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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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February 16, 2012

When Reagents Attack!

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Posted by Derek

Well, since I was just talking about a reagent that can potentially take off without warning, I wanted to solicit vivid experiences from the crowd. What's a compound that you've made that did something violently unexpected? I can recall making some para-methoxybenzyl chloride in grad school (for a protecting group; I was running out of orthogonal protecting groups by that time). It's not hard - take the benzyl alcohol and some conc. HCl and swoosh 'em around. But the product you get by that method isn't the cleanest thing in the world, and on storage, well. . .a vial of it blew out in my hood after the acid had had a chance to work on it.

My most vivid reagent-gone-bad story is probably this one; that's a time I literally came down counting fingers. What other things have you had turn on you?

Comments (78) + TrackBacks (0) | Category: How Not to Do It | Life in the Drug Labs


1. Mike on February 16, 2012 11:24 AM writes...

In graduate school I was doing a Birch reduction in cooled liquid ammonia. After the reaction had been going steadily for a few hours, it suddenly within seconds changed color and rapidly warmed. As I was standing a few feet from it, the entire contents of the two liter reaction flask then immediately geysered out leaving a coating of dry material on the roof of my hood. The flask was completely empty. I could smell nothing but ammonia for the next day or so.

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2. Travis on February 16, 2012 11:44 AM writes...

My first semester of grad school I was doing an ortho-formylation of a phenol using MgCl2, Et3N and paraformaldehyde. After heating the mixture to reflux, paraformaldehyde can be seen repolymerizing on the walls of the condenser. My first time doing a large scale-up I used a narrower-bore condenser than usual for some reason and during the reflux the condenser must have plugged. The resulting pressure blew off the condenser and sprayed my entire fume hood with a sticky, canary-yellow polymer.

Fortunately no one was hurt but it took 5 hours to scrape off the gunk from the hood.

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3. Biotechtranslated on February 16, 2012 11:44 AM writes...

My worst reagent experience was a pretty innocuous one: Fe/AcOH

I was doing a reduction of an aromatic nitro compound and Fe/AcOH was the only one that worked half-decent.

The procedure called for mixing the nitro compound with AcOH, heating to 50C, then adding the iron powder.

I have the solution heated, ready to add the iron powder. I add the iron in one charge and then put the condenser back on. I watch the temperature and it goes 50C..60C..90C..115C in about 10 seconds. I go to remove the heating mantle and WOOSH....

The condenser popped off and I was sprayed with a nice mixture of acetic acid, iron powder and partially reduced nitro compound.

I quickly rinsed by face off (safety glasses for the win!) since acetic acids stings when it hits your lips.

I had visions of my skin coming off in sheets, but luckily no damage was done. I had to use abs. ethanol to remove the waxy nitro compound from my skin (including in my ears). I'm sure my liver appreciated the exposure.

Lesson learned! Never try and save a reaction, just shut the hood and walk away. You can always clean it up later.


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4. anonymous on February 16, 2012 11:46 AM writes...

I made an unexpectedly pyrophoric compound (a silicon analogue of bis-vinyl zinc(II)) which quite surprised me.

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5. LittleGreenPills on February 16, 2012 12:01 PM writes...

In my limited synthetic exposure I have had three experiences:

1. As an inexperienced undergrad I picked up an old 4L bottle of diisopropyl ether that had a lot of some sort of grey material in the bottom. The instant I picked it up it bubbled like a bottle of champagne. Fortunately it was stoppered with a cork, which shot out also like a champagne cork. Still not sure how I did not drop the bottle.

2. Working up a LAH reduction on a very rainy night, I was left holding a flask crusted with a white solid. As I held it I noticed a strange black spot that was growing. Then noticed that it was surrounded by a red ring. As it dawned on me that it was burning, in a state of panic I had to decide, do I put it back in the hood with the L of THF from the reaction or leave it out? I put it at the far end of the hood closed the sash and watched.

3. Trying to rearrange an allylic alcohol. I added H2SO4 to a flask of the alcohol. It began to bubble, then smoke, then whistle, and finally with a little poof sound, a puff of smoke came out and I had a flask of expensive charcoal.

I now do very little synthesis.

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6. Opps on February 16, 2012 12:05 PM writes...

I can't forget the multiple times I have seen someone's mineral oil heating bath go up in flames upon high heating. "Opps, I though that was a silicon oil bath."

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7. baluba on February 16, 2012 12:22 PM writes...

I recently moved to process chemistry after grad school and postdocs and soon came to realize how many things are HIGHLY underestimated in academic labs and "small scale" environments. Many simple work up (quenching acid chlorides for instance) can go very badly even moving to say 100g batch size. And NO training in process safety is available at any stage of grad school careers!

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8. AlMe3 on February 16, 2012 12:22 PM writes...

Trimethylaluminum-mediated amidation of an ester on 100g scale: I quenched the reaction by quickly adding a few mLs of ammonium chloride solution and it shot up like a volcano (on the day of a lab safety audit no less). The next time I ran the reaction (on the same scale), I found that pouring the reaction mixture into rapidly stirring, cold ammonium chloride solution only resulted in a fizzle.

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9. p on February 16, 2012 12:31 PM writes...

baluba makes a great point about scale up. The "best" reaction I ever had was a Simmons-Smith. I did the reaction on 50mg at 0 C and it went beautifully. I then scaled up to 2 grams, still at 0 C, and blew a flask, addition funnel and ice bath to smithereens (pun intended). My advisor saw me after clean up and said, "You know, I was thinking about your reaction. When you scale up you probably ought to cool it to -78". Yep.

But, yeah, scaling up creates hazards out of stuff you don't think will be all that bad.

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10. MnO2 on February 16, 2012 12:33 PM writes...

I once added activated MnO2 to a secondary benzylic/propargylic alcohol and the flask shot flames out of it with such force that it made the sound of a train whistle for several seconds. After the fireworks were over and I cleaned out my pants, I decided to TLC the reaction mixture. To my surprise the reaction was complete and clean enough to proceed with a workup and column. The best part of the story was that I achieved 75% isolated yield of the desired ketone after purification.

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11. Calvin on February 16, 2012 12:33 PM writes...

Ozonolyis followed by oxidative work up with peracetic acid. Ozonolysis fine, work up not so much. Needed a bit of heat and a decent amount of peracetic acid to get it going which was fine on mg scale but on gram scale was pretty hard to judge. Monitor temp inside the reaction and in the oil bath and cool v quickly when there was a difference netween the two. One time I was a bit slow and it exploded out the top of the flask and covered the inside of the hood in stick goo. I managed to get the sash down in time to prevent myself getting covered in it but it did make a mess of the hood. Some of it is probably still there to this day.

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12. canchem on February 16, 2012 12:38 PM writes...

First reaction I was ever instructed to do involved alkylation of an alcohol using NaH as base. I was told to wash the NaH with hexanes. I did, but thinking the supernatant was what I wanted, dumped the grease into my reaction and left about 4g of this funny grey powder in an erlenmeyer.

That alkylation reaction didn't work. A reaction did take place when I tossed some dil. HCl into that erlenmeyer before washing it. Kept my eyebrows, but only barely.

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13. NJBiologist on February 16, 2012 12:40 PM writes...

Does a loose rhesus monkey count as "a reagent that can potentially take off without warning"? 'Cause that will get your heart rate up pretty fast....

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14. processchemist on February 16, 2012 12:41 PM writes...

A 4-nitrophenylglycoside unexpectedly exploded: it happened during the recrystallization of a second crop.

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15. anon the II on February 16, 2012 12:48 PM writes...

Many years ago, when I left big pharma to try out biotech (or was I leaving NJ for NC), my new boss was emphatic that we save money whenever possible. My idea of saving money was different from one of my new coworkers who had spent a few years in the fields during the Cultural Revolution. One day, after rotavaping off thionyl chloride from a reaction, he poured the contents of the rotavap trap into a bottle for the next time he needed the “expensive” reagent. Oh yeah, he tightened the cap on the bottle real tight. Who knows how much pressure was in that bottle when it finally gave way in the back of his hood. Luckily, he was at the sink and I was at my desk when it went. The largest piece of glass we found was maybe a couple of mm’s long. The former bottle of hydrazine that was sitting next to the recovered prize helped form a nice white smoke in the aftermath of the event.

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16. Doubja on February 16, 2012 12:48 PM writes...

A few years ago I wanted to convert a secondary amine to the corresponding methyl carbonyl carbamate using methyl isocyanatoformate (CAS# 5843-42-5). I found a bottle in an adjacent lab that was a couple of years old according to our inventory system. It came from a lab where I trusted the guys to take care of their chemicals. The Aldrich website and the label on the bottle made me expect a white powder. The actual content of the 5 g bottle appeared to be a liquid. I didn’t think too much about it and fortunately unsuccessfully tried (and I am not one of those lab whimps) to unscrew the lid. Luckily the next thing I tried was INSIDE the hood. I started tapping the edge of the vial against an edge thinking the thread got dirty and stuck. After the second tap the bottle (thankfully only a small 5 g bottle) exploded in my hands with a bang that made my ears ring and the guys from the lab next door to run over to see if I had killed myself. Needless to say I disappointed them. Aside from the shock I stayed unharmed. I couldn’t even find any shards from the vial which to this day freaks me out. In hindsight the change in physical appearance should have given me a hint and set off a couple of alarm bells. Fortunate for me I got to live and learn. I wont bore you with the chemistry that went on in the vial but the experts in the audience will immediately figure out what happened to the reagent.

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17. NI3 on February 16, 2012 12:54 PM writes...

Not an accident. But once we made a large batch of nitrogen triiodide (safe when wet, contact explosive when dry) for a high school demonstration. Before we could set it off on our own with a long meter stick with a feather on the end, a fly landed on the the dry powder - KABOOM. Caught everyone (especially the fly) by surprise

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18. anchor on February 16, 2012 1:15 PM writes...

This story goes long back to a time when we accidentally made active manganese dioxide. We carried out exhaustive oxidation of a natural product (several kilos) with KMnO4. None of us anticipated that the byproduct manganese dioxide would be super reactive enough. The filtration of the heterogeneous mixture was smooth but the pad of manganese dioxide along with residual organic caught fire and had us all surprised! After putting off fire and exercising caution we stored the manganese oxide in several containers for disposal. The manganese dioxide worked like charm for selective allylic/benzylic oxidation for several months. I have used other variants of manganese dioxide (active) that is sold commercially these days, but I reckon that the one we made accidentally was the best!

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19. Yazeran on February 16, 2012 1:16 PM writes...

Well my most unexpected chemical reaction was way back in high school when I was fiddeling with a variety of redox reactions (read ways to create home made fireworks). I had read through our chemistry textbook and found that the entry on amonium nitrate mentioned that a significant part of the world production went to military use...

Not surprised, I worked out that NH4NO3 liberates excess oxygen, and that could be used to burn things. I also looked up the melting point and found that it melts before it decomposes, and by accident the melting point is similar to that of plain sucerose.

Bingo I thought, the perfect mixture for making solid rocket fuel.
So I carefully worked out the exact ratio of amonium nitrate to sugar and slowly melted the amonium nitrate in my parents kitchen. As soon as it had melted, I removed it from the stove and slowly added the sugar while stirring. Initially it went ok, but after a few seconds the mixture became first brownish yellow, and then gradually darker untill it was almost black while iot starterd to smoke. As it dit this, it also became more and more sticky, and I was in a bit of a loss as to how I was to explain a completely gunked pot to my mom.

I did a fast thinking and rememberred that both the amonium mitrate and the sugar is water suluble, so quickly added some water to quency/clean while the substance was hot and likely to be still disovlvable.

What I didn't count on was that as soon as the first drop of water hit the mixture, the complete batch exploded (it didn't detonate fortunately, it only burned extremely fast).

I can still with dread remember how the window in front of me suddenly looked to be blurred as the hot gasses from the reaction literally made a meter and a half jet up from the pot. Incidently I must have added just a bit too much sugar, as afterwards most of the kitchen was covered in extremely fine black particles (soot) which took more than an hour top clean up as I had to wash almost all surfaces to remove all traces.

The pot you say? It was completely clean afterwards!

I only told my parents about that incident some 10 years afterwards...

Yours Yazeran

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20. Seth on February 16, 2012 1:36 PM writes...

I was working with an old bottle of thioacetic acid, when I went to syringe some out the needle aided in the degassing of what I presumed to be H2S. This resulted in the thioacetic acid being redistributed all over the hood and me. The smell was something on the order of a skunk and dog poo, which my wife didn't really care for.

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21. Superted on February 16, 2012 1:40 PM writes...

Not exactly a reaction gone bad, but... we used to have a small kugelrohr kit that we used to distill products from Rh and Ir catalysed reactions we were running. I used to use conc. sulfuric acid and hydrogen peroxide to clean it which was always entertaining, but on one occasion the exotherm resulted in the entire mixture erupting out, just as I was cleaning up in the rest of the hood. Result: labcoat sleeves a mess, and scars on one arm that are still visible today, 20 years later.

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22. okemist on February 16, 2012 1:54 PM writes...

I would like to thank everyone for these posts. They contain valuble information. Two of my worst experiences were:
1. after cooling a hot distillation of ether and opening it to air, the mixture was reheated and it exploded. I learned to always work in an inert atmosphere, it take a lot longer when you scale to large vessles, but it is worth the patience.
2. 800g of LiAlH pellets in a crys dish ignited just with static, we had used dailey for years with out problem. opened a tank of lN2 to smother it but it would not extinguish. finally buried it in cat litter (clay) about 100 lbs did the trick. Thank you all again for sharing your experiences.

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23. newton on February 16, 2012 1:57 PM writes...

Back at my postdoc, I prepared a 50g batch of MoOOPH to oxidize thioethers. The material looked beautiful as I collected it by filtration, but as I scooped it out of the funnel it went up in smoke and gave off a not-so-surprisingly awful smell. The resulting cloud and odor chased the entire floor out of the building. Luckly the lab had windows that still opened (probably not a good idea, but probably saved a few years of my life).

Another reference for the prep of MoOPH said that if all the solvents are not removed from the intermediate steps the product could be pyrophoric. Wish I read that one first.

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24. ProteinChemist on February 16, 2012 1:57 PM writes...

Back in my first year of grad school I was working in a lab that needed a lanthanum oxide solution (not sure why now). To get it soluble, it was recommended at the time that I use concentrated nitric acid. Not thinking about the exothermic nature of the reaction, I combined 200g of lanthanum oxide and about 150mL of nitric acid in a 1L erlenmeyer. It looked a lot like those science fair volcanoes, except that sure wasn't baking soda. Needless to say, next time I dissolved it a bit at a time and over ice.

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25. ScientistSailor on February 16, 2012 2:19 PM writes...

Not me, but in the next lab over, a grad student was doing a large-scale Diels-Alder with butadine in a sealed tube. When it blew, destroyed everything in the hood and even pushed the walls of the hood out. Fortunately, the lab was empty at the time.

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26. James on February 16, 2012 2:49 PM writes...

I was making bis TMS peroxide through the DABCO-peroxide adduct. I had filtered the white complex and left the bench for a minute to retrieve something before treating with trimethylsilyl. In the meantime I heard a terrible hissing noise and came back to find the adduct, blackened and smoking, consuming my filter flask. Not the kind of compound that should be left out in air for long.

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27. John Wayne on February 16, 2012 3:15 PM writes...

Heh ... I've got a few of these:

1. In graduate school I was making an enolate with sodium sand based on a pretty old procedure. I had the sodium suspended in solvent in the round bottom flask and adding the ketoester in solution slowly via addition funnel. It all added, but nothing seemed to happen, so I let the reaction warm up a little ... when the whole thing exothermed it shot the additional funnel through my manifold and covered the hood in little bits of sodium and solvent. Fortunately, I saw the internal temperature starting to spike and closed my hood sash in time; the only part of the addition funnel I ever found was the teflon stopcock.

2. I had just performed a reaction wherein I had washed sodium hydride with hexanes repeatedly to get most of the oil out of it. Everything went well, and the reaction was proceeding, but the hexane washes needed to be quenched. I added water via wash bottle slowly, got impatient, and it got away from me right as the professor I was teaching for walked into the lab to talk to me. He walks up to a graduate student putting out a reasonably sized fire with a towel and his gloved hands and says, "I can come back if you're busy." I got the fire out just at that moment and replied, "My schedule just cleared up; what can I do for you?"

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28. MTK on February 16, 2012 3:17 PM writes...

Fire, Flood, Explosion.

The unholy trinity of chemistry.

I've had 'em all.

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29. gippgig on February 16, 2012 3:24 PM writes...

Did anyone figure out what it was in that para-methoxybenzyl chloride that did the actual exploding? Are there any compilations of the chemistry behind these unexpected explosions etc.? It seems like an interesting and useful topic to study.

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30. Neil on February 16, 2012 3:44 PM writes...

@Yazeran - I had almost the exact same thing happen to me, while in high school. A friend and I were mixing up our own solid-rocket fuel (to re-fuel our spend model rockets), and were also in the kitchen at the time.

We were heating the mixture in a small metal pot, stirring constantly. My friend noted that a small amount of smoke was present, when the whole thing blew up on us!

Anyone who knows the old ammonium nitrate and sugar bit will also know of its use as a smoke powder...and smoke it did! My friends kitchen was more or less instantly filled with a dense sweet-smelling smoke. His mom was outside at the time, but ran screaming into the house when she saw the billowing clouds of smoke emanating from the kitchen door (which my friend had thrown open to help clear the mess).

We were lucky, however, and did our cooking in the sink! After a good hour or so the kitchen was clear and clean.

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31. Anonymous on February 16, 2012 3:48 PM writes...

#19 reminds me of a very similar reaction that surprised me by working precisely as advertised - I never would have dreamed of trying it, but the greybeard doing the serious chemistry on our team swore by it.

As with Yazeran, we were making a rocket propellant, but we specifically wanted to nitrate the (proprietary) polymer we wer using. So, mix polymer with the right amount of NH3NO4 and heat to just shy of the melting point. Result, a molten eutectic that isn't hot enough for ammonium nitrate to decompose outright, but close enough for individual nitro groups to jump over to the energetically-favorable carbon right next door. Wait for the ammonia to stop bubbling out of the mix, cool, and wash. Or, when we were planning to use ammonium nitrate as an oxidizer, just arrange for there to have been a sufficient surplus in the first place.

Worked just fine (and yes, we were doing this in a shielded test cell in a bunker designed for experimental rocket propellant work).

I suspect something similar may have been going on in the nitrate/sugar melt incident, save that the result would have been crude sucrose octanitrate. "...hitherto proved of little practical value as an explosive on account of its extreme sensitivness and liability to spontaneous decomposition" (Hoffman and Hawes, JACS, 1919).

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32. Jonathan on February 16, 2012 4:20 PM writes...

I wonder if possibly my finest moment as a young PhD student back in the 1990s counts? As a pharmacologist, I didn't really have to worry about blowing up the lab so much as accidentally poisoning myself with the fruits of someone else's reactions. We did roll our own radioimmunoassays though, which involved heating and stirring the buffer to get the gelatin to dissolve. For reasons I can't quite remember, I had been making up my buffer in a lab on the second floor, despite the radioactive lab being on the ground floor. The floor in-between was where the ice machine was located, and I stopped on the way down to fill up a large tray with the necessary ice to perform the assay. Only having two hands (and presumably no functioning brain), I decided that the easiest way to get everything back to the lab was to carry the bottle of buffer in the tray of ice. Did I mention that the bottle was hot? Or that it was made of glass?

I think I made down a flight of stairs before a loud bang and lots of tiny bits of glass announced to me that negative thermal expansion had done its thing. Bloody good job I was wearing glasses!

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33. Anon on February 16, 2012 4:55 PM writes...

When I was a graduate student, a post-doc across the hall decided to purify ~100g of impure TBS-Cl. This is a solid at RT and purified by vacuum distillation (with a gently warmed short-path condenser).

The Post-doc had not done it before and chilled the condenser with water. He got ~10g over before the distillation stopped.... so he cranked up the temperature... WAY UP because it wouldn't distill..... You can probably guess what happened.

The condenser had sealed off with solid TBS-Cl, so the vacuum was not longer applied to the still pot. By cranking up the temperature (on a now sealed system), the pressure built until the still-head popped out explosively venting a massive amount of hot TBS-Cl vapor that created clouds through his lab bay. I only saw the aftermath of clouds, shattered Still-head, water (from the condenser) and a spray of TBS-Cl all over the interior of the hood. Fortunately, he was at his desk when the "eruption" occurred so no one was hit with flying glass.

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34. anon on February 16, 2012 5:38 PM writes...

Where's milkshake? Go back in his blog and he has had more excitement with energetic molecules than anyone I ever heard of. Mostly in Prague,as I recall.

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35. Gene on February 16, 2012 5:40 PM writes...


Not in a lab, but how about turning a 40-foot garbage compactor container barrel shaped (think of Mrs Puff after Spongebob crashes the boat again)? I'm an environmental regulator and got called out to the rail loading yard here because, "A container has exploded." When I got there the container was on its side next to the train and the fire department had three 2 1/2" hoses blasting into it full force with heavy smoke pouring out. So I started collecting info on what had happened.

Trash and garbage here go to transfer stations where it's dumped into pits and compacted into 40-foot, heavily reinforced containers which go on trucks to the loading yard where they are put on trains to the landfill. This train had been loaded with containers and was getting ready to depart soon, so one of the yardbirds was walking the train ensuring everything was in good shape for the trip. As he said, "I was about two cars past that one when I heard a loud boom behind me. I turned around and it was all blowed up and falling off the car." Luckily, it was top loaded, if it had been the one on the bottom it would have been a whole lot more interesting.

After much investigation (by another agency, I deal with what goes to sewers) here's what was discovered: A few days before an employee at a heat-treating/metal finishing/welding company was cleaning up and discarded what he thought was waste to the dumpster. They regularly put waste into the sealable metal tins that welding rods come in. This dumpster had gone where dumpsters go and its contents had been compacted into the container along with many tons of other stuff, much of it wet, then sealed. It turns out that the "waste" was granular CaC2, so as the CaC2 was getting wet in the container it was producing C2H2, which at some point reached the right concentration/pressure/ignition source/incompatible substance and went BOOM! It blew the container barrel shaped, blew the doors off (or they fell off due to distortion) and knocked the container off the train car.

That energetic enough?