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.
Text-books (or e-books) invariably show path (a). But the Baeyer-Villiger showed us that involvement of an additional acid as a proton transfer agent via a cyclic (7 or 11-membered) transition state was possible. So how about path (b, R=H), calculated using wB97XD/6-311G(d,p)/SCRF=dichloromethane?
The IRC (intrinsic reaction coordinate) shows us the more detailed steps in the mechanistic dance. This tells us that the transition state shown above corresponds to the final stage of the reaction, path (c) in fact. The requisite reorganisation of the protons has already happened, and the reaction is happening from the zwitterionic intermediate shown in (c), with a barrier of only ~ 4 kcal/mol from that species.
The transition state for the formation of the zwitterionic intermediate is itself shown below. One proton is clearly moving (to the carbon), but is the other? Again, an IRC is needed to tell us.
It seems that the two acid molecules do not co-operate with each other. The mechanism really does simply involve a protonation of the diazomethane by a molecule of acid to form a zwitterionic intermediate, following by attack by the anion of the acid on the diazonium cation to displace the nitrogen, path (a).
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May 18th, 2012
Text books (is this a misnomer, much like “papers” are in journals?) in a higher-educational chemistry environment, I feel, are at a cross-roads. What happens next?
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Tags: author, Bob Hanson, energy, GBP, iPads, PDF, skilful author, Steve Job, tablet devices, textbook author, USD
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May 7th, 2012
The 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.
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Tags: 200th post, pericyclic, S bridge
Posted in Historical, Interesting chemistry | 3 Comments »
April 30th, 2012
During 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.
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Tags: computational chemist, computational chemistry, pericyclic, sigmatropic shifts, tracer labelling
Posted in Chemical IT, Historical, Interesting chemistry | No Comments »
April 22nd, 2012
Astronomers 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.
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Tags: condensation, energy, gas-phase optimised geometry, Houk-List, smallest steric exchange energy, so-called single-point solvation energy correction, steric exchange energy
Posted in Historical, Interesting chemistry | 3 Comments »
April 6th, 2012
Chemists love a mystery as much as anyone. And gaps in patterns can be mysterious. Mendeleev’s period table had famous gaps which led to new discovery. And so from the 1890s onwards, chemists searched for the perbromate anion, BrO4-. It represented a gap between perchlorate and periodate, both of which had long been known. As the failure to turn up perbromate persisted, the riddle deepened. Finally, in 1968, the key was found, but talk about sledgehammer to crack a nut! It was done by alchemical-like radioactive transmutation of selenium into bromine:
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Tags: alkaline sodium hypobromite solution, chemical synthesis, metal catalysis, present chemical knowledge, speculative chemist
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March 13th, 2012
I wrote in an earlier post how Pauling’s Nobel prize-winning suggestion in February 1951 of an (left-handed) α-helical structure for proteins was based on the wrong absolute configuration of the amino acids (hence his helix should really have been the right-handed enantiomer). This was most famously established a few months later by Bijvoet’s definitive crystallographic determination of the absolute configuration of rubidium tartrate, published on August 18th, 1951 (there is no received date, but a preliminary communication of this result was made in April 1950). Well, a colleague (thanks Chris!) just wandered into my office and he drew my attention to an article by John Kirkwood (DOI: 10.1063/1.1700491) published in April 1952, but received July 20, 1951, carrying the assertion “The Fischer convention is confirmed as a structurally correct representation of absolute configuration“, and based on the two compounds 2,3-epoxybutane and 1,2-dichloropropane. Neither Bijvoet nor Kirkwood seem aware of the other’s work, which was based on crystallography for the first, and quantum computation for the second. Over the years, the first result has become the more famous, perhaps because Bijvoet’s result was mentioned early on by Watson and Crick in their own very famous 1953 publication of the helical structure of DNA. They do not mention Kirkwood’s result. Had they not been familiar with Bijvoet’s result, their helix too might have turned out a left-handed one!
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Tags: California, chiroptical spectroscopies, computational chemistry, Imperial College, Institute of Technology, John Kirkwood, Pasadena, spectroscopy
Posted in Interesting chemistry | 1 Comment »
