musings on music and life

April 6, 2016

Classics in Organic Chemistry, Part I

Filed under: Classics in Organic Chemistry — Tags: — sankirnam @ 1:07 pm

I’ve decided to start a new series of posts where I discuss classic old papers from the organic chemistry literature. Of course, my focus will be on Physical Organic Chemistry, but anything that I deem important will be discussed.

I’ve decided to start this series with a paper by Prof. J. C. Martin from 1979. I gave a brief overview of his work earlier; I remember coming across it when I was studying for my qualifying exams and got instantly hooked. The nature of his work is fascinating and unorthodox, and led to developments in “elemento-organic” chemistry; that is, organo-iodine, organo-sulfur, organo-selenium, organo-tellurium, organo-bromine, organo-bismuth, and many other new types of chemistry. These were all developed around a growing understanding of the nature of “hypervalent” bonding. Previously, VSEPR theory invoked the use of s,p, and d orbitals in order to generate trigonal bipyramid and octahedral geometries. However, this was slowly coming under attack, and the “hypervalent” bond, which is the apical-apical bond in trigonal bipyramid and octahedral complexes, came to best be described as a “3-center 4 electron” system stabilized by electronegative ligands. Our knowledge of this type of bonding is still being refined by theoreticians today.

The significance of this manuscript is that it describes the characterization of the first 5-coordinate compound of carbon! This is distinct from the “onium” ions such as CH5+, that are best described as “5-center 8-electron systems”. In this case, you’re actually trying to cram extra electron density onto the central carbon so that it has 5 formal bonds (although one should recall that in the perfect SN2 transition state, the total number of bonds is still 4, as the bond-forming and bond-breaking events are synchronous).


The synthesis of this compound is a few steps from the starting 1,8-dichloroanthraquinone, which is commercially available. Previous studies with similar model compounds had shown they underwent a “bell-clapper” rearrangement; the result being that the central carbon underwent reversible binding with the apical atoms, and the resulting compounds had a fluxional structure with a moderate activation enthalpy (10 kcal/mol) for rearrangement. In this case, the asymmetric structures and the p-quiniodal dicationic structures are ruled out on the basis of 1H-NMR shift assignments.

However, more concrete evidence in favor of this structure is lacking. As Prof. Martin mentions in the communication, they were unable to grow X-ray crystals in order to provide conclusive proof of structure. This is consistent with my experience; growing X-ray crystals of charged substances is incredibly difficult, as these tend to be more sensitive to handle. 13C NMR evidence was also lacking, and was only published much later; the follow-up articles to this communication were only published in 1993! The 13C NMR peak of the central carbon is δ 109.3, which is in the range for an sp2 carbon, but at the same time not shifted quite as dramatically as one would expect for an extremely electron-rich carbon (remember, it now has 10 electrons instead of 8)! Theoretical studies would serve as a very useful complement to this extremely nice experimental work. For instance, it would give a useful handle on the activation energy to desymmetrization, as well as what orbitals are actually involved in bonding. J. C. Martin also published some follow-up electrochemical studies on this compound as further proof of the hypervalent nature of the central carbon atom. Further work in this area is being continued by Prof. Kin-Ya Akiba in Japan; I remember seeing some nice experimental work published by him over the years attempting to isolate different types of “hypervalent” boron and carbon compounds.

In any case, this is a really nice piece of work, and all serious students of organic chemistry should be aware of this. I think that is probably my main motivation for this series of posts – I’ll be writing about papers that all students of organic chemistry should be aware of at any level (whether it is high school, bachelors, masters, PhD, postdoc, or professional). Of course, this will be biased towards what I am aware of and what I feel is important, so bear with me!


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