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[cite]10.1073/pnas.37.4.205[/cite] 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[cite]10.1038/168271a0[/cite] 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[cite]10.1063/1.1700491[/cite] 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[cite]10.1038/168271a0[/cite] result, their helix too might have turned out a left-handed one!
Confirming the Fischer convention as a structurally correct representation of absolute configuration.
March 13th, 2012Spotting the unexpected. The hydration of formaldehyde.
March 12th, 2012In 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?
Spotting the unexpected. The trifluoromeric effect in the hydration of the carbonyl group.
March 9th, 2012The equilibrium for the hydration of a ketone to form a gem-diol hydrate is known to be highly sensitive to substituents. Consider the two equilibria:
The blog post as a scientific article: citation management
February 27th, 2012Sometimes, 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.
The hydroboration-oxidation mechanism: An updated look.
February 26th, 2012One 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. Read the rest of this entry »
E2 elimination vs ring contraction: anti-periplanarity in action.
February 20th, 2012The 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). Read the rest of this entry »
An exothermic E2 elimination: an unusual intrinsic reaction coordinate.
February 6th, 2012The 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.
An orbital analysis of the stereochemistry of the E2 elimination reaction
February 4th, 2012The 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. Read the rest of this entry »
Secrets of a university tutor: dissection of a reaction mechanism. Part 2, the stereochemistry.
January 30th, 2012In 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. Read the rest of this entry »
Secrets of a university tutor: dissection of a reaction mechanism.
January 25th, 2012Its 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.