all blogs

The biology of named reactions

25 February 2017 - a review reviewed

Lin, McCarty and Liu have authored an interesting review in Angewandte titled "The enzymology of Organic Transformations" (DOI). It is of course well known that synthetic organic reactions exist with a biological enzymatic counterpart but this review exposes the true scale, especially for the so-called named reactions. Reactions described in the review are the Claisen condensation, Michael addition ,Morita-Baylis-Hillman Reaction[, Henry reaction and the Ugi reaction (!).

In the case of Pictet-Spengler Condensation it is sad to learn that the Pictet-Spenglerases are apparently named after the frauds who stole their invention in the first place. Dieckmann cyclases and Diels-Alderases share their fate.

CCN three minus

09 February 2017 - Chemical Zoo

CCN Jach 2017.PNGIn the chemical zoo this week: CCN three minus, that is acetonitrile stripped of all its protons as reported by Jach et al. in The Angewandte (DOI). The recipe was unsurprisingly complex: a mixture of barium nitride (made from barium and nitrogen at 550K), elemental tantalum, sodium azide and graphite was reacted at at 920 K for 24 hours forming solid Ba5(TaN4)(C2N) as orange plates. The necessity of the sodium azide is not explained, the article only mentions that after the reaction all nitrogen has evaporated and that sodium metal did assemble at the top of the reaction vessel. Hydrolysis yields acetonitrile again. The lab was stocked with X-ray diffraction, solid-state NMR spectroscopy, ironically named INADEQUATE AND REDOR for full analysis. In the crystal structure layers of CCN and barium alternate with nitridometalate layers. QTAIM suggests two double bonds (C=C=N) in the structure.

Wikipedians not amused

06 February 2017 - Wikipedia in the literature

wikipediachemicalstructureexplorer.PNGThe chemistry Wikipedians have had a difficult week! Someone pointed them in the direction of a paper that, although already published in 2016 took them by surprise. Titled "Glaring Chemical Errors Persist for Years on Wikipedia" in the Journal of Chemical Education and authored by Michel Mandler (DOI) it basically states that the Wikipedia chemistry section is rubbish in chemical structure drawings. In the ensuing discussion here it is mentioned that the errors found are "pretty obscure examples" and correcting errors "often took hours". The most damning comment is that the author "looked for a shortcut to his 15 minutes of fame by belittling a community he knows nothing about". Other commentators let it know they did not have a beef with the author.
In the discussion there was another mention of an article about Wikipedia (this one from 2015 and certainly unknown to me) and this one was definitely favourable! In it Peter Ertl et al. describe a chemical substructure search engine based on the Wikipedia chembox templates (DOI). The thing is, Wikipedia is not just an encyclopaedia, it is a database of molecules as well and easily extractable. The practical result is search engine page at http://www.cheminfo.org/wikipedia/ preloaded with a 2 MB json file containing the entire Wikipedia chemical structure collection (15200 entries). Combined with a Javascript molecular editor and substructure search software also based on JS it is a complete frontend search engine. Examples: a search for brome-hexane also yields bromoadamantane and BOMT. The oxetane group also includes diketene, malonic anhydride and merrilactone A. The article describing the search engine does report the Wikipedia chemboxes contain errors but apparently to a manageable extent.