Corante

About this Author
Derek Lowe
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

Chemistry and Pharma Blogs:
The Science Business
Org Prep Daily
Kilomentor
On Pharma
Kinase Pro
Chemical Quantum Images
The LouRoe
One in Ten Thousand
Periodic Tabloid
Chemical Musings
C&E News Blog
Chemiotics II
Noel O'Blog
In Vivo Blog
Chirality
BBSRC/Douglas Kell
Drug Discovery Opinion
The Chemblog
Realizations in Biostatistics
Heterocyclic Chemistry Blog
Molecule of the Day
Chemjobber
WSJ Health Blog
PK/PD
Social Detritus
ChemSpider Blog
Node in the Noosphere
Pharmagossip
Organometallic Current
Useful Chemistry
Great Molecular Crapshoot
No Name No Slogan
Post Doc Ergo Propter Doc
SimBioSys
Culture of Chemistry
The Curious Wavefunction
Chemical Sabbatical
Totally Synthetic
Molecular Philosophy
Zusammen
Pharma's Cutting Edge
My Chemical Journey
The F- Blog
Chemical Professionals
Generally Chemistry
Chemistry World Blog
Eigenfunction/Eigenvalue
Synthesizing Ideas
Carbon-Based Curiosities
Business|Bytes|Genes|Molecules
Eye on FDA
Sigma-Aldrich ChemBlogs
Peter Murray-Rust
Chemical Forums
Depth-First
Curly Arrow
ChemCafe
Power of Goo
Fetz the Chemist
Carbon Tet
Chemical Crosspatch
Sceptical Chymist
Atomchuxky
Lamentations on Chemistry
Computational Organic Chemistry
Mining Drugs
Henry Rzepa
Making Graphite Work
Realm of Organic Synthesis
Liquid Carbon
Pharma Blog Review


Science Blogs and News:
The Loom
Uncertain Principles
Fierce Biotech
Blogs for Industry
Omics! Omics!
Young Female Scientist
Notional Slurry
Life of a Lab Rat
Nobel Intent
SciTech Daily
Is This Thing On?
Science Blog
Eastern Blot
FuturePundit
Flags and Lollipops
Aetiology
Gene Expression (I)
Gene Expression (II)
Sciencebase
Pharyngula
Adventures in Ethics and Science
Terra Sigillata
Transterrestrial Musings
Slashdot Science
A Scientist's Life
Living the Scientific Life
Humans in Science
Speculist
Science, Shrimp and Grits
Cosmic Variance
The Capsule
Zeroth Order Approximation
Science Library Blog
Biology News Net


Medical Blogs
Med Tech Sentinel
DB's Medical Rants
Science-Based Medicine
GruntDoc
The Health Care Blog
Respectful Insolence
Black Triangle
Diabetes Mine


Economics and Business
Marginal Revolution
Arnold Kling
The Volokh Conspiracy
Knowledge Problem
The Stalwart


Politics / Current Events
Virginia Postrel
Tinkerty Tonk
Instapundit
Megan McArdle
Mickey Kaus
Colby Cosh
Alien Corn
No Watermelons


Belles Lettres
Two Blowhards
Critical Mass
Arts and Letters Daily
God of the Machine
Armavirumque
About Last Night

In the Pipeline

Category Archives

October 23, 2009

Things I Won't Work With: Straight Dimethyl Zinc

Email This Entry

Posted by Derek

Organometallic reagentss come from large tribes, and there are always wild cousins up in the hills. A good place to look for the livelier ones is in the simplest alkyl derivatives, and you should go all the way down to the methyls if you want to know their real character. Ignore the halides. Methylmagnesium bromide you can get in multiliter kegs; they might as well sell it in Pottery Barn.

Dimethylmagnesium, though, is not an article of commerce. I've made it myself. So although it's definitely something you want to keep an eye on, I can't very well say that I won't work with it. And the other metals? Dimethyl mercury I will not get within yards of, for very well-founded reasons. Trimethylaluminum is a flamethrower extraordinaire, with a solid reputation among pyromaniacs. I've used the stuff, although I wasn't whistling while I was syringing it out. Handling it in solution, as I did, is less stressful than using the pure stuff - I'd definitely want to sit down and think about that one.

But neat dimethyl zinc. . .no, I don't think so. A colleague of mine made some in graduate school, and came down the hall to us looking rather pale. He'd disconnected a length of rubber tubing from his distillation apparatus and seen it go up in immediate, vigorous flames. "This stuff makes t-butyllithium look like dishwater" is the statement I remember from that evening. You can buy the pure stuff from Alfa, if you're inclined to run a head-to-head comparison. Do make sure to post the video on YouTube; that's as close as I want to get.

One problem is that it's a pretty volatile compound, boiling at 46C, so there's plenty of vapor around to start a party. The diethyl analog is a bit better, but it's nearly as pyrophoric. The Library of Congress discovered this in the 1980s and 1990s, during a long-running project to deacidify old documents. The diethyl zinc reacts with the acid in aged wood-pulp papers, neutralizing it, lightening the color, and stiffening the paper, so you'd think it would be ideal. Well, except for the instant-bursting-into-ravenous-flames part. Making sure that all the reagent was gone before opening the hatch, that was rather important. The pilot plant for this process suffered from some regrettable explosive bonfires before the whole idea was abandoned. Interestingly, one of the biggest problems seems to have been that the treated books were (at least at first) rather odorous, and some colored book covers were initially affected. You can sense a certain testiness about these issues in the Library's final report on the subject:

It has also been established that tight or loose packing of books; the amount of alkaline reserve; reactions of DEZ with degradation products, unknown paper chemicals and adhesives; phases of the moon and the positions of various planets and constellations do not have any influence on the observed adverse effects of DEZ treatment.

You'll notice that the LOC didn't even bother with the dimethyl compound, and I think I'll take a tip from them.

Comments (26) + TrackBacks (0) | Category: Things I Won't Work With

June 11, 2009

Things I Won't Work WIth: Thioacetone

Email This Entry

Posted by Derek

My recent entries in this category have, for the most part, been hazardous in a direct (not to say crude, or even vulgar) manner. These are compounds that explode with bizarre violence even in laughably small amounts, leaving ruined equipment and shattered nerves in their wake. No, I will not work with such.

But today's compound makes no noise and leaves no wreckage. It merely stinks. But it does so relentlessly and unbearably. It makes innocent downwind pedestrians stagger, clutch their stomachs, and flee in terror. It reeks to a degree that makes people suspect evil supernatural forces. It is thioacetone.

Or something close to it, anyway. All we know for sure is that thioacetone doesn't like to exist as a free compound - it's usually tied up in a cyclic thioketal trimer, when it's around at all. Attempts to crack this to thioacetone monomer itself have been made - ah, but that's when people start diving out of windows and vomiting into wastebaskets, so the quality of the data starts to deteriorate. No one's quite sure what the actual odorant is (perhaps the gem-dimercaptan?) And no one seems to have much desire to find out, either.

There are sound historical reasons for this reluctance. The canonical example (Chemische Berichte 1889, 2593) is the early work in the German city of Freiburg in 1889 (see page 4 of this textbook), which quotes the first-hand report. This reaction produced"an offensive smell which spread rapidly over a great area of the town causing fainting, vomiting and a panic evacuation.". An 1890 report from the Whitehall Soap Works in Leeds refers to the odor as "fearful", and if you could smell anything through the ambient conditions in a Leeds soap factory in 1890, it must have been.

The compound shows up sporadically in the literature until the mid-1960s, when several groups looked into thioketones as sources of new polymers. The most in-depth analysis took place at the Esso Research Station in Abingdon, UK, where Victor Burnop and Kenneth Latham got to experience the Freiburg Horror for themselves:

"Recently we found ourselves with an odour problem beyond our worst expectations. During early experiments, a stopper jumped from a bottle of residues, and, although replaced at once, resulted in an immediate complaint of nausea and sickness from colleagues working in a building two hundred yards away. Two of our chemists who had done no more than investigate the cracking of minute amounts of trithioacetone found themselves the object of hostile stares in a restaurant and suffered the humiliation of having a waitress spray the area around them with a deodorant. The odours defied the expected effects of dilution since workers in the laboratory did not find the odours intolerable ... and genuinely denied responsibility since they were working in closed systems. To convince them otherwise, they were dispersed with other observers around the laboratory, at distances up to a quarter of a mile, and one drop of either acetone gem-dithiol or the mother liquors from crude trithioacetone crystallisations were placed on a watch glass in a fume cupboard. The odour was detected downwind in seconds."

Now that's a compound to be taken seriously. How do you work with something that smells like hell's dumpster? Like this:

"The offensive odors released by cracking trithioacetone to prepare linear poly(thioacetone) are confined and eliminated by working in a large glove box with an alkaline permanganate seal, decontaminating all apparatus with alkaline permanganate, eliminating obnoxious vapors with nitrous fumes generated by a few grams of Cu in HNO3, and destroying all residues by running them into the center of a wood fire in a brazier."

So there you have it - just install a fireplace next to your hood (what every lab needs, for sure) and remember that, in a thioacetone situation, fogging the area with brown nitrogen oxide fumes will actually improve the air. (This is from Chemistry and Industry, 1967, p. 1430, if you need more details, and I hope you don't).

Comments (40) + TrackBacks (0) | Category: Things I Won't Work With

March 18, 2009

Things I Won't Work With: Chalcogen Polyazides

Email This Entry

Posted by Derek

The Klapötke group at Munich are some of the masters of alarming chemical structures, and they basically seem to own the field of chalcogen azides. Perhaps the competition for this class of compounds is not as intense as it might be - the other labs doing this sort of thing are collaborations between USC and various military research wings. But they're still interesting beasts.

A few years ago, both groups reported the synthesis of tellurium azides, with the Munich group sending in their paper a few days before the USC/Air Force team sent in theirs. The parent tetra-azide was explosive, to be sure, but could be kept at room temperature without necessarily blowing up. Klapötke's group and the USC group (led by Karl Christe) then teamed up to tackle the corresponding selenium analogs, which were reported in 2007.

And they're a livelier bunch. The selenium tetra-azide is another yellow solid, like the tellurium compound, but it's rather harder to keep it down on the farm. Taking some selenium tetrafluoride (see below) and condensing it with trimethylsilyl azide at -196 °C did the trick. After warming things up (you'll note the relative use of that term "warming"), they saw that:

"Within minutes, the mixture turned yellow, the color intensified, and a lemon-yellow solid precipitated while the reaction proceeded. Keeping the reaction mixture for about 15 min at -64 °C resulted in a violent explosion that destroyed the sample container and the surrounding stainless-steel Dewar flask."

Did I mention that this prep was performed on less than one millimole? Spirited stuff, that tetra-azide. The experimental section of the paper enjoins the reader to wear a face shield, leather suit, and ear plugs, to work behind all sorts of blast shields, and to use Teflon and stainless steel apparatus so as to minimize shrapnel. Hmm. Ranking my equipment in terms of its shrapneliferousness is not something that's ever occurred to me, I have to say. It's safe to assume that any procedure which involves considering which parts of the apparatus I'd prefer to have flying past me will not get much business in my lab, no matter how dashing I might look in a leather suit.

That procedure deserves a closer look, though. You can't just crack open a can of selenium tetrafluoride whenever you feel the urge, you know. That stuff has to be made fresh, as far as I can see, and the way these hearty sons of toil make it is by reacting selenium dioxide with chlorine trifluoride. Yep, that stuff, the delightful compound that sets sand on fire and eats through asbestos firebrick.

So if you're going to make selenium polyazides, your day starts with chlorine trifluoride and I'm sure that it just rolls along from there. Before you know it, you've gone from viciously reactive halogens, paused to prepare some disgusting selenium fluorides, made some violently unstable azides that explode if you stick your tongue out at them and hey, it's dinnertime already. . .

Comments (21) + TrackBacks (0) | Category: Things I Won't Work With

January 7, 2009

Things I Won't Work With: Azidotetrazolate Salts

Email This Entry

Posted by Derek

An early favorite has appeared in my “most alarming chemical papers” file for this year. Thomas Klapoetke and Joerg Stierstorfer from Munich have published one with a simple title that might not sound unusual to people outside the field, but has made every chemist I’ve shown it to point like a bird dog: “The CN7 Anion”. The reason that one gets our attention is that compounds with lots of nitrogens in them – more specifically, compounds with a high percentage of nitrogen by weight – are a spirited bunch. They hear the distant call of the wild, and they know that with just one leap of the fence they can fly free as molecules of nitrogen gas. And that’s never an orderly process. If my presumably distant cousin Nick Lowe does indeed love the sound of breaking glass, then these are his kinds of compounds. A more accurate song title for these latest creations would be “I Love the Sound Of Shrapnel Bouncing Off My Welder’s Mask”, but that sort of breaks up the rhythm.

These Bavarian rowdies have prepared a series of salts of the unnerving azidotetrazolate anion. As they point out, the anion was described back in 1939 (in what I hope was a coincidental association with the outbreak of the Second World War), but its salts are “rarely described in the literature”. Yes indeed! People rarely spray hungry mountain lions with Worcestershire sauce, either, come to think of it.

After reading this paper, I’m considering taking my chances with the mountain lions. The authors report a whole series of salts, X-ray structures and all, which range from the “relatively stable” lithium and sodium derivatives all the way to things that couldn’t even be isolated. In the latter category is the rubidium salt, which they tried to prepare several times. In every case, the solution detonated spontaneously on standing. And by “spontaneously”, they mean “while standing undisturbed in the dark”, so there’s really just no way to deal with this stuff. It’s probably a good thing they didn’t get crystals, because someone would have tried to isolate the hideous things. The cesium salt actually did give a few crystals, which they managed to pluck from the top of the solution and get X-ray data on. A few hours later the remaining batch suddenly exploded, though, which certainly must have been food for thought.

The authors went on to investigate the thermal behavior of these wonderful compounds, another risky move. As it turns out, they have calorimetry data on only five of the salts, because when they got to the sodium derivative, “a violent explosion destroyed the setup”. They also did sensitivity tests, using a standard drophammer rig from the Bundesanstalt fuer Materialforschung, evocatively abbreviated as BAM. These, along with the friction and spark tests, put these compounds well into the “primary explosive” category. Well, the ones that they could get data on, that is: the potassium and cesium compounds blew up as they tried to get them into the testing apparatus. So it’s safe to assume that they’re a bit touchy, too.

One of my favorite parts of the paper is the mention (found in much of the recent high-energy materials literature) that high-nitrogen compounds are worth investigated as “green” explosives, which makes me think that the whole environmental-rationale business must be reaching its end points. The notion of a more environmentally friendly way to blow things up aside, I have to salute the paper’s authors. They’ve made compounds that no one will have to make again, and survived the experience. Read the paper and be glad that this wasn’t your PhD project. . .

Comments (26) + TrackBacks (0) | Category: Things I Won't Work With

October 21, 2008

Things I Won't Work With: Triazadienyl Fluoride

Email This Entry

Posted by Derek

Now this is a fine substance. Also known in the older literature as fluorine azide, you make it by combining two other things that have already made my “Things I Won’t Work With” list. Just allow fluorine (ay!) to react with neat hydrazoic acid (yikes), and behold!

Well, what you’re most likely to behold is a fuming crater, unless you’re quite careful indeed. Both of those starting materials deserve serious respect, since they're able to remove you from this plane of existence with alacrity, and their reaction product is nothing to putz around with, either. The first person to prepare the compound (John F. Haller back in 1942) survived the experience, and made it (rightfully) the centerpiece of his PhD dissertation. But relatively few buckaroos had the fortitude to follow his trail over the years, and it’s not hard to understand why. Haller himself wrote on the subject in 1966 from an industrial position at Olin Mathieson, and got right to the point:

”(Fluorine azide) is described as a greenish-yellow gas at room temperature, liquefying at −82°C when diluted with nitrogen and freezing to a yellow solid at −143°C. Evaporation of this solid generally results in violent explosion.”

Yes, it does, and that does tend to slow down the march of science a bit. Not until 1987 was an improved procedure published, from Helge Willner and group in Hannover. (We'll see him again - most of his publication list falls into the "Things I Won't Work With" category, and I really have to salute the guy). Basically, it was the same reaction, but done slowly and Teutonically. You start off by making absolutely pure anhydrous hydrogen azide, which is a proposal that you don't hear very often around the lab, and is the sort of thing that leads to thoughts of career changes. (Maybe I could go into the insurance business and sell policies to whoever took over the prep). The next step is introduction of the fluorine, and when elemental fluorine is the most easily handled reagent in your scheme, let me tell you, you're in pretty deep. After the reaction, attention to painstaking fractional evaporation at very cold temperatures, in the best traditions of German experimental chemistry, is needed to clear out the reactants along with some silicon tetrafluoride, difluorodiazene, and other gorp. Willner's group managed to make about 20 milligrams of the pure stuff, but strongly recommend that no one ever make more than that. As far as I can tell, no more than a few drops of the compound have ever existed at any one time. This is not really a loss:

”The synthesis of pure N3F by the method described above was repeated more than 30 times without explosion. But if N3F is cooled to -196 C or N3F is vaporized faster than described, very violent explosions may occur. One drop of N3F will pulverize any glass within a 5-cm distance.”

They managed to get pretty full spectroscopic data on the compound while they had it, which was good of them, and even explored its chemistry a bit. Life must have a peculiar vividness when your job is to come in and see if triazadienyl fluoride does anything when you expose it to fluorine monoxide. (Oddly, they report that that reaction is OK – go figure). Still, most of the literature on this compound remains computational, rather than experimental (other than Willner's lab), and unless it turns out to be the secret to faster-than-light travel or something, that situation will continue to obtain. It's already good for accelerating Pyrex fragments past the speed of sound, but there are easier ways.

Comments (21) + TrackBacks (0) | Category: Things I Won't Work With

July 14, 2008

Things I Won't Work With: Cyanogen Azide

Email This Entry

Posted by Derek

Cyanogen bromide is not a nice reagent. It’s not quite on my list of things that I refuse to use, but it’s definitely well up on the list of the ones I’d rather find an alternative to. The stuff is very toxic and very volatile, and reactive as can be.

But it’s not the worst thing in its family. A good candidate for that would be cyanogen azide, which you get by reacting the bromide with good old sodium azide. Good old sodium azide, which is no mean poison itself, will do that with just about any bromide that’s capable of being displaced at all. Azide is one of the Nucleophiles of the Gods, like thiolate anions – if your leaving group doesn’t leave when those things barge in, you need to adjust your thoughts about it. Cyanogen bromide (or chloride) doesn't stand a chance.

Cyanogen azide is trouble right from its empirical formula: CN4, not one hydrogen atom to its name. A molecular weight of 68 means that you’re dealing with a small, lively compound, but when the stuff is 82 per cent nitrogen, you can be sure that it’s yearning to be smaller and livelier still. That’s a common theme in explosives, this longing to return to the gaseous state, and nitrogen-nitrogen bonds are especially known for that spiritual tendency.

There were scattered reports of the compound in the older German and French literature, but since these referred to the isolation of crystalline compounds which did not necessarily blow the lab windows out, they were clearly mistaken. F. D. Marsh at DuPont made the real thing in the 1960s (first report here, follow-up after eight no-doubt-exciting years here). It's a clear oil, not that many people have seen it that state, or at least not for long. Marsh's papers are, most appropriately, well marbled with warnings about how to handle the stuff. It's described as "a colorless oil which detonates with great violence when subjected to mild mechanical, thermal, or electrical shock", and apologies are made for the fact that most of its properties have been determined in dilute solution. For example, its boiling point, the 1972 paper notes dryly, has not been determined. (The person who determined it would have to communicate the data from the afterworld, for one thing).

The experimental section notes several things that the careless researcher might not have thought about. For one thing, you don't want to make more than a 5% solution in nonpolar solvents. Anything higher and you run the risk of having the pure stuff suddenly come out of solution and oil out on the bottom of the flask, and you certainly don't want that. You also don't want to make a solution in anything that's significantly more volatile than the azide, because then the solvent can evaporate on you, making a more concentrated stock below, and you don't want that, either. Finally, you don't want to put any of these solutions in the freezer - a particularly timely warning, since that's one of the first things many people might be tempted to do - because that'll also concentrate the azide as the solvent freezes. And you don't want that. Do you?

Actually, the careless researcher shouldn't even work with cyanogen azide, or anything like it, but you never can tell what fools will get up to. The compound has around a hundred references in the literature, a good percentage of which are theoretical and computational. Most of the others are physical chemistry, studying its decomposition and reactive properties. You do run into a few papers that actually use it as a reagent in synthesis, but I believe that those can be counted on the fingers, which is a good opportunity to remind oneself why they're all still attached.
tetrazine.gif
In fact, the reason I got to thinking about this wonderful little reagent was a recent paper in Angewandte Chemie, which details the preparation of horrible compounds like the one shown. But what does the experimental section spend the most time warning you about? The cyanogen azide used to make them. Enough said.


Comments (27) + TrackBacks (0) | Category: Things I Won't Work With

February 26, 2008

Sand Won't Save You This Time

Email This Entry

Posted by Derek

In a comment to my post on putting out fires last week, one commenter mentioned the utility of the good old sand bucket, and wondered if there was anything that would go on to set the sand on fire. Thanks to a note from reader Robert L., I can report that there is indeed such a reagent: chlorine trifluoride.

I have not encountered this fine substance myself, but reading up on its properties immediately gives it a spot on my “no way, no how” list. Let's put it this way: during World War II, the Germans were very interested in using it in self-igniting flamethrowers, but found it too nasty to work with. It is apparently about the most vigorous fluorinating agent known, and is much more difficult to handle than fluorine gas. That’s one of those statements you don’t get to hear very often, and it should be enough to make any sensible chemist turn around smartly and head down the hall in the other direction.

The compound also a stronger oxidizing agent than oxygen itself, which also puts it into rare territory. That means that it can potentially go on to “burn” things that you would normally consider already burnt to hell and gone, and a practical consequence of that is that it’ll start roaring reactions with things like bricks and asbestos tile. It’s been used in the semiconductor industry to clean oxides off of surfaces, at which activity it no doubt excels.

There’s a report from the early 1950s (in this PDF) of a one-ton spill of the stuff. It burned its way through a foot of concrete floor and chewed up another meter of sand and gravel beneath, completing a day that I'm sure no one involved ever forgot. That process, I should add, would necessarily have been accompanied by copious amounts of horribly toxic and corrosive by-products: it’s bad enough when your reagent ignites wet sand, but the clouds of hot hydrofluoric acid are your special door prize if you’re foolhardy enough to hang around and watch the fireworks.

I’ll let the late John Clark describe the stuff, since he had first-hand experience in attempts to use it as rocket fuel. From his out-of-print classic Ignition! we have:

”It is, of course, extremely toxic, but that's the least of the problem. It is hypergolic with every known fuel, and so rapidly hypergolic that no ignition delay has ever been measured. It is also hypergolic with such things as cloth, wood, and test engineers, not to mention asbestos, sand, and water-with which it reacts explosively. It can be kept in some of the ordinary structural metals-steel, copper, aluminium, etc.-because of the formation of a thin film of insoluble metal fluoride which protects the bulk of the metal, just as the invisible coat of oxide on aluminium keeps it from burning up in the atmosphere. If, however, this coat is melted or scrubbed off, and has no chance to reform, the operator is confronted with the problem of coping with a metal-fluorine fire. For dealing with this situation, I have always recommended a good pair of running shoes.”

Sound advice, indeed. I'll be lacing mine up if anyone tries to bring the stuff into my lab.

Comments (48) + TrackBacks (0) | Category: Things I Won't Work With

May 30, 2006

Things I Won't Work With: Frisky Perchlorates

Email This Entry

Posted by Derek

Perchloric acid almost makes my list by itself, although technically I can't quite include it, since I've already used it. I used the commercial grade, which is 70% strength in water, and it's pretty nasty stuff. It'll chew through your lab coat and give you burns you'll regret, as you'd expect from something that's rather stronger than nitric or sulfuric acid.

But it has other properties. The perchlorate anion is in a high oxidation state, and what goes up, must come down. A rapid drop in oxidation state, as chemists know, is often accompanied by loud noises and flying debris, particularly when the products formed are gaseous and have that pesky urge to expand. If you take the acid up to water-free concentrations, which is most highly not recommended, you'll probably want to wear chain mail, because it's tricky stuff. You can even go further and distill out the perchloric anhydride (dichlorine heptoxide) if you have no sense whatsoever. It's a liquid with a boiling point of around 80 C, and I'd like to shake the hand of whoever determined that property, assuming he has one left.

Perchlorate salts show similar tendencies. The safety literature is just full of alarming stories about old lab benches that had had perchlorates soaked into them years before and exploded when someone banged on them. They're a common component of solid rocket fuels and fireworks, as you'd figure. As with other lively counterions, the alkali metal salts (lithium, sodium, etc.) are comparatively well-behaved, with things heading downhill as you go to larger and fluffier cations. I've used things like zinc and magnesium perchlorate, but I would refuse, for example, to share a room with any visible samples of the lead or mercury salts.

People have made organic perchlorate esters, too, which doesn't strike me as a very good idea - unless, of course, you're actively searching for a way to blow up your rota-vap. Which is exactly what happened in the paper I saw on the synthesis of ethyl perchlorate, as I recall. If you'd like to make your mark, this seems to be a relatively unexplored field. The problem is, the mark you're most likely to make is in the nature of a nasty stain on the far wall.

Perhaps the most unnerving derivative I know of is fluorine perchlorate. That one was reported in 1947 (JACS 69, 677) by Rohrback and Cady. It's easily synthesized, if you're tired of this earthly existence, by passing fluorine gas over concentrated perchloric acid. You get a volatile liquid that boils at about -16 C and freezes at -167.3, which exact value I note because the authors nearly blew themselves up trying to determine it. The liquid detonated each time it began to crystallize, which is certainly the mark of a compound with a spirited nature.

The gas, meanwhile, blows up given any chance at all - contact with a rough surface, with tiny specks of any type of organic matter, that sort of thing. The paper notes that it has "a sharp acid-like odor, and irritates the throat and lungs, producing prolonged coughing". My sympathies go out to whichever one of them discovered that. No, if it's all the same to science, I think I'll let others explore the hidden byways of perchlorate chemistry. . .

Comments (26) + TrackBacks (0) | Category: Things I Won't Work With

May 23, 2006

Can't Buy These Thrills

Email This Entry

Posted by Derek

There are a number of reagents that you used to be able to buy which are no longer around. Some of these have just fallen out of favor, but a compound has to go pretty far down the list before no one sees any profit in selling it. The more common reasons for the disappearance are a bit more dramatic.

A notorious example is "Magic Methyl" (methyl fluorosulfonate). Flurosulfonate is about as good a covalent leaving group as nature provides, and Magic Methyl was accordingly one heck of a way to methylate anions that turned up their noses at anything difficult. Problem was, though, that it also tended to methylate the user. There was at least one fatality in the 1970s from a not-very-large spill of the stuff, and by the time I got to grad school it had been pulled from commercial supply. It's never coming back, either. You can still make the stuff and use it yourself, and people do once in a while (not to mention things that are even more reactive, although that one's not volatile, at least). But there are research organizations that forbid even that.

There are substitutes, but nothing's quite in the same league. Methyl triflate is the closest thing going, as far as I know. It's an open question as to how much less nasty that one is - you can still buy it by the gallon. No one's been killed by it, but if someone dropped a bottle near me I'd still hold my breath and dive out the door.

Dess-Martin reagent is one that's appeared and disappeared over the years. It's a useful oxidizing reagent, which tends to react very cleanly and on some substrates that are hard to work with otherwise. Making it has always been a nerve-wracking process, though. The reagent itself shouldn't be heated, but is reasonably well-behaved. But the intermediate compound in the synthesis (IBX) has been known for some time to be erratically explosive, especially if it's allowed to dry out. It's sensitive to impact, which always made for a good time when it was time to get it out of the funnel after filtering it.

The fun didn't stop there. The last step in the synthesis, right after the IBX formation, was famously wonky, and has only been ironed out in recent years. Or so I'm told - I made a couple of hundred-gram batchs of the stuff, fifteen years ago, going two for three in attempts on the last step, and do not plan to do so again. You can buy the reagent at the moment, but it's been dropped from catalogs before (as Aldrich did during the 1990s).

Comments (10) + TrackBacks (0) | Category: Things I Won't Work With

March 3, 2005

Things I Won't Work With: Carbon Diselenide

Email This Entry

Posted by Derek

Column VI of the periodic table doesn't start out smelly, but that's probably just because we run on its first element, oxygen. Animal ancestors of ours who felt woozy all the time from the stench of oxygen didn't leave much of a legacy, so we're all pretty positive about it. But when you start moving down into the next rows, everything changes.

Sulfur's next, and its fame as a reeking element is well deserved. Skunks, rotten eggs, burning tires - they all have delightful sulfurous tang, and we have sulfur compounds in the lab that are worse yet. But most people don't think about the elements to come.

The next heavier element in the series is selenium, which most people will have heard of primarily from its presence in health food stores. It is indeed an essential trace element, although I'd think that if your cuisine includes a reasonable amount of garlic (as it should!) then you're getting all the selenium you need. You don't want to overdo it, because this essential dietary factor is also a pretty efficient poison, which is a useful First Lesson in Toxicology right there. (And no, I don't think it's possible to get selenium poisoning from eating too much garlic; I think many other effects would kick in before you noticed any selenium-related problems.)

Selenium compounds are, if anything, more intrinsically noxious than sulfur ones. Imagine a sort of hyperskunk, scattering its enemies before it and making them carom off trees and dive into ponds. The heavier selenium atoms tend to make the compounds less volatile, though, so you don't always get their full bouquet. The smaller compounds get in their licks, though. One of the simpler selenium-rich compounds, for example, is carbon diselenide, an exact homolog of the carbon dioxide in your breath and in your glass of soda. Instead of a gas, the selenide is an oily liquid with a higher boiling point than water. Most of us organic chemists have never seen it.

Which is just fine. The first report of the compound in the chemical literature is from a German university group from 1936, and it was a memorable debut. A colleague of mine had a copy of this paper in his files, and he treasured a footnote from the experimental section which related how the vapors had unfortunately escaped the laboratory and forced the evacuation of a nearby village. The authors stressed the point that its aroma was like nothing that they'd ever encountered.

The compound made a few appearances over the next couple of decades, but one of the next synthetic papers dates from 1963. (That's Journal of Organic Chemistry 28, 1642, for you curious chemists.) The authors are forthright:

"It has been our experience that redistilled carbon diselenide has an odor very similar to that of carbon disulfide. However, when (it is) mixed with air, extremely repulsive stenches are gradually formed. Many of the reaction residues gave foul odors which were rather persistent (and) it should be noted that some of the volatile selenium compounds produced may be extremely toxic as well as foul."

Something for everyone! At least it lets you know when it's coming. Interestingly, in recent years, the compound has actually made a comeback, with more references to it in the past twenty years than in the fifty before. It's been used to prepare a number of odd compounds that have shown promise as organic semi- and superconductors, and there's actually a commercial source for the disgusting stuff (which may be a first.) I'd like to see what they ship it in.

Comments (14) + TrackBacks (0) | Category: Things I Won't Work With

November 16, 2004

Things I Won't Work With: Ozonides

Email This Entry

Posted by Derek

I've never done an ozone reaction myself. In fact, I haven't seen anyone else do an ozonolysis in years now, and I wonder if this reaction is passing into chemical history. These guys are hoping not.) Many chemistry departments have an electric gizmo to produce ozone in small quantities, and I get the impression that they're mostly gathering dust.

Ozone attacks a carbon-carbon double bond, initially making an ozonide, a hair-raising five-membered ring that has three oxygens in a row. That rearranges to a still-alarming one with two on one side, separated by carbons from the other. That falls apart on workup to two carbonyl compounds (or other things, depending on what you add to the reaction.) It's a very clean way to oxidize a double bond and make reactive handles out of its two ends.

But it tends to be something that's done on a small scale, because those ozonides are packed with energy and ready to hit the town. In general, we chemists shy away from compounds with lots of single bonds between the elements on the right-hand side of the periodic table. Those guys tend to have a lot of electron density on them, and bonding between them is a careful, arm's-length affair, sort of like porcupines mating. Two oxygens single-bonded make a peroxide, and those generally blow up. A small ring with more oxygens in it than carbons will almost invariably blow up if you try to concentrate it or handle it too briskly.

I'd do an ozonolysis if I needed to (although first I'd have to find our machine and see if it even works.) But you couldn't pay me to try to isolate the intermediate ozonides. But you can pay some people, like Prof. Pat Dussault, who was a post-doc down the hall from me when I was in graduate school. He's made a career out of oxygen-oxygen bonds, no small feat.

Comments (13) + TrackBacks (0) | Category: Things I Won't Work With

August 26, 2004

Things I Won't Work With: Polyazides

Email This Entry

Posted by Derek

The azide group (three nitrogens bonded together in a row, for the non-chemists in the crowd) has several personalities. Unfortunately, most of them are hostile. Azide anion, as you find in sodium azide, is pretty toxic. It shuts down several important enzymes, and it's often used in biology labs as a general metabolic poison.

Covalent azides are a different sort of beast. Having something directly bonded to the group stops it from being an enzyme-killer, for the most part, but you have a new problem to worry about: explosiveness. In general, reasonably high molecular weight azides are OK to handle (e.g., the early anti-HIV drug azidothymidine). I've made some of that sort, since azide displacement is a classic (and useful) way to get a nitrogen into your molecule. But the smaller ones aren't worth the risk.

That's because the higher the percentage of nitrogens in the formula, the more you have to worry. Thermodynamically, nitrogens bonded to each other are always regarded as guilty until proven innocent - there's always the fear that they're going to find a way to throw off their civilized clothes and revert to wild nitrogen gas. That's a hugely stable compound. If your structure goes that route, all that extra bonding energy it used to have ends up diverted into flying shrapnel and loud noises.

A few years ago I saw some Israeli escape artists has prepared triazidomethane, which I wouldn't touch with somebody else's ten-foot titanium pole. One carbon, one hydrogen, and nine nitrogens - look at the time! Gotta run! But there's always worse. Just today I was reading a soon-to-be-published paper in Angewandte Chemiefrom some daredevils at USC. They've prepared titanium tetraazide, of all things. One titanium and twelve nitrogens: whoa! Podiatrist appointment! See you later!

You can isolate the stuff, it seems, as long as you handle it properly. It turns out that brutal treatments like, say, touching it with a spatula, or cooling down a vial of it in liquid nitrogen - you know, rough handling - make it detonate violently. I think that staring hard at it is OK, though. The authors recommend using everything you have for protection if you're zany enough to follow their lead: goggles, blast shield, face shield, leather suit (!) and ear plugs. Those last two suggestions are unique in my experience, and quite. . .evocative of what you have to look foward to with these compounds. (We don't have any leather suits around where I work, although I'm sure I'd look dashing in one.)

Some of the folks on the paper have a joint appointment with an Air Force missile propulsion research lab. They've found a home. Me, I'll be way over here.

Comments (7) + TrackBacks (0) | Category: Things I Won't Work With

August 4, 2004

Things I Won't Work With: A Nasty Condensed Gas

Email This Entry

Posted by Derek

If you cool things down enough, you can turn almost anything into a liquid (or into a solid, if you're really insane about it.) Chemists use liquid ammonia fairly often, for example, though it's been some years now since I've needed any. People outside the field think of the aqueous solution of ammonia gas (household ammonia) when you say "liquid ammonia", but I'm talking about the pure stuff. Cool the gas down below about -33 C, and you'll condense it out to a clear liquid that's sort of like a thinner version of water.

It's easy enough to do, with an ammonia tank and a condenser full of dry ice. But once, over twenty years ago, I had a chance to see someone use one of those rigs to condense something a bit more exotic: pure hydrogen cyanide. That's another one that people confuse with the aqueous solution. But pure HCN has a fairly high boiling point, for such a small molecule, and condensing out is no problem - as long as you have more nerve than you have sense.

The fellow doing it was down the hall from me in graduate school, and he was doing an obscure reaction which forms a geminal dinitrile, which themselves are rather obscure compounds. (That's probably because this bug-eyed route is the best way to make 'em.) He was dressed in full suit and respirator gear, for which he'd had to get trained. Everyone else had cleared out of the lab, but someone was watching him at all times from the hallway, just in case.

I thought to myself, "When am I going to get the chance to see pure liquid HCN again?", and went down to see, ready to bail out if anything started going wrong. It looked just like ammonia, clear drops rolling down the cold condenser and dripping into the round-bottom flask below. But there was enough HCN in there to kill off the lot of us, if (im)properly handled.

I've worked with plenty of cyanide since then, and even plenty of reactions that have produced small whiffs of HCN vapor. (As I think I've mentioned, it doesn't smell as much like almonds as it's said to, in my opinion.) But I doubt very much if I've worked with enough of it to match the amount that I saw in that flask, that day - there must have been a couple of moles of it in there. A lifetime supply that was, in many sense of the word. . .

Comments (8) + TrackBacks (0) | Category: Things I Won't Work With

March 28, 2004

Thing I Won't Work WIth (2): Nickel Carbonyl

Email This Entry

Posted by Derek

Synthetic organic chemists rely a lot on inorganic chemistry. We let metals do a lot of work for us, particularly when it's time to do the real arc-welding of carbon-carbon bond formation. I have a pretty typical synthetic background, and over the years I've used palladium, platinum, sodium, iron, copper, rhodium, aluminum, mercury, silver, manganese, lithium, titanium, chromium, cobalt, zinc, ruthenium, vanadium, tin, magnesium, cerium, potassium, and probably a few more that escape me right now. Never sit near a chemist and give him any excuse to rattle off a list of elements.

I've never used elemental nickle metal, but I have broken out some of its salts from time to time. I especially enjoy the vivid green of nickel chloride, whose solutions look for all the world like lime jello. Not that you'd want to substitute that in your favorite recipe: nickle salts are rather toxic, and are suspected carcinogens to boot. But I'd work with them all day long to avoid dealing with another nickel compound, its tetracarbonyl.

That's a complex of nickel with carbon monoxide. CO has a good amount of electron density left on its carbon, and it'll line up on a metal atom, slotting into its electron orbitals and making itself at home. You can find carbonyl complexes of all the transition metals, as far as I know. Many of them are liquids, which is rather disconcerting when you consider their metal heritage.

Nickel carbonyl is a liquid, but it can barely restrain itself from being a gas. It boils at 43 C, so it has a pretty substantial vapor pressure, and that's a real problem. Said vapor, as you'd imagine, is rather weighty. It's not one of your wafting-away-on-the-summer-zephyr sort of vapors; it's more like a sort of ghostly molasses. It's so heavy that you really can't rely on a standard laboratory fume hood to contain it, because that's not the sort of hazard they're built for. Depending on the air flow and the sash, the stuff can just ooze right out the front of the hood and pour out into the lab.

You don't want it there. Breathing it is most unwise, because those CO ligands are not stapled on very well. If they find another metal that appreciates them more, they'll bail out, and an excellent candidate is the iron in your hemoglobin. There go four equivalents of carbon monoxide into your blood cells, and there's only so long you can keep that up. And there's the nickle, too - alone, bereft, with only your proteins to complex to. Wonderful. Recall that the metal is toxic all on its own, and you've now dosed in the most bioavailable manner possible. If you make it through the carbon monoxide spike, you have long-term metal poisoning to deal with.

Even if the vapor doesn't get the chance to wander around poisoning you, it can amuse itself right in your fume hood. If it rolls across a hot surface, of which there are no shortage in most working hoods, then it can explode, leaving behind a vile haze of carcinogenic nickle soot. An exploding toxin with a high vapor pressure - I just don't know what else you could ask for in a laboratory reagent. No doubt it does many interesting and useful reactions. They can save 'em for me, because I'm not that desperate yet.

Comments (0) | Category: Things I Won't Work With

March 3, 2004

Things I Won't Touch (1)

Email This Entry

Posted by Hylton Jolliffe

I'm still working on my reply to the Matthew Holt article I mentioned yesterday, so I thought I'd do one of the awful reagents that I spoke of. I'll kick things off with hydrogen fluoride.


The chemically inclined members of my audience might be saying "Hold it! You said yesterday that you'd used hydrofluoric acid!" And that's true, and that stuff is certainly bad enough on its own merits. It gives terribly painful burns, and it eats through glass, to pick two of its fine qualities. But if you're going to be precise, hydrofluoric acid is a water solution of hydrogen fluoride, HF. That's a gas, and it's a lot worse.


Actually, it's just barely a gas. In a cool room it'll condense out as a liquid (it boils at about 20 degrees C, which is 68 F.) The straight liquid must really be a treat, but I've never seen it in that form, and would only wish to through binoculars. It's sold compressed in metal cylinders, like other gases, but it needs some care in packaging. The stuff is so corrosive that special alloys need to be used, usually ones high in nickel. If you stick an ordinary gas regulator on top of an HF cylinder, you're in for trouble, and the complete destruction of the regulator is the least of your worries.


HF has actually been used right out of the cylinder for a long time in Merrifield peptide synthesizers. It's the traditional way to cleave the peptide off the resin at the final step, so there are actually a lot of people who've used the stuff. But it's in a dedicated apparatus that is (that had better be) well sealed, and people treat it with due respect. At a former employer of mine, there was an accident with one of these machines right before I joined the company. The shout "HF LEAK!" went out into the halls, and I'm told that the whole area set a never-to-be-equaled evacuation record. This was one of those drop-things-right-where-you-stand type evacuations, a real sauve qui peut moment.


I've caught some whiffs of HCl, like any chemist has, and it'll wake you up for sure. And I was wrestling with a lecture bottle of HBr gas in grad school, only to have it start to hiss onto my shirt - which was never the same afterwards. But I've never smelled HF, and I hope I never will. As bad as it is on metals and glass, it's much worse on living tissue, although (as I mentioned) a lot of synthetic peptides can stand up to it.


Oddly enough, it's not that strong an acid in the traditional sense. The fluorine doesn't want to let go of the proton enough. It's strong enough to burn, but the big problem is how penetrating it is. As soon as it hits anything moist - like your lungs - it dissolves in the water and turns into hydrofluoric acid again. And that soaks into tissue very readily, with the acid part doing its damage along the way, and the fluoride merrily poisoning enzymes and wreaking havoc. The damage isn't immediately apparent, and there are terrible cases of people who've been exposed and didn't realize it for hours - by which time a lot of irreversible damage had been done.


Fortunately, I have very little cause to even think about using HF. I don't do Merrifield peptide synthesis, and the only times I even use the solution forms of the reagent are on a very small scale and in weakened form (like its complex with pyridine.) Should some lunatic discover a wonderful reaction that requires the gas, I will respectfully pass. As will everyone else.

Comments (0) + TrackBacks (0) | Category: Things I Won't Work With