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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: Twitter: Dereklowe

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May 11, 2004

By Any Other Name

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Posted by Derek

I mentioned the smell of organosilane compounds the other day, which makes me think of the ambiguous place that smells have in modern organic chemistry. In theory, we're not supposed to smell anything in the lab, or even to be able to. Air-handling systems are supposed to whisk all that stuff away, and besides, we're supposed to be doing all that work inside the fume hood, anyway. Sniffing a compound to find out what it is? A thing of the past - in theory.

But the nose is just too useful. If I have two flasks full of clear liquid, there's no faster way to find out which one has ethyl acetate in it (as long as I'm sure that neither one of them has, say, acetic acid instead.) But it's true that the labs do smell much better than they did years ago. How many years depends on what sort of lab you're talking about. Industrial labs have long been safer places to work than academic ones, and they've long been less smelly, too. I've been in university labs that would knock you down even when no one was working in them, just from the stuff that had permeated the room, and which the air flow clearly couldn't keep up with.

When I was a teaching assistant in the early 1980s, I supervised a standard organic lab where the sophomores made phenyl Grignard reagent. They did it in ether, out on the flippin' bench, because there wasn't enough hood space for everyone to work in. And man, was the ether thick. It has a rollicking vapor pressure under any circumstances, of course, and as the Grignard reactions warmed up you could almost see the mirage-like shimmers in the air as waves of vapor went rolling around.

I taught three lab sections a week that semester, which was the last time I ever TA'ed. The first day was unpleasant, what with all that missing oxygen, for which ether is a poor replacement. The next section was worse, definitely worse. I'd never really minded the smell of ether, but I was finding it a little too much to take. I finished up the afternoon with a terrible headache and a powerful urge for the open air. But come the third lab of the week, I knew that I was in trouble as soon as the first gusts hit me. I had to teach that one from the hallway: "Can you hold that up for me? Higher? Yeah, OK, that looks fine." The only way I could go into the lab without gagging was to hold my breath, exhaling slightly the whole time to avoid the noxious ether fumes.

There's no way that a drug company lab would put up with those conditions, or allow them to happen unless some sort of emergency was in progress. But we still get whiffs of things all the time, weighing reagents out and transferring things around. It's unavoidable, and in such small amounts, relatively harmless. And like anyone with lab experience, I've had small transient exposures to some rather poisonous stuff (cyanide, for example, which doesn't smell as much like almonds as popular lore has it). You can get away with that, but there are some things that you don't want to smell at any level, stuff compared to which hydrogen cyanide fumes are as lilac blossoms on the spring breeze.

The fine chemicals in my "Things I Won't Work With" category over there on the right are in this category. To give another example, here's an entry from the Merck Index whose entry I've always enjoyed, from a distance - fluorine monoxide, the fluorine homolog of water. It's at least a hundred times worse than cyanide, to judge from the toxicity data. According to Merck, it's a ". . .colorless gas. Yellowish-brown when liq. Peculiar smell. Attack lungs. More poisonous than fluorine; delayed appearance of symptoms." Raised eyebrows, followed by a thoughtful silence, is the usual chemist's reaction to the news of something that's worse to inhale than fluorine. And I like that notation of "peculiar smell." Very helpful, that, and it makes you wonder who first noticed it. Probably the poor guy's last words.

Fortunately, fluorine monoxide is unstable, unstorable, unhandleable, and unobtainable. And thus unweaponizable. Anyone who tries is welcome to poison themselves in the attempt, and good riddance, too.

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


1. Klug on May 11, 2004 10:06 PM writes...

Not to turn this into "Real Stories of the TA Patrol", but even better than the stunning smell of solvents in teaching labs is the student who will thrust their reaction, flask and all, into your face and say "Does this look right?"

I might add that I would guess that sophomore students work in fully ventilated areas now, their own (!) fume hoods.

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2. Derek W on May 13, 2004 4:12 PM writes...

So is flourine monoxide different than OF2 (oxygen difluoride)? That seems to be available as a gas or liquified, but still rather hazardous.

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3. Derek Lowe on May 14, 2004 10:45 AM writes...

Those are the same thing, all right - just depends on whether you're naming it as a fluorine derivative or an oxygen one. (Both sound funny, actually.)

And I hadn't realized at all that it was an article of commerce, but checking the supplier databases, I see that it is, barely. How on earth do they ship the stuff?

Looking through the literature, I see that it's been used as an exotic fluorination agent, and it shows up a bit in the semiconductor industry (which uses a number of terrible gases). There's an alarming paper from the Univ. of Munich in 1999, where they reacted the stuff with cesium azide. No thanks. Otherwise, it's mostly theoretical studies.

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4. Steven Den Beste on May 16, 2004 2:13 PM writes...

Gah! That stuff seems as if it should embody nearly every dreadful property of any noxious chemical you can think of. I can well believe that it's preposterously toxic, but it also ought to be horribly corrosive, and I bet it's also explosive. Keryst; I bet it could combust with nitrogen gas. Yikes!

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