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Derek Lowe The 2002 Model

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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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May 15, 2007

Into The Trackless Wilderness

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Posted by Derek

I had an e-mail the other day from a reader who pointed out that when anyone tells you something is simple or obvious in indole chemistry, that you should run for cover. He expressed similar worries about amino acids, and I take his point. There are some areas of organic chemistry that have huge encrustations of literature all over them, which can be a warning sign.

One way you get a literature jungle is for few general methods to work. That's always been my impression of indole chemistry - each reaction has its limited area of jurisdiction, but if you start messing around you find yourself in the lawless borderlands pretty quickly. I did my PhD work using carbohydrates for natural product synthesis, and I have to say that they've got the same problem. All kinds of interesting, funky things start happening when you do something so (apparently) innocent as using a galactose scaffold instead of glucose.

Of course, there's another way to pile up a lot of different reactions, which is for most all of them to work, more or less. I think that's been the situation for many years in the palladium-catalyzed reaction field. As I've said before, I believe that just about any Pd coupling can be made to work, if you're willing to devote enough of your life to tweaking the conditions. Can you imagine a comprehensive review of some of these reactions? You'd need a special nine-volume run of Organic Reactions to even have a hope, and where would you find the maniacs to write it all?

Readers are invited to submit other examples of literature swamps - another one I can think of, from the old days, are all those steroid transformations. But I know that there are others lurking out there. . .

Comments (16) + TrackBacks (0) | Category: The Scientific Literature


1. Three _Cheers_For _Polymer_Chemistry on May 15, 2007 10:11 AM writes...

From a medical device perspective, sifting through cell adhesion literature is a nightmare. For every positive in-vitro model there seems to exist another article disputing it...

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2. Devices R Us on May 15, 2007 11:03 AM writes...

I agree with 3-cheers, except in our lab the same model only works on even number dates.

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3. Carbs on May 15, 2007 11:13 AM writes...

You think Glu to GAl is bad? Just try removing an hydroxyl and going from Galactose to Fucose. Ouch!

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4. HB on May 15, 2007 11:40 AM writes...

Answer: Massachusetts

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5. Matt on May 15, 2007 12:37 PM writes...

Just some nomenclature...
Glc is the correct abbreviation for glucose. Glu is for glutamate, and going from that to galactose would indeed be a feat.

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6. Zany on May 15, 2007 12:38 PM writes...

Gold catalysis in synthetic chemistry is getting there. Quickly. Unlike Pd catalysis, however, it unfortunately appears many of these transformations are useful for exactly......nothing except getting JACS communications published.

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7. LNT on May 15, 2007 1:08 PM writes...

Copper promoted amidations & aminations. There's an infinite number of catalyst, ligand, base, and solvent combinations to choose from. And given the right combination, you can slap an amine on practically any halide, triflate, tosylate, and even acetate. Like Pd chemistry, it is very useful -- but nearly impossible to figure out in advance what the best reaction conditions are for your particular system.

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8. SynChem on May 15, 2007 1:29 PM writes...

I laughed out loud at the "Massachusetts" comment. It's well known that certain reactions and high yield are only obtainable in Boston.

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9. weirdo on May 15, 2007 1:46 PM writes...

Do you mean Boston or Cambridge?

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10. Wavefunction on May 15, 2007 2:59 PM writes...

Add La Jolla to Cambridge. Especially the reduction of an ester to an aldehye with DIBALH, which works in these two places, does not work in State College, PA.

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11. SynChem on May 15, 2007 3:27 PM writes...

Cambridge is more accurate. Hey Wavefunction, I was thinking about La Jolla too :)

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12. Jose on May 15, 2007 3:57 PM writes...

As for the DIBAL red, I've heard from several sources that if you monitor the *internal* temp via a thermocouple very carefully, it is possible; but have not tried it me-self.

Other Fire-Swamps? I'd vote for thiadiazoles and cousins, along with any guanidines or amidines.

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13. eugene on May 15, 2007 6:41 PM writes...

Well, there is Pd coupling where you tweak the conditions to get the best yields for known substrates. But I think that the fundamental advances literature for Pd couplings and transformations, would be a lot shorter. There is still room to discover entirely new processes, or to rationally design a great system, rather than throwing stuff together.

If March could write "Advanced Organic Chemistry", someone can write: "Encyclopedia of Pd catalyzed transformations".

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14. milkshake on May 16, 2007 12:58 AM writes...

I think of synthetic photochemistry. There are very few general reaction there that you can remember or rely on, and the rest is, like peat. Running the experiments on a practical, one-gram scale in a photoreactor is also less-thanexhiliriating

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15. MTK on May 16, 2007 7:57 AM writes...

Recently, we've been working within a multidisciplinary team of chemists, biologists, MD's, on a grant headed by non-chemists. There are two chemistry groups and we were charged with scaling up to 1 gram, a synthesis the other group had conducted. (I won't go into the politics of why that occurred.) As soon as I looked at the synthesis, I knew we'd have a tough time due to a number of things, but primarily due to a tricky step which is a specialty of the other group. Well, we couldn't do it. It went back to the other group and they were able to do it, albeit on smaller scale. You can imagine the PI's opinion of us, which they have not hidden.

I should send them the URL to this discussion.

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16. aa on May 16, 2007 4:32 PM writes...

the friedel-crafts literature is a swamp.... do you have any idea how many zeolites, clays, silica gels, metal chlorides, metal triflates, solid supported sulfonic acids can activate acid chlorides, acids, esters, anhydrides, iminiums, acetals, alcohols, alkyl halides towards attack by benzene, furan, indole, pyrrole, thiophene, naphthalene, styrene and on and on?

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