Management of research (data) outputs is a hot topic in the UK at the moment, although the topic has been rumbling for five years or more. Most research-active higher educational establishments have or are about to publish general guidelines, which predominantly take the form of aspirational targets rather than actionable examples or use-cases.‡ Because the concepts remain somewhat abstract, one can encounter questions from researchers such as “how should I go about achieving such RDM (research data management)?” I thought it might be useful for me to here summarise some key features in the form of an FAQ that can help answer that question. I will concentrate purely on the sub-set chemistry about which I know most.
This post is prompted by the appearance of a retrospective special issue of C&E news, with what appears to be its very own Website: internet.cenmag.org. It contains articles and interviews with many interesting people, along with several variations on the historical (albeit rather USA-centric) perspectives and a time-line covers many of the key innovations (again, from a USA-perspective). Some subjects are covered in greater depth, including computational chemistry. The periodic table too gets coverage, but surprisingly that is not of Mark Winter’s WebElements, which carries the impressive 1993-2015 continuous timeline (hence 22 in the title!).
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 Crystallogr C, 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