July 12th, 2012
Years 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.
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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
Tags: Cambridge, chemist, conformational analysis, free energy, Historical, Internet era, London, pericyclic, perturbation energy, re-analysis using modern algorithms, Reaction Mechanism, Skolnik
Posted in Interesting chemistry, reaction mechanism | 1 Comment »
July 9th, 2012
Sometimes, 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.
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Tags: alkyne, gas phase, gas phase model, perepoxidation, Reaction Mechanism, semantic web tools
Posted in Curly arrows, reaction mechanism | 3 Comments »
July 5th, 2012
Back 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.
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Tags: Historical, MPEG, Peter Schreiner, Skolnik
Posted in Chemical IT, Interesting chemistry | 3 Comments »
June 10th, 2012
This 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).
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Tags: Baldwins rules, free energy, hydrogen bond network, immediate product, Reaction Mechanism
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June 2nd, 2012
The Baldwin rules for ring closure follow the earlier ones by Bürgi and Dunitz in stating the preferred angles of nucleophilic (and electrophilic) attack in bond forming reactions, and are as famous for the interest in their exceptions as for their adherence. Both sets of rules fundamentally explore the geometry of the transition states involved in the reaction, as reflected in the activation free energies. Previous posts exploring the transition states for well-known reactions have revealed that the 4th dimension (the timing of the bond formations/breakings) can often spring surprises. So this post will explore a typical Baldwin ring formation in the same way.
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Tags: Baldwins rules, free energy barrier, immediate product, potential energy surface, Reaction Mechanism, Tutorial material
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May 28th, 2012
Streptomycin 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]‡
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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
Tags: Albert Schatz, candidate for its formula, Historical, laboratory of Selman Waksman, MS, muse, pence, Rutgers University, tuberculosis, X-ray
Posted in Interesting chemistry | 1 Comment »
May 25th, 2012
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.
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Tags: acetic acid, Reaction Mechanism, Tutorial material
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May 24th, 2012
HCl 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.
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Tags: acetic acid, Tutorial material
Posted in Interesting chemistry | 2 Comments »
May 19th, 2012
Many 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.
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Tags: e-books, Tutorial material
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