NaH: Magical Oxidizing Pixie Dust Part II: The Revenge

July 23rd, 2009 by excimer

My buddy D.C., who is a consummate scientist as well as a snappy dresser, decided to do the notorious oxidation/reduction/alchemy/etc.. Here’s what he said:

Did this overnight in our box with oil free NaH and SDS THF, no reaction. 1 hr open to air this mornin’, ~80% yield by NMR.

That pretty much tells me everything I needed to know, along with Tot. Syn.’s attempt. Waiting for the errata/retraction for this paper in 3…2…1…

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37 Comments »

Comment by Will
2009-07-23 10:46:07

Score 1 for blog-reviewed research.

 
Comment by Joel
2009-07-23 11:01:32

Who needs peer review when you can have blog review?

 
Comment by MJenks
2009-07-23 11:41:56

Looks like your friend just secured himself a JACS paper.

 
Comment by Hap
2009-07-23 11:53:35

Wouldn’t this still be useful as an alternative oxidation for secondary aralkyl alcohols? It doesn’t seem useless – just poorly delineated (and reviewed/edited, perhaps).

Comment by Ψ*Ψ
2009-07-23 12:08:14

I think it’s a kinda cool reaction, and maybe more likely to be used now that people have verified that it does work and kinda figured out why. It would be awesome to see some of the more finicky reactions get this treatment, too.

Comment by European Chemist
2009-07-23 14:08:56

I would have to disagree on the “people are more likely to use this reaction now that it has been checked”. It is still using an excess of sodium hydride (a strong base) to do an oxidation that any weak oxidant (like MnO2) can accomplish… furthermore, the need to open it to air or somehow include oxygen in a kind of erratic way makes this simply a case of sloppy working.

Sorry if I sound too harsh, but aerobic oxidation of metal alkoxydes (also called “autoxidation of metal alkoxydes”) is not new and was surely not invented in 2009….

I do agree that this reaction could ONLY get this kind of treatment because it was so damn easy to try! Reagents needed are stuff that exists in every single Org Chem laboratory. Try repeating an exotic reaction using a 4-step ligand bound to an exotic transition metal precursor, using a substrate with 3 triple bonds and 2 double ones…. :-D lol

Comment by Hap
2009-07-23 14:43:27

I’ve never run it, but I thought MnO2 reactions are sort of a pain (because the MnO2 has to be activated, which can be annoying). Swern is cryogenic and stinks. Chromium oxidations generate, well, chromium salts. Dess-Martin reagent is either expensive if bought or made with (some) effort. Parikh-Doering might be OK, but is probably harder than this. These are easier oxidation conditions than any of these for aralkyl alcohols (more convenient, likely cheaper).

Also, most of the references brought don’t explore the reaction systematically – they approach the reaction mechanistically rather than as a synthetically useful reaction. This paper delineates the substrate scope well (if not the mechanistic claims of the title) – if you know where you can use a reaction, it becomes a lot more useful than a 1968 JOC with two substrates (with no synthetic emphasis). It shouldn’t have been in JACS, but if the inputs are clarified, it could be a good OL. You don’t have to invent a reaction to get your name on it – you just have to make it useful.

Comment by Cat Herder
2009-07-23 15:33:06

I would say that Parikh-Doering is about as straightforward operationally, more chemoselective, and much faster than the NaH “method”. As long as you don’t mind the smell, it is definitely the oxidation of choice. I suspect if someone could actually make this reaction catalytic somehow, it would be of use.

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Comment by Hap
2009-07-23 15:49:48

The smell probably would turn people off, though. I assume pyridine-SO3 is commercially available, but NaH is probably lying around everyone’s lab (well, people who have one). The only caveat might be (other than base sensitivity) the possibiliy/likelihood of generating peroxides and related oxidized O species – there might only be catalytic peroxides around, but with 2 equiv. NaH, there’s plenty of room to make more, and unless you quench, the peroxides might accumulate either in the reaction solvent or the NaH filtered out. Process people won’t like that at all. It should be easy enough to use for appropriate substrates to be pretty useful.

 
 
Comment by Moody Blue
2009-07-23 16:03:53

I do like the oxidative amidation. They have shown it works with NaH and MHMDS (M=Na, K) as well. There is certainly some level utility factor from the data in this paper. If you don’t like Xs NaH at the end of the reaction, I am pretty sure powdered KOH or NaOH will do the trick.

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Comment by uncle sam
2009-07-23 17:12:54

What’s wrong with chromium salts? They fall out of solution when you add non-polar solvents and a small column can take care of the rest of the trouble in ten minutes… It’s stoichiometric in chromium though.

PCC rocks. Swern oxidation all the way if PCC and PDC fail. The smell is not actually all that bad. It’s mostly hype. It’s true that the Swern oxidation is a much, much bigger pain to do than with chromium.

When I did a reaction similar to one reported in this paper, I used MnO2 I believe, but I wouldn’t quote me on that. I don’t have that lab book anymore. It worked pretty well. Most of the examples in this paper involve benzylic alcohols of a pyridine. Those alcohols tend not to be too stable for long times under air just by themselves in my experience. Especially if they already have small impurities in them. It’s the non-pyridine examples that grabbed my attention.

Anyways, to comment on the main story, the glove box experiment excluding air was a necessary control. And it proved the mechanism mentioned can’t work. It was thermodynamically unreasonable and the only hope they had was driving off the H2 by equilibrium to force the reaction forward. Another good control would have been to ‘prove’ that the NaH was catalytic by using substoichiometric amounts and getting catalytic yields and then recycling the catalyst. Still, failing the oxygen control is good enough.

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Comment by Ψ*Ψ
2009-07-23 21:23:01

Hype my ass! The Swern oxidation smell makes me nauseous. Ugh. One of the few things I don’t miss about my last lab.

 
Comment by excimer
2009-07-23 21:35:45

I don’t hate Swerns. I hate people who do them who don’t know how to work it up properly. Bleach, people! Fucktons of it!

 
 
 
 
 
 
Comment by Uncle Al
2009-07-23 11:59:54

Air-based Green chemistry is Officially kewl! Uncle Al would repeat the foreplay with some 18-crown-6 or suitably-sized cryptand added to try for hydrogen emission. A claimed chemical fuel tank for the H*Y*D*R*O*G*E*N car is R&D DoE mucho buckarinees even if it is engineering crap. Second round is (t-Bu)2CHOH, then (adamantane)2CHOH, then then 1-carbon bridge norbornanol, then… isolobal organometallics! Then argue n- and p-doped semiconductor electrodes to make the H*Y*D*R*O*G*E*N/hybrid car. Then add a fat UV blast because that makes things happen.

“We project hdrogen storage densities exceeding the most fevered politically expedient extrapolations given adequate funding.”

 
Comment by European Chemist
2009-07-23 12:01:31

Actually, I can see blog review being much more interesting than normal peer-review. People here come from all different backgrounds, and you do end up getting well over the “3 opinions from Professors who are anyway too busy to really care and do the thoughtful research that this requires”.

Comment by Ψ*Ψ
2009-07-23 12:05:43

I agree. We have a lot of commenters (and one blog author) who are extremely good at what they do and who usually have some awesome insights to impart here. I’d like to see more of this in the future (though perhaps not just for synthetic chemistry because I have nothing to offer those discussions).

 
 
Comment by milkshake
2009-07-23 12:54:31

ninja1.jpg

 
Comment by bridgedragon
2009-07-23 23:52:17

I thought they are nice reactions with solid supporting materials. At least, we need to test these reactions before we make our claims.

Well, there is really some bad junks such as using 1 micro M melamine to detect 1 nano M melamine in the following paper,

Hydrogen-Bonding Recognition-Induced Color Change of Gold Nanoparticles for Visual Detection of Melamine in Raw Milk and Infant Formula
Kelong Ai, Yanlan Liu and Lehui Lu

pp 9496–9497

Publication Date (Web): June 18, 2009 (Communication)

DOI: 10.1021/ja9037017

Completely fictionalized. No real data at all.

Comment by excimer
2009-07-24 00:38:50

solid supporting materials? Are you kidding me? They took NMRs of their products. Big fucking deal- they could have bought them, as most of the oxidation products are commercially available or easily made other ways. That’s not the issue at hand. The issue is their claim of sodium hydride as an oxidant, and they are completely wrong about that. There is an egregious lack of data to support their claims that what they think is happening is actually happening. They do no control experiments, none- do it in the glove box, it doesn’t work. As far as I am concerned, there is absolutely no data to support any of their claims in this paper. They show results experiment after experiment, with no controls and no precedent for their claims. The quality of the science in this paper was atrocious.

The paper you claim to be shitty isn’t half as bad by contrast, particularly because their claims aren’t nearly as outrageous- melamine-cyanuric acid is an archetypal supramolecular aggregate, and red solutions of AuNPs turn blue upon aggregation- everyone knows this. And they do (some) controls! (though they should have done more) How about that. Its practicality is debatable, but it is a cute application (and one backed by precedent holy fuck), and in general I think modern chemists tend to shun colorimetric indicators for fancy expensive equipment when it’s not really necessary to do so. Is that paper “JACS-worthy?” I don’t really care, but I believe their conclusions far more readily and that is what really matters.

Comment by Ψ*Ψ
2009-07-24 01:15:28

dude! CTFD or the ninjas will come after you.

Comment by excimer
2009-07-24 01:56:03

duty_calls.png

 
 
Comment by bridgedragon
2009-07-24 02:59:59

You seem to support the authors to falsify the experimental results by using the precedent holy fuck. None of the data in paper ja9037017 is true. Look at the images, spectra (UV-Vis absorption, proton NMR, and ESI-MS), all were fictionalized.

I believe the results from paper ja904224y and your checking data. These authors might draw wrong conclusion and incorrectly delineate the corresponding reaction mechanism. But they did not fictionalize their data. The complains should go to their strict experimental condition, control data and poor organic background.

The base assisted oxidation is well-known as well. As I experienced, for instance, hydrazine derivatives can be easily oxidized to diazo derivatives using sodium methoxide in the air. I hope that there is no role of oxygen played in it.

Comment by excimer
2009-07-24 09:21:12

That is an very damning statement you are making, and not only because I disagree with it. You are claiming they falsified the data in this publication, a most serious claim of scientific dishonesty. If you really believe this is the case, then you should take up your complaints with the JACS editors and not post such accusations on a blog anonymously, especially when you have no evidence to verify your claim.

 
Comment by Ψ*Ψ
2009-07-24 12:20:08

There are appropriate places to take claims like this, but this blog isn’t one. Please seek a more appropriate channel for your grievances. We don’t want to get involved with this.

 
Comment by Hap
2009-07-24 12:55:39

Other people have reproduced some of this though – while it sure doesn’t seem to be NaH doing the oxidation (not without help from O2, likely), the authors would have had to get really lucky to have happened to fake a reaction that already works, particularly on readily available substrates (because if it failed on substrates they tried and they claimed it worked, someone would ask a whole lot of questions). There doesn’t appear to be any other paper giving the scope of the oxidation of substrates like this (some precedent, but with very limited substrate scope), so there isn’t anything to copy. Without that, it isn’t clear that you could throw a bunch of aralkyl alcohols at this reaction and have it work.

It’s pretty difficult to believe someone would be stupid enough to fake something that could not only be easily verified by any interested party, but could be more easily done legitimately than faked. Without significantly evidence (no solvent peaks/misplaced solvent peaks/no satellites in NMR spectra, testimony, unavailability of relevant reagents and equipment, for example) there isn’t any reason to believe you. Thanks for playing though.

Comment by Hap
2009-07-24 13:03:41

Sorry, I r stupid – I thought you were referring to the wrong paper. Dumbass.

Still, if you’ve got evidence for your claims, I’m sure there are people who could actually do something who would listen. Dropping anonymous claims isn’t really going to change anything (well other than changing the comments policy here).

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Comment by Moody Blue
2009-07-24 13:14:58

Looks like bridgedragon has taken his grievances to the proper place. It’s a copy of the complaint s/he has sent to JACS editor that has been ccd here.

 
Comment by Moody Blue
2009-07-24 13:15:26

Looks like bridgedragon has taken his/her grievances to the proper place. It’s a copy of the complaint s/he has sent to JACS editor that has been ccd here.

 
Comment by excimer
2009-07-24 13:37:28

And said complaint will not be posted here.

 
Comment by Hap
2009-07-24 14:14:08

But then isn’t the JACS editor the appropriate place to send it first without posting it here? If you think the editor’s circular filing it, the granting agencies for the research are another good place to go (I would assume government agencies might get cranky about supporting bogus research). Maybe he’s tried those and not gotten a response, so he filed it openly so that it couldn’t be round filed, but other than that it makes no sense to cross post it here. There isn’t much that people here can do that would be helpful, and it seems to be a libel threat, so there isn’t a real reason to post it here. Maybe Chemical Forums/The Chemistry Blog would be a better place, but I don’t know if it would go well there for similar reasons. There are people who can validly assess the paper (Chip has replies on the other post that seem sensible), but even then claims of fraud are probably beyond any blog’s ability to assess – people can tell that something is funny and potential not reproducible, or that there are inconsistencies in the paper, but the real evidence is likely to be elsewhere (lab notebooks, etc., to which we have no access), if it exists at all.

I was a dumbass in the first reply, though. Sorry.

 
Comment by KNP
2009-07-24 14:52:39

Not that this is the place for an witch hunt on JACS papers, but I must say that bridgedragon had a point and indicated those inconsistencies in his post. I have seen FAR worse discussions on these blogs in discussion of LaClair’s fabrication (albeit there is really damning proof in that case). Not that I have any great point, but I am sure bridgedragon felt “called out” on his initial statement, and therefore provided his proof. The supporting information for that paper is quite weird. The pre-addition of 1 microM melamine before the “test” melamine (nanoM) addition is quite weird (third paragraph of SI). Perhaps it was a language discrepancy and it comes across wrong on paper? I am not making any judgements from this data however.

 
Comment by Hap
2009-07-24 16:53:36

I think that’s the key, though – the evidence was pretty strong to make a claim of dishonesty there – the lack of evidence for his synthesis (no SI or data for compounds – and its lack of provision years after publication), the questionable data that was there (shifted solvent peak, no satellites), the nature of some of the reactions (Mitsunobu reactions at tertiary centers (subsequently done, but hard to plan on in the middle of a synthesis), unprecedented [4+2] cycloadditions in strained systems with multiple dienes without ene reactions), the prepn. of the actual compound by Porco and its comparison with both the data given by LaClair and the that calcd. by Rychnovski all point to something rather hinky. Even then, the most damning/libelous claims (Kyle’s post, the post on tenderbutton about a rambling discussion given by La Clair on his synthesis) were either amended or removed. In this case, there might be evidence, but probably not enough to claim fraud.

With hexacyclinol, there were also a lot of bloggers and others interested in it, and so people were willing to put themselves on the line for what they believed. It’s sort of different to put someone else on the hook for libel based on what you believe to be fraud. The people running the blog have the right to decide when to put themselves on the line and expose themselves to legal action and when not to do so – it’s not reasonable to presume that they will do so based on someone’s word alone, particularly when they don’t know the person. While I can understand not being willing to reveal oneself openly for fraud investigations for fear of reprisal (whistleblower laws provide about as much coverage as a bikini on a 300 lb. man in Edmonton in February), it’s not reasonable for someone to expect others to accept consequences for one’s beliefs that one isn’t willing to accept for oneself. If people look at the paper and decide for themselves that something is wrong, then they can do as they feel right, but it’s not reasonable to assume that people are willing to accept libel/slander charges on your behalf – since they are liable for the consequences, they get to decide for themselves what to do.

 
Comment by milkshake
2009-07-24 17:21:09

In US it is extremely difficult to sue for libel. Corporate lawyers may try to send you ominously-sounding letters to harass you (or your IP provider) into submission but there is no realistic chance of you losing such a case against you, unless they can prove that you were knowingly spreading false accusations with a malicious intent. This tactics can actually back-fire because the case can get much wider publicity then it would have otherwise (“A giant company is trying to strong-arm poor blogger for posting critical stuff”) and there are freedom-of-speech advocacy groups willing to lend you a support.

Far more realistic approach for a big company lawyers shutting you up is going after your employer. Say, you work for at University or Institute that gets occassionally donations/research sponsorship from industry, or there are close personal contacts with some professors being on advisory scientific boards of the said corporation and sending their graduates to there… Or you are employed with a little company that has a weasel for HR boss or your group manager. Your employer can order you to remove the contentious post and strongly recommend you to stop posting stuff online because this could become a distraction in your job. Would you risk your job in situation when so many other chemists are unemployed?

 
Comment by Hap
2009-07-24 18:08:05

Appealing to the granting agency probably wouldn’t do much for him. I don’t know how well Chinese granting agencies would deal with problems or respond to them. On the other hand, I don’t know how much leverage they would have here.

It isn’t fair to the people running the blog, though, to drop fraud claims. One might get a blog of one’s own and post one’s suspicions, questions, and evidence there – you could refer people there if they have questions. It’s more polite to ask people if they see a problem and point to your claims and evidence than to put others at risk (even if the risk is minimal).

 
Comment by uncle sam
2009-07-25 02:59:32

“It isn’t fair to the people running the blog, though, to drop fraud claims.”

True, that’s why I only go after stuff that the blog author has posted. There is too much crap that doesn’t work in the chemical literature and a good percentage of it is probably a little fraudulent. With stuff like yield and substrate scope. There are many many times I’ve tried to repeat some procedures…. Demanding bosses and depressed students is a recipe for disaster. Just ignore it and move onto the next procedure.

It’s one of the reasons why I really want to leave chemistry as a career even though I like it well enough. Not a major reason, but it’s one nonetheless. After I travel around the world doing postdocs for a bit of course.

 
 
 
 
 
 
2009-07-31 08:56:38

[...] Missed it.  Do this in a glove box and it doesn’t work.  Open it up to air and you get 80% yield.  [...]

 
2009-08-02 23:45:14

[...] But where are all the hardcore materials folk?  Hiding out while everyone else aruges about NaH?[1]  Perhaps I can entice some delurking with a picture of some solar [...]

 
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