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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

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February 20, 2007

Something From Nothing

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Posted by Derek

I have some down time here at the Hartford airport, which gives me a chance to talk about one of the routine, but pleasurable, things about doing organic chemistry: making stuff. By that I mean making something that most certainly wasn't there when you started.

For example, in the post the other day about the odors of various lab solvents, someone mentioned 2,2-dimethoxypropane. That's not in my top five, but it is pretty nice, and certainly distinctive. You can buy it by the liter, but it's also not hard to make (as grad students in underfunded academic labs know). You take some acetone, which as I mentioned the other day has a clear, strong solvent smell to it, and some methanol - thin and harsh. Add a couple of drops of sulfuric acid or the like, which you can forego enjoying the aroma of unless you're downright perverse), and heat it up.

After a few hours at a gentle boil, you can distill off the product. It's a clear liquid, and looks identical to the solvents you started with. The first clue is the different boiling point, and the second is the smell - strong and somewhat herbaceous. It's new, all right, and you made it with your own hands. (This sort of distillation has its own pleasures, which I'll go on about in another post sometimes - I really haven't done much of it in recent years, and that's a bit of a loss).

The effect is even more dramatic when you have liquid starting materials that produce solid crystalline products. All chemists enjoy crystals - if you don't, you either shouldn't get into synthesis, or you should strongly consider getting out. Having a forest of bright needles or beveled plates come out from what was, a few hours before, a mixture of thin, smelly liquids is something I've never tired of. It's something that would have passed for magic a few hundred years ago, and in a way, it still is.

Well, I've just been unexpectedly upgraded to first class, so this is already looking like a good trip. I'll try to blog some during the conference tomorrow, when I get a chance.

Comments (15) + TrackBacks (0) | Category: Life in the Drug Labs


COMMENTS

1. Jane Galt on February 20, 2007 1:58 PM writes...

If you're around this evening, I'm coming back early; my train gets into Union Station at 7:45 if you want to grab a drink. Email me at janegalt -at- gmail.com with a cell # if so . . .

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2. Outofthelab... on February 20, 2007 3:15 PM writes...

My favorite was the first step in the synthesis of 3-bromofuran - a commercially available chemical I was not allowed to purchase as a grad student: A D/A reaction between furan and maleic anhydride. If memory serves, you simply add maleic anhydride briquettes (yes they look just like charcoal, except white) to an excess of furan at rt. Over the course of a couple hours, the anhydride dissolves, but by the time you come in the next morning you have a white slurry of D/A adduct in furan. Filter, wash and record your all-too-infrequent 95+% yield!

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3. paiute on February 20, 2007 4:32 PM writes...

Outofthelab:

I was running an undergraduate lab one day long ago where this type of reaction was being run. There were two dozen or so students and only a couple of hoods, so the maleic anhydride bricks were ground per the procedure (not mine!) on the open benchtop. I thought nothing of it, as there were no volatiles involved. To my surprise, I had to take several of the students to the infirmary - and one to the hospital. It turns out that the maleic anhydride "dust" consists of jagged little razor-sharp spears that lodge happily in the cornea.

Luckily there were no pre-law students in the lab, and no lawsuits were filed. Because you know that the University would have had my back.

Ha ha! I kill myself. Actually, if there had been any trouble, I would have been villified and sacrificed.

Lesson: hoods are your friend. Because even students who were wearing full goggles, not just safety glasses, were nailed.

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4. lar on February 20, 2007 5:32 PM writes...

Just out of curiosity Derek, do you use your Dr. title for booking flights and does this increase your chances of an upgrade? I'm reluctant to use mine in case of a medical emergency and the flight staff come looking for a medical doctor. "Well, I could certainly help you make the stuff you require if you would just supply me with two round bottomed flasks, a heating mantle..."

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5. dearieme on February 20, 2007 5:59 PM writes...

I avoid using "Dr" in everyday life. But once I used it by accident and it worked wonders. In Hong Kong.

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6. n on February 20, 2007 7:08 PM writes...

This is exactly why I like chemistry!

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7. eugene on February 20, 2007 8:23 PM writes...

Yes, crystals are great, but there is a bad side to them as well. I have a lot of compounds that crystallize over the span of five minutes. Two days ago, as I was collecting column fractions in the rotovap, after I took my flask off, I would stare at it for a long time minutes until it all crystallized and only then would add more fractions. I must have wasted a lot of time doing that.

Then again, I probably waste a lot of time in other places anyways since grad students have that luxury:

"Reaction should be done now, better check the GC/TLC... Naahhh, let it reflux for another hour while I relax with coffee in front of the latest literature/in the pipeline post. Another hour or two of reflux can't hurt. Besides, it's not like I'm going home before 10 p.m. anyways".

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8. eugene on February 20, 2007 8:27 PM writes...

The best is when you've got a clear liquid, and you drop a little, invisible seed crystal in, and it starts crystallizing and growing bigger.

"Run, little liquid run! But you can't escape... Ha ha ha! Yes, try to escape up the walls, but you can't! Soon, your pathetic liquid life will be over. You're slowly turning SOLID, SOlid, solid, sooolllll....."

For the record, I'd like to note that I'm not, in fact, crazy.

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9. Hap on February 20, 2007 8:39 PM writes...

It's sort of offtopic, but did the snow last week remind anyone of a reaction product? The snow was pretty, lustrous crystals, and it made think of a reaction I ran in grad school, the product of which I can't remember (and I ought to, since so few of my reactions actually gave anything resembling crystals). I can see the nice crystals on the Buchner , but I can't remember what they were...

The snow was pretty though.

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10. Don on February 20, 2007 9:39 PM writes...

We hid the magnificent crystals (sitting in a petri dish) of the final product of a difficult long synthesis of another student in graduate school, as he went out to lunch to celebrate his success. (ie. his thesis !!) We replaced this with an identical petri dish with old vacuum pump oil in place of his crystals. Well, he didn't lose his lunch anyway, but it was quite a reaction !! Nothing like Organic Chemistry !!

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11. bcpmoon on February 21, 2007 2:32 AM writes...

Making something unique and new is certainly the best part in chemistry! Re crystals: I think the guys in inorganic chemistry crave crystals even more as they are into exotic complexes and nothing beats a nice structure of a zillion-bond wolfram complex. More often than not serendipity comes into play, not only did I witness the harvest of never-before-seen crystals from a freezer containing the remains of a thesis long finished, but it happened to me as well: I already had some xrays from a series of reactions when the xray-lab called me and asked if it could perhaps be possible that there was some Pd in my stuff. Voilá, a pi-allyl complex. I loved it .

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12. molecularArchitect on February 21, 2007 4:24 AM writes...

That is what makes organic chemistry different from most of the other sciences: we create something new, something that didn't previously exist. This is what I love about this profession. Biologists and most other scientists are passive observers: they perturb a natural system and then sit back and see if the system responds according to their hypotheses. Organic chemistry is a blend of science (will it work? is it stable? will it have the desired biological or physical activity/properties, etc.), engineering (how to make it?), and architecture/art (designing the molecule, the most elegant way to make it, etc.) which stimulates both the intellect and the senses (crystals, boiling liquids, odors, etc.).

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13. eugene on February 21, 2007 12:58 PM writes...

"I think the guys in inorganic chemistry crave crystals even more as they are into exotic complexes"

And a good crystal structure will bump your publication up to a better journal if the complex is novel and important. I heard that Andjewandte likes crystal structures. Is there any truth to that?

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14. eugene on February 21, 2007 1:00 PM writes...

molecularArchitect

I actually tried the: "I'm a molecular engineer" line during an evening out to make me sound more important and successful. I think it really helped and it did wonders for me. I eventually cracked and admitted that I'm a chemist though. Bad mistake...

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15. molecularArchitect on February 21, 2007 2:42 PM writes...

Eugene,

Trying to impress a girl huh?

You say you admitted that you're a chemist as though it is something to hide. I'm proud to say I'm a chemist. Most non-technical types are intimidated by chemistry so I do my best to explain it in common terms. e.g. "we design and build little tiny structures just like engineers or architects - you just can't see them"

Actually, when asked what I do, my preferred reply is "I make drugs (long pause.................) to treat cancer. You can almost see their relief that I'm not making illegal drugs.

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