Field of Science

Wrong data makes me happy

Well, it's not that simple, but a couple of months ago, I did a NOESY analysis of an alkaloid. I acquired the spectrum, integrated the peaks, and got the interproton distances, which looked fine. Then I tried to do a similar analysis for the salt. That's it, nothing much different, just the salt. And now, try as I may, I could never get decent distances. Most of my distances seemed too short (<2.4 A) I reran the NOESY with different parameters, integrated the peaks tediously, and everything looked fine. But again, when I calculated the distances from the intensities, everything was messed up. Finally, the cost-benefit analysis of spending the time on the compound and getting it done from an expert was carried out, and it was quickly decided that it would be best to send it to an expert.

A couple of days ago, we got the intensities of the peaks from the expert, and guess what. The distances are still terrible, at least most of them. So that means that maybe it was not my fault. Maybe it wasn't me, it was you (you=the machine, the parameters, the molecule itself). I am not blaming the expert, because there seems to some unique feature of the molecule itself that's causing trouble. So in some ways, I am happy that it wasn't just me. But I am also sad that this means that our analysis is even further prolonged. This is a project which I want to get done with and publish. And it never seems to be getting close to that goal.

But this also is making the situation more chemically interesting. Why would a simple transformation from the alkaloid to its salt make the analysis so much more difficult? The 1D spectra look ok, so we are pretty sure no decomposition/chemical transformation has taken place. And yet the problem suddenly became thorny because of such a simple change. It seems that the vagaries of SAR reflect in SNR (Structure-NMR Relationships) too.


  1. I have never had the opportunity to determine H-H distances via NOESY, do you happen to have a lead reference on the technique?

  2. There's a reference from 1992 (J. Am. Chem. SOC.. Vol. 114, No. 9, 1992, p 3272-3277) in which there are two methods for getting distances from peak intensities in NOESY. As for the intensities themselves, there is a straightforward procedure in the Varian INOVA 600 spectrometer that we use, which I am guessing would be similar for others (eg. Bruker). I would be happy to give you the procedure if you are interested.

  3. The JACS ref answered all! Thanks!


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