zenodo.19272
- O.M. Gonzalez-James, X. Zhang, A. Datta, D.A. Hrovat, W.T. Borden, and D.A. Singleton, " Experimental Evidence for Heavy-Atom Tunneling in the Ring-Opening of Cyclopropylcarbinyl Radical from Intramolecular 12 C/ 13 C Kinetic Isotope Effects ", J. Am. Chem. Soc., vol. 132, pp. 12548-12549, 2010. http://dx.doi.org/10.1021/ja1055593
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. If you really want to learn (almost) everything about these strange species, go read the wonderful review by Zurek, Edwards and Hoffmann, including a lesson in the history of chemistry stretching back almost 200 years.
- 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 Crystallographica Section C Crystal Structure Communications, vol. 44, pp. 1374-1376, 1988. http://dx.doi.org/10.1107/S0108270188002847
- 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
Recollect this earlier post on the topic of the Baeyer-Villiger reaction. In 1999 natural abundance kinetic isotope effects were reported 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.
- 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
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.
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. 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. 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. 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, and improved. Here I explore how measured and calculated KIE can be reconciled.
- 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
- 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
- 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
- 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
- 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