Fine-tuning a (hydrogen) bond into symmetry.

January 23rd, 2015

Sometimes you come across a bond in chemistry that just shouts at you. This happened to me in 1989[1] with the molecule shown below. Here is its story and, 26 years later, how I responded.

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  1. P. Camilleri, C.A. Marby, B. Odell, H.S. Rzepa, R.N. Sheppard, J.J.P. Stewart, and D.J. Williams, "X-Ray crystallographic and NMR evidence for a uniquely strong OH ? N hydrogen bond in the solid state and solution", Journal of the Chemical Society, Chemical Communications, pp. 1722, 1989.

A convincing example of the need for data repositories. FAIR Data.

January 15th, 2015

Derek Lowe in his In the Pipeline blog is famed for spotting unusual claims in the literature and subjecting them to analysis. This one is entitled Odd Structures, Subjected to Powerful Computations. He looks at this image below, and finds the structures represented there might be a mistake, based on his considerable experience of these kinds of molecules. I expect he had a gut feeling within seconds of seeing the diagram.

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The demographics of a blog readership – updated

January 8th, 2015

About two years ago, I posted on the distribution of readership of this blog. The passage of time has increased this from 144 to 176 countries. There are apparently between 189-196 such, so not quite yet complete coverage! 2015
Of course, it is the nature of the beast that whilst we can track countries, very little else is known about such readerships. Is the readership young or old, student or professor, chemist or not (although I fancy the latter is less likely). Another way of keeping tabs on some of the activity are aggregators such as Chemical Blogspace, which has been rather quiet recently. Perhaps we have become too obsessed by metrics, and with the Internet-of-things apparently the “next-big-thing”, the metrics are only likely to increase. This will only encourage “game playing“, and I urge you to see a prime example of this in the UK REF (research excellence framework), the measure which attempts to rank UK universities in terms of their “excellence”.

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Chemistry in the early 1960s: a reminiscence.

December 22nd, 2014

I started chemistry with a boxed set in 1962. In those days they contained serious amounts of chemicals, but I very soon ran out of most of them. Two discoveries turned what might have been a typical discarded christmas present into a lifelong career and hobby.

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Data discoverability

December 17th, 2014

I have written earlier about the Amsterdam Manifesto. That arose out of a conference on the theme of “beyond the PDF“, with one simple question at its heart: what can be done to liberate data from containers it was not designed to be in? The latest meeting on this topic will happen in January 2015 as FORCE2015.

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Cyclopropanation: the mechanism of the Simmons–Smith reaction.

December 14th, 2014

These posts contain the computed potential energy surfaces for a fair few “text-book” reactions. Here I chart the course of the cyclopropanation of alkenes using the Simmons-Smith reagent,[1] as prepared from di-iodomethane using zinc metal insertion into a C-I bond.

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  1. H.E. Simmons, and R.D. Smith, "A NEW SYNTHESIS OF CYCLOPROPANES FROM OLEFINS", J. Am. Chem. Soc., vol. 80, pp. 5323-5324, 1958.

Halogen bonds 4: The strongest (?) halogen bond.

December 7th, 2014

Continuing my hunt, here is a candidate for a strong(est?) halogen bond, this time between Se and I.[1].
The features of interest include:

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  1. H. Maddox, and J.D. McCullough, " The Crystal and Molecular Structure of the Iodine Complex of 1-Oxa-4-selenacyclohexane, C 4 H 8 OSe.I 2 ", Inorganic Chemistry, vol. 5, pp. 522-526, 1966.

Halogen bonds 3: “Nitrogen tri-iodide”

December 1st, 2014

Nitrogen tri-iodide, or more accurately the complex between it and ammonia ranks amongst the oldest known molecules (1812). I became familiar with it around the age of 12-13, in an era long gone when boys (and very possibly girls too) were allowed to make such substances in their parent’s back gardens and in fact in the school science laboratory, an experiment which earned me a personal request to visit the head teacher.

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Halogen bonds 2: The DABCO-Iodine structure.

November 30th, 2014

Pursuing the topic of halogen bonds, the system DABCO (a tertiary dibase) and iodine form an intriguing complex. Here I explore some unusual features of the structure HEKZOO[1] as published in 2012[2] and ask whether the bonding between the donor (N) and the acceptor (I-I) really is best described as a “non-covalent-interaction” (NCI) or not.

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  1. Peuronen, A.., Valkonen, A.., Kortelainen, M.., Rissanen, K.., and Lahtinen, M.., "CCDC 879935: Experimental Crystal Structure Determination", 2013.
  2. A. Peuronen, A. Valkonen, M. Kortelainen, K. Rissanen, and M. Lahtinen, "Halogen Bonding-Based “Catch and Release”: Reversible Solid-State Entrapment of Elemental Iodine with Monoalkylated DABCO Salts", Crystal Growth & Design, vol. 12, pp. 4157-4169, 2012.

Halogen bonds: Part 1.

November 29th, 2014

Halogen bonds are less familiar cousins to hydrogen bonds. They are defined as non-covalent interactions (NCI) between a halogen atom (X, acting as a Lewis acid, in accepting electrons) and a Lewis base D donating electrons; D….X-A vs D…H-A. They are superficially surprising, since both D and X look like electron rich species. In fact the electron distribution around X-X (A=X) is highly anisotropic, with the electron rich distribution (the “donor”)  being in a torus encircling the bond, and an electron deficient region (the “acceptor”) lying along the axis of the bond.

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