If you have not previously visited, take a look at Nick Greeves’ ChemTube3D , an ever-expanding gallery of reactions and their mechanisms. The 3D is because all molecules are offered with X, Y and z coordinates. You also get arrow pushing‡ in 3D. Here, I argue that we should adopt Einstein, and go to the space-time continuum! By this, I mean one must also include the order in which things happen. To my knowledge, no compendium of (organic) reaction mechanisms incorporates this 4th dimension. My prelude to this post nicely illustrated this latter aspect. Here I continue with an exploration of the mechanism of forming an acyl chloride from a carboxylic acid using thionyl chloride. The mechanism shown at ChemTube3D is as below and will now be tested for its reasonableness using quantum mechanics.
The mechanism (in 4D) of the reaction between thionyl chloride and a carboxylic acid.
May 25th, 2012Surprises (?) in the addition of HCl to a carbonyl group.
May 24th, 2012HCl reacting with a carbonyl compound (say formaldehyde) sounds pretty simple. But often the simpler a thing looks, the more subtle it is under the skin. And this little reaction is actually my prelude to the next post.
Mechanism of the diazomethane alkylation of a carboxylic acid.
May 19th, 2012Many reaction mechanisms involve a combination of bond formation/cleavage between two non-hydrogen atoms and those involving reorganisation of proximate hydrogens. The Baeyer-Villiger discussed previously illustrated a complex dance between the two types. Here I take a look at another such mechanism, the methylation of a carboxylic acid by diazomethane.
Reductive ozonolysis: the interesting step.
May 7th, 2012The mechanism of the reaction of alkenes known as ozonolysis was first set out in its modern form by Criegee. The crucial steps, (a), (b) and (d), are all pericyclic cycloaddition/eliminations. The last step (e) is known as reductive ozonolysis, and this step is often treated as an afterthought, part of the work-up of the reaction if you like (it is not illustrated in Criegee’s review for example). Here, I will attempt to show that it is actually a very interesting mechanistic step.
The mechanism of the Baeyer-Villiger rearrangement.
May 7th, 2012The Baeyer-Villiger rearrangement was named after its discoverers, who in 1899 described the transformation of menthone into the corresponding lactone using Caro’s acid (peroxysulfuric acid). The mechanism is described in all text books of organic chemistry as involving an alkyl migration. Here I take a look at the scheme described by Alvarez-Idaboy, Reyes and Mora-Diez[cite]10.1039/b712608e[/cite], and which may well not yet have made it to all the text books!
The Dieneone-phenol controversies.
April 30th, 2012During the 1960s, a holy grail of synthetic chemists was to devise an efficient route to steroids. R. B. Woodward was one the chemists who undertook this challenge, starting from compounds known as dienones (e.g. 1) and their mysterious conversion to phenols (e.g. 2 or 3) under acidic conditions. This was also the golden era of mechanistic exploration, which coupled with an abundance of radioactive isotopes from the war effort had ignited the great dienone-phenol debates of that time (now largely forgotten). In a classic recording from the late 1970s, Woodward muses how chemistry had changed since he started in the early 1940s. In particular he notes how crystallography had revolutionised the reliability and speed of molecular structure determination. Here I speculate what he might have made of modern computational chemistry, and in particular whether it might cast new light on those mechanistic controversies of the past.
Stereoselectivities of Proline-Catalyzed Asymmetric Intermolecular Aldol Reactions.
April 22nd, 2012Astronomers who discover an asteroid get to name it, mathematicians have theorems named after them. Synthetic chemists get to name molecules (Hector’s base and Meldrum’s acid spring to mind) and reactions between them. What do computational chemists get to name? Transition states! One of the most famous of recent years is the Houk-List.
A golden age for (computational) spectroscopy.
April 2nd, 2012I mentioned in my last post an unjustly neglected paper from that golden age of 1951-1953 by Kirkwood and co. They had shown that Fischer’s famous guess for the absolute configurations of organic chiral molecules was correct. The two molecules used to infer this are shown below.