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.
Archive for May, 2015
R-X≡X-R: G. N. Lewis’ 100 year old idea.
Friday, May 22nd, 2015As 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.
References
- G.N. Lewis, "THE ATOM AND THE MOLECULE.", Journal of the American Chemical Society, vol. 38, pp. 762-785, 1916. http://dx.doi.org/10.1021/ja02261a002
Impact factors, journals and blogs: a modern distortion.
Thursday, May 21st, 2015A 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!
The Bürgi–Dunitz angle revisited: a mystery?
Tuesday, May 12th, 2015The Bürgi–Dunitz angle is one of those memes that most students of organic chemistry remember. It hypothesizes the geometry of attack of a nucleophile on a trigonal unsaturated (sp2) carbon in a molecule such as ketone, aldehyde, ester, and amide carbonyl. Its value obviously depends on the exact system, but is generally taken to be in the range 105-107°. A very good test of this approach is to search the crystal structure database (this was how it was originally established[1]).
References
- H. B:urgi, J. Dunitz, J. Lehn, and G. Wipff, "Stereochemistry of reaction paths at carbonyl centres", Tetrahedron, vol. 30, pp. 1563-1572, 1974. http://dx.doi.org/10.1016/S0040-4020(01)90678-7