Posts Tagged ‘Institute of Technology’

Confirming the Fischer convention as a structurally correct representation of absolute configuration.

Tuesday, 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!

I record all this because I was today asked to provide an abstract for an NSCCS Themed Workshop shortly to be held at Imperial College on the uses of the Gaussian computational chemistry program in synthetic chemistry. One of the themes will be chiroptical spectroscopy. Gaussian of course deploys much of the theory developed by Kirkwood in the 1950s to make exactly the same sort of predictions that Kirkwood himself used to verify the Fischer convention in 1951. Whilst the majority of modern determinations of absolute configuration are still based on Bijvoet’smethod, catching rapidly up are those based on chiroptical calculations. Perhaps in 2012 they are trusted more than they were in the 1950s? At any rate, such calculations are nowadays very much part of a modern undergraduate laboratory experience (slightly less so still in research laboratories I fear).

Here is another coincidence. Both Pauling and Kirkwood worked in the same department (Institute of Technology, Pasadena, California). One can only speculate on whether Kirkwood might have wandered into Pauling’s office in late 1951 to alert him that the protein helix should be right rather than left-handed (oh to have been a fly on Pauling’s blackboard). So alerted, would Pauling have foreseen that eventually such determinations would be routinely made using the very quantum mechanics that he had popularised?

Historical detective stories: colourful crystals.

Friday, October 21st, 2011

Organic chemists have been making (more or less pure) molecules for the best part of 180 years. Occasionally, these ancient samples are unearthed in cupboards, and then the hunt for their origin starts. I have previously described tracking down the structure of a 120 year-old sample of a naphthalene derivative. But I visited a colleague’s office today, and recollected having seen a well-made wooden display cabinet there on a previous visit. Today I took a photo of one of the samples:

One of the "Hofmann" collection.

No date, no name, but a structure! As I noted before, when it comes to structures, you have to research the conventions (and numbering) used at the time. Thus note the apparent cyclohexane rings, the N(Me)2 group and the lack of stereochemistry around the alkenes. The former dates the sample to before 1950, whilst the use of Me to mean methyl puts it in the 20th century. Which is shame, since it had been known as the “Hofmann” collection, meaning some sort association with August von Hofmann, the first professor of organic chemistry in the UK, who occupied that position from 1845-1864. Samples that old are very rare. The one above by the way is very deep green (the photo does not do it justice), and very crystalline! Tracing the history of where the display cabinet might have been did indeed reveal that it probably started its life at the same institute as Hofmann was working in (and where I now work), but little more than this was known about it.

A search of the Beilstein database (nowadays known as Reaxys) revealed a collection of samples corresponding to the above structure (with benzenes of course, not cyclohexanes), but co-crystallised with different molecules, and dating from 1921. These were known as the Heilbron collection, and this was encouraging, since Heilbron was indeed a successor to Hofmann, being active in the 1920s. During his career, he and his students probably made 100s, if not 1000s of compounds, so why did they go to the considerable expense of having beautiful wooden cases built to house these particular samples? Probably because the basic colour varied from yellow to black (perhaps 400nm difference in λmax) and for which they had no explanation! So, much like some people are cryofrozen in the hope an advanced civilisation might bring them back to life in the future, these samples were mounted in a display cabinet in the hope that someone would find out the origins of their variable colour.

Well, in 1984 (some 63 years after the event) researchers in the Technion-lsrael Institute of Technology, Haifa, came upon the 1921 article (but not the samples; if they read this they might be amazed that these still exist!), repeated (most of the) syntheses, and determined the crystal structure of three of the molecules (but conspicuously not the one above). One 3D structure is shown below. The colours were ascribed to charge-transfer interactions between the components of the molecules.

DADZIR. Click for 3D

As I noted previously, it is well worth preserving chemical samples for future generations (and sometimes that generation is 120 years in the future!). Sadly, health and safety aspects (real or imagined) mean that such collections are being lost to posterity at an every increasing rate. Soon, there may be no collections of old chemicals left. That would be indeed a loss to science. So if you know of a lovingly preserved case of old chemicals, go take a look at it. And if it’s in danger of being put in the skip, then rescue it. There is no telling what may be scientifically interesting about it.