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Synthetic pepsin

24 July 2015 - Sensational headlines

Hie amide hydrolysis 2015.PNGThe one reaction missing on the amide Wikipedia page: amide hydrolysis. Better leave that one to nature's proteases. Their grandpa (called pepsin) was discovered as early as 1836. The amide bond is simple too strong (resonance stabilised) and will resist any nucleophile. Good to know then that in one particular synthetic chemical configuration featuring nickel, amide bond cleavage is indeed possible with many thanks to Hie et al. (DOI) of the Kendall Houk laboratory who report about it in the journal Nature.

Here is a typical batting order: substrate N-methyl-N-phenyl-benzamide, solvent toluene (110°C), catalyst bis(cyclooctadiene)nickel(0), carbene ligand SIMes (both 0.1 eq.) , methanol (1.2 eq.) and product methyl benzoate in a 88% reported yield. Not strictly a hydrolysis more like a amide to ester conversion. Naturally, success critically depends on the type of substrate. The Weinreb amide N-methoxy-N-methyl-benzamide (differs from substrate 1 by a single oxygen) yields only 22% of product. Luckily the report is able to trace the substrate's fortunes to a single parameter: the computed Gibbs free energy. With respect to reaction mechanism the reaction is a classic oxidative addition - ligand exchange - reductive elimination.

Au9 cluster snapped

13 July 2015 - Image of the month

Bosch Navarro 2015.PNGThe image on display in this week's image of the month (new item) is brought to you by Bosch-Navarro & Rourke both from the University of Warwick. (DOI) What you see is a very organised gathering of 9 gold atoms on a carbon surface. And not by coincidence.

For this TEM image to happen graphene oxide (GO) was treated with potassium thioacetate to generate GO covered with thiol groups (GOSH!) As the carbon material was also partially reduced it was expected to behave like graphene.

The gold cluster Au9(PPh3)8(NO3) was then selected. This particular molecule has one gold atom surrounded by 8 others. As GOSH was stirred with this gold compound in DMSO it attached itself by exchanging a surface sulfur atom for a phosphine ligand. GOSH@Au9 was then transferred from DMSO solution (simply by drying out) on so-called lacey carbon which is a carbon-copper supported grid designed for TEM.

The TEM images show discrete clusters with variations with respect to the surface. If the resolution was just a tiny bit higher all 9 individual atoms would be visible. The experimental configurations were backed up by TEM image simulations. In time-lapse mode the rotation of the gold wheel around it's sulfur attachment point can even be observed.

Next move in Dutch Elsevier boycott

04 July 2015 - The War on Elsevier

As reported earlier here in the beginning of the year, the Dutch universities have started a war on publisher Elsevier demanding a better deal for their journal subscription preferably open-access. This war has now entered stage two: all university personnel is kindly requested to abandon their second jobs at Elsevier (source NRC). Currently 46 such people moonlight as chief-editor at an Elsevier publication and another 835 hold regular editor positions. Key in the contract dispute are the fees that universities pay Elsevier for open-access publications even when the universities already pay a regular subscription. That does not sound fair. Elsevier in the meanwhile complains that a transition to the proposed new model will take millions of euros in investments and that national governments should fund them. Apparently it was possible to fool the UK government in supplying this money but so far the Dutch counterpart is not convinced Elsevier has a case. To be continued!