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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: derekb.lowe@gmail.com Twitter: Dereklowe

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In the Pipeline

« I Don't See How This Qualifies As Bliss | Main | Some Perspective »

November 23, 2004

Chemistry Geekery

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Posted by Derek

Since I mentioned the other day that I've never done an ozonolysis reactions, I thought I should come clean about some other classic reactions that I've never had the need to perform: I've never run a real aldol reaction, for one. That's partly because I did a lot of carbohydrate-based synthesis early in my career, so I already had all the aldol-like products I needed. Now, I've run a few retro-aldol reactions, but none of them deliberately, I'm sad to report. They just up and happened, and at unfortunate times.

I've never run a diazotization (Sandmeyer) reaction. I've nothing against them (well, except on large scale, maybe), but I've never quite needed one. I've never used selenium for anything. I've never made diazomethane (although I've used someone else's, parasite that I am.) Nor have I ever done a Fischer indole synthesis, a Skraup reaction, or a Nazarov cyclization. They've waited this long; they can wait some more.

I've never done an olefin metathesis reaction, which means that the trend started without me and will leave without me. I've yet to use samarium iodide for anything, although it's been close a few times. The Hell-Vollhardt-Zhelinsky reaction has passed me by, as has the Oppenauer oxidation, the Wacker oxidation, and doubtless several others.

What have I done? Most of the remaining famous ones, as far as I can tell. Sometime I'll unleash a list of the more obscure ones that I've run (Shapiro reaction, anyone?), and we'll have a name-reaction fiesta.

Comments (4) + TrackBacks (0) | Category: Life in the Drug Labs


COMMENTS

1. Tony on November 24, 2004 8:01 AM writes...

How about the [2,3] Wittig rearrangement, obscure as it is?

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2. Jimmy on November 24, 2004 8:32 PM writes...

Is there going to be an obligatory Tryptophan reaction joke anytime soon? I'd like to have one to make my family moan at the depths of geek humor. Thanks & happy Thanksgiving.

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3. Chris Hoess on November 29, 2004 10:07 PM writes...

Ah, the Skraup reaction. That was the one that helped drive me towards molecular biology, after spending a summer running it on an up-to-half-kilogram scale. For the lay audience, this involves mixing up glycerol, some aminated aromatic (the original substrate was aniline), and an oxidizing agent (if you're lucky, a nitroarene that can be converted to your starting material; we weren't lucky).



Then you dump in the sulfuric acid and reflux the *tar* out of the lot. Did I say tar? Yes, there's plenty of that floating around after the sulfuric acid chews into the glycerol; after it's done, the reaction mixture looks like Satan's own coffee cup.

And then there's the workup. The way we were doing it, at least, we had to bring the pH up to about 9 or 10, steam-distill, and salt out and extract into ether. On a 0.5 kg scale this is, to put it mildly, not a joke. Particularly given the amount of sulfuric acid in the reaction vessel. We spent a lot of time slowly spooning in NaOH pellets, waiting for the overhead stirrer to kick them around enough to dissolve, spooning in more, checking the pH, spooning in more...at least initially. Then came the day we tried to improve the quality of life during the distillation by filtering out the huge quantities of sodium sulfate sludge that inevitably formed on the bottom. Not surprisingly, it quickly clogged the filter, so we left the rest of the mixture in the flask and let things drain while we went for lunch.



We came back just in time to observe the three-necked flask lurching on its corkstand in a manner not normally associated with laboratory glassware. A quick examination revealed that the contents were boiling furiously and periodically bumping from one of the necks to splatter at the bottom of the hood. We slammed down the sash and ran for a bucket of ice, but by the time we got back the flask was erupting continuously and impossible to get near.



Cleaning up the charnel sludge from the hood after it had cooled enough to approach, we discovered...a huge wad of NaOH pellets. It seems that the sodium sulfate had sufficiently impaired the overhead stirring that most of the NaOH had slipped quietly to the bottom and begun to fuse. While we were at lunch, it had been (exothermically) dissolving in the remaining contents of the flask, and ran away just as we got back. After that, we made our own *saturated* NaOH and used that instead. Syrupy stuff, considerably more dense than water, which can absorb an absolutely ridiculous amount of NaOH, and kept in plastic bottles, of course.



(I'll stop hijacking the comments section now, but I haven't told half the fun we had with that thing.)

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4. A chemist on December 3, 2004 3:36 PM writes...

Hmm, that Skraup sounds lovely ;) Mind you, the only time I've done one the quinoline crashed out nice and easily, no tar whatsoever (but it was only on a gram scale)...

As to the other reactions, I guess it's true that in academia you get to play around and "invent" reactions, whereas (in my experience) in industry you tend to stick to tried and trusted methods the majority of the time.

Anyway, question for the panel..

I've been having fun getting interviews etc for organic chem positions (at grad and slightly higher level in the UK), and generally good feedback off them, except for one nagging point, which goes along the lines of "We like you, but we're not going to take you on as you haven't done much in the way of [insert reaction type here]" - is this 'valid'? After all, if [reaction type] is e.g. reductive alkylation, and I haven't had to make many secondary amines for my projects in the past is it my fault?

Is there some subtext that I'm not getting here, or should I start bending the truth about the chemistry I've done - I assume the interviewee would pick up if I was starting to "wing it" and that's a *bad thing*, right...?

Thanks in advance for any thoughts.

S

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