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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: Twitter: Dereklowe

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June 25, 2013

Picking Out Incorrect Natural Products

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Posted by Derek

Once in a while, you see people who've gone to the trouble of synthesizing a natural product, only to find that its structure had been incorrectly assigned. (Back in the days when structure elucidation was much harder, R. B. Woodward had this on his list of reasons to do total synthesis, although it wasn't number one).

Now there might be computational method that could flag incorrect structures earlier. This paper describes a carbon-13-NMR-based neural-network program, from a training set of 200 natural products, that seems to do a good job of flagging inconsistencies. It won't tell you that the assigned structure is right (there's probably a list of plausible fits for any given NMR), but it will speak up when something appears to be wrong.

And that's the mode I see this being used in, actually. I suspect that some groups will be motivated to go after the misassigned compounds synthetically, if they can come up with a believable alternative, in order to revise the structure. I'm not sure what happens if you put one of those South Pacific marine toxins into it, the ones that practically need a centerfold to publish their structures in a journal, but this looks like it could be a useful tool.

Comments (4) + TrackBacks (0) | Category: Analytical Chemistry | Natural Products


1. InfMP on June 25, 2013 9:00 AM writes...

Woodward's opinion structure elucidation and prediction of the future is seen here in this footnote (yes, footnote) from the Strychnine Full article (Tetrahedron, 1963, 19, 247). Break out your dictionary.

It will not be lost upon the reader-nor was it on at least some of the observers of the chemical
scene in the late nineteen forties- that the almost simultaneous outcomes of the decades-long chemical degradative assault, and the incomparably shorter X-ray crystallographic investigations, presaged a future in which so singular an edifice as the chemical structure determination of strychnine was unlikely to find parallels.
…This short history should give pause to those whose talent for despair is lavished upon an organic chemistry ornamented and supplemented, or as they fancy, burdened-by magnificent new tools
which permit the establishment in days or weeks of enlightenments which once would have required
months or years. While it is undeniable that organic chemistry will be deprived of one special and highly satisfying kind of opportunity for the exercise of elan and experimental skill when
the tradition of purely chemical structure elucidation declines, it is true too that the not infrequent dross of such investigation will also be shed; nor is there any reason to suppose that the challenge for the hand and the intellect must be less, or the fruits less tantalizing, when chemistry begins at the advanced vantage point of an established structure.
Of course, men make much use of excuses for activities which lead to discovery, and the lure of unknown structures has in the past yielded a huge dividend of unsought fact, which has been of major importance in building organic chemistry as a science. Should a surrogate now be needed, we do not hesitate to advocate the case for synthesis.

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2. MoMo on June 25, 2013 10:25 AM writes...

Your prose sounds like ol' RB Woodward himself! Good job emulating his writing style!

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3. a. nonymaus on June 25, 2013 12:33 PM writes...

Re: 2
Um, it sounds like Woodward because he's quoting a footnote written by Woodward.

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4. WaterTech on June 25, 2013 1:35 PM writes...

Might need to include a link to a "centerfold" to help the younger generations understand what that's about! Love your writings!

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