Singleton and co-workers have produced some wonderful work showing how dynamic effects and not just transition states can control the outcome of reactions. Steve Bachrach’s blog contains many examples, including this recent one.
Dynamic effects in nucleophilic substitution at trigonal carbon.
July 16th, 2012More joining up of pieces. Stereocontrol in the ring opening of cyclopropenes.
July 12th, 2012Years ago, I was travelling from Cambridge to London on a train. I found myself sitting next to a chemist, and (as chemists do), he scribbled the following on a piece of paper. When I got to work the next day Vera (my student) was unleashed on the problem, and our thoughts were published[1]. That was then.
References
- M.S. Baird, J.R. Al Dulayymi, H.S. Rzepa, and V. Thoss, "An unusual example of stereoelectronic control in the ring opening of 3,3-disubstituted 1,2-dichlorocyclopropenes", Journal of the Chemical Society, Chemical Communications, pp. 1323, 1992. https://doi.org/10.1039/c39920001323
Joining up the pieces. Peroxidation of ethyne.
July 9th, 2012Sometimes, connections between different areas of chemistry just pop out (without the help of semantic web tools, this is called serendipity). So here, I will try to join up some threads which emerge from previous posts.
Connections in chemistry. Anti-malaria drug ↔ organocatalysis.
July 5th, 2012Back in 1994, we published the crystal structure of the molecule below (X=H), a putative anti-malarial drug called halofantrine. Little did we realise that a whole area of organo catalysis based on a thiourea catalyst with a similar motif would emerge a little later. Here is how the two are connected.
The direct approach is not always the best: ethene + dichlorocarbene
June 12th, 2012The reaction between a carbene and an alkene to form a cyclopropane is about as simple a reaction as one can get. But I discussed before how simple little molecules (cyclopropenyl anion) can hold surprises. So consider this reaction:
Transition state models for Baldwin dig(onal) ring closures.
June 10th, 2012This is a continuation of the previous post exploring the transition state geometries of various types of ring closure as predicted by Baldwin’s rules. I had dealt with bond formation to a trigonal (sp2) carbon; now I add a digonal (sp) example (see an interesting literature variation).
Streptomycin: a case study in the progress of science.
May 28th, 2012Streptomycin is an antibiotic active against tuberculosis, and its discovery has become something of a cause célèbre. It was first isolated on October 19, 1943 by a graduate student Albert Schatz in the laboratory of Selman Waksman at Rutgers University. I want to concentrate in this post on its molecular structure. Its initial isolation was followed by an extraordinarily concentrated period of about three years devoted to identifying that structure, culminating in a review of this chemistry in 1948 by Lemieux and Wolfram.[1] This review presents the structure as shown below (left). The modern rendering on the right is based on a crystal structure done in 1978.[2]‡
References
- R. Lemieux, and M. Wolfrom, "The Chemistry of Streptomycin", Advances in Carbohydrate Chemistry, pp. 337-384, 1948. https://doi.org/10.1016/s0096-5332(08)60034-x
- "The crystal and molecular structure of streptomycin oxime selenate tetrahydrate", Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences, vol. 359, pp. 365-388, 1978. https://doi.org/10.1098/rspa.1978.0047
The mechanism (in 4D) of the reaction between thionyl chloride and a carboxylic acid.
May 25th, 2012If 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.
Surprises (?) 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.