Field of Science

Samoquasine is perlolidine after all

Here is another nice example of the application of C13 chemical shifts calculated using quantum chemistry to solve a dispute concerning the structure of a natural product. This one is from Peter Wipf's group at Pittsburgh who use C13 shifts calculated at the B3LYP/6-31+G(2d,p) level to ascertain that an alkaloid named samoquasine is identical to another one named perlolidine.

Samoquasine was isolated in 2000. At the time the original authors thought that they had isolated a new alkaloid and gave it a new name. Then in 2002 they proclaimed that the "new" substance was actually the same as an earlier identified substance called perlolidine. Then along came some other chemists in 2003 who again said that in fact samoquasine is different from perlolidine. Time to put an end to the squabble!

To resolve the dispute, Wipf's group constructed 48 isomers that could correspond to all combinations of samoquasine/perlolidine. They calculated chemical shifts for all 48 isomers and found out that only the chemical shifts of one particular isomer (perlolidine!) showed the least deviation with measured C13 chemical shift for samoquasine/perlolidine. This indicated that the original authors' assertion, that samoquasine was identical to perlolidine was in fact correct. Not only were the latter authors wrong, but Wipf also castigates their melting point and their lack of measurement of UV spectra that could have helped settle the dispute back then. In short, the previous study was not exactly a nice piece of experimental work. Ouch.

Carl Djerassi once said that the great value of computers in structure determination is to generate several straw men and then identify which ones are in fact straw men. This study serves to drive that point home and again shows the value of computational prediction of NMR chemical shifts in organic chemistry. However, I also wonder how much the results would have changed had the authors used the MPW1PW91 functional which has been found to be optimum for such calculations. Also recall that this technique was demonstrated in a famous incident a few years ago.

Cody Timmons, Peter Wipf (2008). Density Functional Theory Calculation of
C13 NMR Shifts of Diazaphenanthrene Alkaloids: Reinvestigation of the Structure of Samoquasine A
The Journal of Organic Chemistry, 73 (22), 9168-9170 DOI: 10.1021/jo801735e


  1. I blogged on this too:


  2. Hi Steven...thanks for the link. Your blog and book are excellent!


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