Corante

About this Author
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: derekb.lowe@gmail.com Twitter: Dereklowe

Chemistry and Drug Data: Drugbank
Emolecules
ChemSpider
Chempedia Lab
Synthetic Pages
Organic Chemistry Portal
PubChem
Not Voodoo
DailyMed
Druglib
Clinicaltrials.gov

Chemistry and Pharma Blogs:
Org Prep Daily
The Haystack
Kilomentor
A New Merck, Reviewed
Liberal Arts Chemistry
Electron Pusher
All Things Metathesis
C&E News Blogs
Chemiotics II
Chemical Space
Noel O'Blog
In Vivo Blog
Terra Sigilatta
BBSRC/Douglas Kell
ChemBark
Realizations in Biostatistics
Chemjobber
Pharmalot
ChemSpider Blog
Pharmagossip
Med-Chemist
Organic Chem - Education & Industry
Pharma Strategy Blog
No Name No Slogan
Practical Fragments
SimBioSys
The Curious Wavefunction
Natural Product Man
Fragment Literature
Chemistry World Blog
Synthetic Nature
Chemistry Blog
Synthesizing Ideas
Business|Bytes|Genes|Molecules
Eye on FDA
Chemical Forums
Depth-First
Symyx Blog
Sceptical Chymist
Lamentations on Chemistry
Computational Organic Chemistry
Mining Drugs
Henry Rzepa


Science Blogs and News:
Bad Science
The Loom
Uncertain Principles
Fierce Biotech
Blogs for Industry
Omics! Omics!
Young Female Scientist
Notional Slurry
Nobel Intent
SciTech Daily
Science Blog
FuturePundit
Aetiology
Gene Expression (I)
Gene Expression (II)
Sciencebase
Pharyngula
Adventures in Ethics and Science
Transterrestrial Musings
Slashdot Science
Cosmic Variance
Biology News Net


Medical Blogs
DB's Medical Rants
Science-Based Medicine
GruntDoc
Respectful Insolence
Diabetes Mine


Economics and Business
Marginal Revolution
The Volokh Conspiracy
Knowledge Problem


Politics / Current Events
Virginia Postrel
Instapundit
Belmont Club
Mickey Kaus


Belles Lettres
Uncouth Reflections
Arts and Letters Daily
In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline

In the Pipeline

« J. Whoozat Sci. | Main | Want To Make an Amide? Have I Got Good News For You! »

September 20, 2010

Sodium Hydride As Oxidant, Again?

Email This Entry

Posted by Derek

Many readers will remember the "sodium hydride as an oxidizing reagent" story from last year. (For the non-chemists in the audience, the problem here is that sodium hydride is most certainly not what you'd think of as an oxidizing reagent, quite the opposite, in fact. Seeing the paper's title was, for an organic chemist, a bit like reading about a new way to sweeten drinks with vinegar).

This was famously live-blogged over at Totally Synthetic and picked up on around the chemical blog world. The current thinking, though, is that adventitious oxygen is really doing the work here. If you run the reaction under strict inert atmosphere conditions, you get no more oxidation. (And it still doesn't appear that any note has been added to the original JACS paper). Update - make that no note added to the abstract page. The paper itself is still accessible, although it does have notes that it was withdrawn.

Well, now we have another one. This paper in press in Tetrahedron Letters claims oxidation of benzoins to benzils with good ol' sodium hydride. In this case, anyway, the authors (from Korea) did try running the reaction under inert atmosphere, and saw their yield go down. Their proposed mechanism involves molecular oxygen, in fact, and is quite plausible. (I've seen anion-oxygen chemistry myself - if you deprotonate Strecker amines of benzaldehydes, you'll convert them into amides via oxygen in your solvent, that is, if you don't saturate things with inert gas first). Still, I'd rather that they titled this paper differently, since it's not sodium hydride that's doing the oxidation here. You could probably get this to happen with NaHMDS, t-butoxide, or the base of your choice.

And, weirdly, the authors (as far as I can see by going over the PDF) manage not to cite the original JACS NaH oxidation paper at all. You'd never think that anyone had tried this before, especially not in one of the most high-profile chemical journals in the world, just last year, with plenty of added press coverage. What does it take a get a paper cited? Update: given the withdrawn-but-still-available status of the original, this becomes a trickier question. The earlier paper seems to have clearly gone through the same sort of chemistry, but the mechanism - and thus the point of the whole paper - was misassigned. Do you cite it, or not?

Comments (14) + TrackBacks (0) | Category: Chemical News | The Scientific Literature


COMMENTS

1. chemist4hire on September 20, 2010 12:31 PM writes...

Well the original JACS paper was retracted.

http://pubs.acs.org/doi/full/10.1021/ja910615z

If you were the author of the paper, would you cite a retracted paper? I have never been in that situation, so do not know what the proper protocol is for such a situation. I thought you treated retracted papers as if they never existed in the literature to begin with.

Permalink to Comment

2. student on September 20, 2010 12:38 PM writes...

It's in tet lett. so it probably never even got peer reviewed.

Permalink to Comment

3. strayxray on September 20, 2010 1:18 PM writes...

Would the editors of Tetrahedron Letters allow a paper to cite a retracted paper?

Permalink to Comment

4. watcher on September 20, 2010 2:15 PM writes...

There is no reason to cite a withdrawn paper. The removal is an acknoledgement that the work was not suitable to be published, so that also means it should not be cited, as the reason for citation assumes an element of previous authority.

Permalink to Comment

5. Henning Makholm on September 20, 2010 3:00 PM writes...

This all depends on what the purpose of citations is supposed to be. To tell the reader where he can read more about such-and-such topic? To document where the authors got their ideas? To back an assertion that the current paper does not have the room to make an independent case for? To prove that the authors are familiar with the relevant literature? To allocate academic brownie points to the authors of the cited paper?

Some of these goals are invalidated by the prior paper being retracted. Some remain as relevant as they ever were.

Permalink to Comment

6. Dr. Smalls on September 20, 2010 3:29 PM writes...

I like using O2 and NaOH to convert fluorene to fluorenone. This is an easy demonstration of O2 oxidation.

Permalink to Comment

7. eugene on September 20, 2010 6:41 PM writes...

Well, if I let a lot of my pyridine derivatives sit around on the shelf and some oxygen gets in under the cap, eventually they'll become oxidized with no base needed at all! Well... I suppose pyridine.

I vote for not citing the original. After all, it's been retracted.

Permalink to Comment

8. syregnask on September 21, 2010 1:50 AM writes...

Not only is the title of that Tetrahedron Lett. paper misleading, but the graphical abstract does nothing to make up for it.

As for citing last year's story, maybe it could be done by citing the RSC piece about it (well, if that had itself been published in a different form that might have been easier).

Permalink to Comment

9. p on September 21, 2010 5:53 AM writes...

Just to add my 2 cents to everyone else's, base and O2 isn't exactly a new-fangled oxidation protocol. I've used it dozens of times, with various bases. As Dr. Smalls says, you could just as easily use NaOH or TEA.

Also, providing an "inert" atmosphere can be tricky. We do chemistry that is sensitive to O2 and simply blowing some argon or N2 in doesn't cut it. It takes work to get rid of O2. So, if they tried to omit O2 and see the yield go down, I'd feel safe saying they simply cut the concentration of O2.

Permalink to Comment

10. ddddddd on September 21, 2010 7:46 AM writes...

You should cite it for sure. Even if it was retracted, just highlight it's dubious nature in the text and cite it anyway. It's helpful to a potential reader and the two are way too similar to not merit a citation imo.

Permalink to Comment

11. Ed on September 21, 2010 8:07 AM writes...

I suspect your inorganic chemistry readership are giggling at their "degassing" procedures

Permalink to Comment

12. Zoltan on September 21, 2010 11:23 AM writes...

@11

Giggling indeed!

I haven't found the "degassing procedures" in the paper, are there any? What's the source of the NaH (in mineral oil) and THF (peroxides in an old flask?). Schlenk line or glove-box?

Mentioning "oxygen-free THF" just doesn't cut it.

Permalink to Comment

13. European Chemist on September 21, 2010 12:12 PM writes...

I was just wondering that letting that NaH oxidation paper into JACS actually got the journal and the authors a lot of media coverage. Even if for the bad reasons. After all this time still can't quite figure out how that stuff got past 3 referees.

Permalink to Comment

14. startup on October 15, 2010 9:58 AM writes...

re: vinegar. You are aware that lead acetate is quite sweet, right?

Permalink to Comment

POST A COMMENT




Remember Me?



EMAIL THIS ENTRY TO A FRIEND

Email this entry to:

Your email address:

Message (optional):




RELATED ENTRIES
Scripps Update
What If Drug Patents Were Written Like Software Patents?
Stem Cells: The Center of "Right to Try"
Speaking of Polyphenols. . .
Dark Biology And Small Molecules
How Polyphenols Work, Perhaps?
More On Automated Medicinal Chemistry
Scripps Merging With USC?