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Pyramidal carbon

15 January 2017 - Molecule of the year 2016

pyramidalcarbonMalischewski2016.PNGThanks to the New Scientist article here for reminding us but the discovery of a pyramidal carbon dication by Malischewski and Seppelt (DOI) must be the chemistry event of the last year (work published 26 November, yeah this blog missed it completely). It is common knowledge that carbon will partner in chemical bonds with up to 4 partners but definitely not more. In fact, if a molecule is depicted in any way with 5 bonds going away from it (clearly an error made) the author is met with ridicule and a specific reserved phrase : Texas carbon, a reference to the Texas five-pointed lone star. As it turns out this ridicule is misplaced! It is possible to create Texas carbon molecules after all. Malischewski and Seppelt made theirs starting from the Dewar benzene of hexamethylbenzene (by a cyclotrimerisation of 2-butyne with aluminum chloride). This compound was epoxidized and then reacted with magic acid. This very strong acid basically strips away O2- leaving behind C6(CH3)62+(SbF6-)2. Read the supplementary info to learn the very thin line between reaction success and reaction black tar. The crystal end-product (produced by adding HF and cooling) is stable at -78°C ready for X-ray diffraction. And how to describe the molecule? It is the adduct of the pentamethylcyclopentadienylium cation and the 1-ethylium-1-ylidene cation CH3C+ cation with 6 bonding electrons shared between them. There is of course the issue of precedence, the dication was already observed by NMR in 1973 (DOI) but an actual crystal structure is always a next step.

Spot the hydrogen atoms

14 January 2017 - Image of the week

paracetamolbyPEDT.PNGDoes the phrase "hydrogen atoms omitted for clarification" sound familiar to you? It is the default text accompanying every crystal structure depiction. The reason? it may be that the presence of the hydrogen atoms is obvious so that there is no need to show them. The actual truth: the accuracy of the position of the hydrogen atoms in a crystal structure is very inaccurate and any depiction of them will hopelessly clutter the picture. Problem is, hydrogen has just one electron, reducing scattering power. But thank science we now have precession electron diffraction tomography (PEDT), a brand new technique pioneered by Czech/French team headed by L. Palatimus as first author who practised it on straightforward paracetamol (DOI). To paint the picture old-fashioned X-ray crystallography has been superseded by electron crystallography which has been superseded by precession electron diffraction and then by its tomography child. Technology moves fast. The instrument is especially suited for working with micro crystals. Challenge: any crystal submitted to PEDT suffers from the radiation and will deteriorate. Solution: build up a picture by moving the electron beam over the crystal and build up the image. Results: the measured C-H distances in paracetamol are 1.15 angstroms (textbook value 1.09 angstroms) and the measured angles deviate by 10 degrees.