Author Archive
Tuesday, March 13th, 2012
I wrote in an earlier post how Pauling’s Nobel prize-winning suggestion in February 1951 of a (left-handed) α-helical structure for proteins[1] 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[2] 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[3] 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[2] result, their helix too might have turned out a left-handed one!
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References
- L. Pauling, R.B. Corey, and H.R. Branson, "The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain", Proceedings of the National Academy of Sciences, vol. 37, pp. 205-211, 1951. https://doi.org/10.1073/pnas.37.4.205
- J.M. BIJVOET, A.F. PEERDEMAN, and A.J. van BOMMEL, "Determination of the Absolute Configuration of Optically Active Compounds by Means of X-Rays", Nature, vol. 168, pp. 271-272, 1951. https://doi.org/10.1038/168271a0
- W.W. Wood, W. Fickett, and J.G. Kirkwood, "The Absolute Configuration of Optically Active Molecules", The Journal of Chemical Physics, vol. 20, pp. 561-568, 1952. https://doi.org/10.1063/1.1700491
Tags:California, chiroptical spectroscopies, computational chemistry, Imperial College, Institute of Technology, John Kirkwood, Pasadena, spectroscopy
Posted in Chiroptics, Historical | 1 Comment »
Monday, March 12th, 2012
In my previous post I speculated why bis(trifluoromethyl) ketone tends to fully form a hydrate when dissolved in water, but acetone does not. Here I turn to asking why formaldehyde is also 80% converted to methanediol in water? Could it be that again, the diol is somehow preferentially stabilised compared to the carbonyl precursor and if so, why?
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Tags:free energy, lowest energy geometry, O Lp, Oxygen Lp, solvation, Tutorial material
Posted in Interesting chemistry | 3 Comments »
Monday, February 27th, 2012
Sometimes, as a break from describing chemistry, I take to describing the (chemical/scientific) creations behind the (WordPress) blog system. It is fascinating how there do seem increasing signs of convergence between the blog post and the journal article. Perhaps prompted by transclusion of tools such as Jmol and LaTex into Wikis and blogs, I list the following interesting developments in both genres.
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Tags:API, chemical terms, chemical/science-savvy blog, chemical/scientific, citation management, Digital Object Identifier, Dublin, Java, LaTex, Skolnik, Sometimes
Posted in Chemical IT | 2 Comments »
Sunday, February 26th, 2012
One thing almost always leads to another in chemistry. In the last post, I described how an antiperiplanar migration could compete with an antiperiplanar elimination. This leads to the hydroboration-oxidation mechanism, the discovery of which resulted in Herbert C. Brown (at least in part) being awarded the Nobel prize in 1979. (more…)
Tags:Tutorial material
Posted in Uncategorised | 10 Comments »
Monday, February 20th, 2012
The anti-periplanar principle permeates organic reactivity. Here I pick up on an example of the antiperiplanar E2 elimination (below, blue) by comparing it to a competing reaction involving a [1,2] antiperiplanar migration (red). (more…)
Tags:conformational analysis, Tutorial material
Posted in Uncategorised | 1 Comment »
Monday, February 6th, 2012
The previous post explored why E2 elimination reactions occur with an antiperiplanar geometry for the transition state. Here I have tweaked the initial reactant to make the overall reaction exothermic rather than endothermic as it was before. The change is startling.
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Tags:conformational analysis, energy, Tutorial material
Posted in Uncategorised | No Comments »
Saturday, February 4th, 2012
The so-called E2 elimination mechanism is another one of those mainstays of organic chemistry. It is important because it introduces the principle that anti-periplanarity of the reacting atoms is favoured over other orientations such as the syn-periplanar form; Barton used this principle to great effect in developing the theory of conformational analysis. Here I explore its origins. (more…)
Tags:conformational analysis, Tutorial material
Posted in Interesting chemistry | 4 Comments »
Monday, January 30th, 2012
In the previous post, I went over how a reaction can be stripped down to basic components. That exercise was essentially a flat one in two dimensions, establishing only what connections between atoms are made or broken. Here we look at the three dimensional arrangements. It all boils down to identifying what the stereochemistry of the bonds marked with a wavy line are. (more…)
Tags:pericyclic, Tutorial material
Posted in Uncategorised | 1 Comment »
Wednesday, January 25th, 2012
Its a bit like a jigsaw puzzle in reverse, finding out to disassemble a chemical reaction into the pieces it is made from, and learning the rules that such reaction jigsaws follow. The following takes about 45-50 minutes to follow through with a group of students.
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Tags:chemical reaction, pericyclic, Reaction Mechanism, Tutorial material
Posted in Uncategorised | 3 Comments »