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Introducing the aromatic ene reaction

23 December 2013 - Orgo

aromatic ene reaction  From the same people who brought you the hexadehydro-Diels-Alder reaction (HDDA), there is now the aromatic ene reaction (Niu & Hoye DOI). The HDDA reaction is a cyclotrimerization of a linear triyne to an aryne. This thermal reaction does not require any reagents and does not leave side-products so the aryne is produced very cleanly. In the subsequent aromatic ene reaction the ene is the methyl hydrogen and the enophile the alkyne. The potentially competing DA reaction is energetically less favourable. The isotoluene intermediate (known to chemistry but very obscure) quickly rearomatises. This step requires a trace amount of water (solvent dichlorobenzene). The isotoluene to toluene isomerization is symmetry forbidden but any proton donor can catalyse the reaction by proton shuttling. With deuterated water, deuterium is prominent on the reformed methyl group.

Table salt not as you know it

20 December 2013 - Inorgo

NaCl7.PNGBored with NaCl? Try NaCl2! or NaCl3, 4, 7?. Reduce your sodium in an unexpected way. Instructions here. NaCl7 is stable at pressures in excess of 142 GPa but the definition of stable here is a broad one: anything more stable than any competitor at the given physical space. The crystal structure is cubic with 4 sodium atoms on the corners and a central chlorine icosahedron. At elevated pressures chlorine is no longer much larger than sodium making these sort of structures possible. The material was prepared in a diamond anvil cell from NaCl with additional chlorine and laser heating and then analysed with XRD and Raman.

Surechem review

14 December 2013 - Chemical databases

Surechem panel.PNGWith thanks to In The Pipeline for the alert, a new open-source chemical database has launched called SureChEMBL / Surechem. The venture boasts a collection of 9 million chemical structures from patents, half of which are not contained in another database.

Registration is easy: as often, even the telephone number is mandatory but otherwise the sign-up process is not a hassle. Surechem offers searches by text query (anything from patent number to company to any wildcarded keyword) or by structure (chemwriter drawing tool). Sticking to the chemical structure theme, searches can include the exact match or any substructure. For example a query for the blockbuster drug aripiprazole yields 313 substructures. While waiting for the results to come flooding in you are treated to a real-time graph developing the number of results found against time which is cool and pointless at the same time. Each of the 313 structures provide access to any number of patents and each patent has a full description (testing was limited though) and presented in a human-friendly way. Compare that to many existing patent websites offering just a summary with or without ugly graphics.

Unable to find out as yet: an option to return to a structure or finding out how the subqueries work but then the venture is only beta. Only problem to work out for the SureChEMBL builders: how to get rid of this antiquated wood-panelled background? A very recent blog from the builders here contains an ambitious list of future plans but no mention of building a reaction database. Why?

See previous report on chemical databases here.

Giants in chemistry are not what you think they are

06 December 2013 - Giantism

giant with far end fading away in the distance.PNGA recent xkcd comic demonstrating various degrees of large in astronomical telescopes reminded this blog of the preoccupation of some chemists with giants. Giants appear to pop up in the strangest of places. Take for example a giant spokewheel here. Considering that this conjugated macrocycle is only 6 nanometer in diameter puts some perspective on the use of the word "giant" in chemistry. Another such giant of chemistry is the Mo72Fe30 cluster Keplerate reported here. In host-guest chemistry if the guest is already big - a fullerene - then the host must certainly by a giant according to the authors of this article. In one of the illustrations the far end of a cage structure is faded. For dramatic effect only because the edge length is just 3.9 nm. How bad can your eyesight be. Supramolecular chemistry is already concerned with molecules larger than your average molecule. So what about the giant metallo-supramolecular cage (1.7  1.7  2.6 nm) in this report, something like the world-champion lightweight boxing. In polymer chemistry molecules are by definition macro but this dendrimer is not just mega-large although in the mega-dalton range but apparently another giant (33 nm diameter).
Physical effects can also suffer from giantism but curiously only in the context of getting significantly smaller. We have giant negative thermal expansion here and a giant photobleaching suppression effect here. It appears chemists have already used up the phrase giant for things that are not really that big. What will they come up with when things get really big or effects really reduced?

Note added: The megaenzymes are coming! DOI