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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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January 23, 2009

The Real Hazards of the Lab

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Posted by Derek

A run of bad accident news today, and all of the same kind. The Chemistry Blog has the story of a fatality in the labs at UCLA. The short and painful details are: inexperienced student, t-butyllithium, flammable clothing, and panic (as in not running toward the safety shower).

This is very sad to hear about, and as with so many lab accidents, one of the saddest parts is how easily it could have been prevented. t-BuLi is, of course, a well-known fire starter, and the student did know about that problem. But one of the keys to working with dangerous substances is to think through what you’ll do if something goes wrong. For a pyrophoric compound, that means knowing where the nearest fire extinguisher and safety shower are. It’s very easy to panic when something goes wrong, but if you’ve rehearsed what to do beforehand, you have a much better chance of doing the right thing in tough circumstances.

I pass this along to the students who read this site, and I’m sure the other experienced lab workers here will agree: always think “OK, what’s the worst thing that can go wrong with this reaction?”, and think about what you’ll do if that happens. Fire? Explosion? Sudden leak of nasty toxic stuff? Think it over. Anyone working in a laboratory should always know where the nearest fire extinguisher is. That is, the nearest appropriate one – if you’ve got a separate Class D model for metal fires, or even just a sand bucket, then when you need it you’re really going to need it. And everyone should know where the nearest safety shower is, because no one ever just sort of needs to use one of those. I’ve had to run and pull one once in my career, and let me tell you, it was a damned good thing that I knew where to go when the chips were down.

The other news I have was communicated to me privately, so I won’t go into details other than to say that it appears to be another fatality, this time involving inhalation exposure to trimethylsilyl diazomethane. The problem with these sorts of reagents is that you might think that they’d cause breathing trouble immediately, but you’d be wrong. Diazomethane, phosgene, methyl bromide and others can actually take hours to kill a person, and for a good part of that time, the only symptoms might be a slight cough. But serious lung damage can be coming on slowly during that period, and by the time it’s clear that there’s a problem it’s usually too late to do very much about it. Unfortunately, in some cases, it’s too late right from the start, but that takes quite a bit of exposure, and indicates a serious mistake somewhere along the line.

Anyone who works with such volatile and damaging reagents needs to be completely aware of what they’re doing, and to only handle them under good ventilation. I’ve used such things many, many times in my career, without incident, and so have most working organic chemists. But we should never lose respect for what we’re holding in our hands.

I’m not trying to scare beginning chemists out of doing lab work. It has it hazards, but so does driving to work in the morning or cutting up food for dinner. (When I was in graduate school, my mother once expressed her worries about my lab work, but I told her that the most dangerous thing I did was to drive 650 miles back home on holidays). But every well-appointed chemistry lab is full of death in screw-capped bottles, and that bears thinking about. Random, unforeseeable accidents are, fortunately, very rare. But that means that the others didn’t have to happen, and that’s painful to contemplate.

Comments (65) + TrackBacks (0) | Category: Chemical News | Graduate School | Life in the Drug Labs


1. NH_chem on January 23, 2009 10:46 AM writes...

Being prepared for the worst and hoping for the best is always what my adviser said. This is something that I always kept in mind.

The time when a POCl3 quench went terribly wrong, I was prepared although it is never fun to inhale that lovely stuff!

Great advice. Chemistry is dangerous but so is driving your car...........

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2. Russ on January 23, 2009 10:55 AM writes...

As you point out, Derek, there are substances which cause no initial irritation but are rapidly absorbed on the pulmonary surface. The subsequent hydrolysis or alkylation is irreversible and can be fatal.

It took years for me to get comfortable with the protection that a hood sash affords the maximum amount of body area possible.

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3. Mark M on January 23, 2009 11:03 AM writes...

This is awful, and, regrettably, preventable.

From the blog you reference:

"Somehow, the syringe plunger popped out or was pulled out of the syringe barrel, splashing the employee with t-bu-Li and pentane. The mixture caught fire, upon contact with air. She was wearing nitrile gloves, safety glasses and synthetic sweater. She was not wearing a lab coat. "

This immediately brings to mind several actions that could have ameliorated this:

1. ALWAYS WEAR A LAB COAT (she would have had her sweater between her and the burning lab coat)

2. work with the hood sash down as far as practical, whenever possible and always when handling pyrophorics or inhalable toxins

3. unless you really know what you are doing, use an 18 gauge needle (not 20 as stated in the report) with a 60 mL glass syringe

4. for the PI:

a) make your newer employees prove to you they know how to use the Ar line before letting them loose in the lab

b) be mindful that females may not have the same hand strenght as males when using a 60 mL syringe--train your people to ask for help for critical manipulations for which they find themselves straining or applying excessive force.

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4. buyproduct on January 23, 2009 11:24 AM writes...

Mark M, you recommend a glass syringe over a plastic disposable one? I always found glass syringes to be more accident prone. I prefer the plastic ones because they have a tighter seal. I always test out the plastic syringe when I measure out a new reagent to ensure it does not react with the plastic and or melt it. Glass slides to easy for me, allowing for pops and less control in dropwise additions.

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5. Petros on January 23, 2009 11:31 AM writes...

Horrific, but no lab coat!

I used bottle of the BuLis while doing ny PhD and while t-BuLi was the worst, and a shock the first time or two as the odd flaming drop fell off the syringe, I soon got used to it. The worst experience was dispsoing of bottles after the cold store they were kept in had been flooded.

As for buyproduct's comment I wouldn't fancy a plastic syringe for t-BuLi

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6. FormerMolecModeler on January 23, 2009 11:50 AM writes...

Very sad. When I did synthesis, there were reagents I always had extra respect for, and alkyl lithiums were at the top of the list. Always wore lab coat + gloves for those.

BuLi is relatively tame (but still dangerous), but tBuLi is nasty. Very easy for syringe to get jammed.

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7. Kai on January 23, 2009 11:52 AM writes...

Despite your attempt to not scare off young chemists, it is for these reasons that I am no longer in chemistry. After three years in my undergraduate research lab, I would see accidents occur to others, hear horror stories from others, and once had an unexpected spray of hydrofluoric acid come off of our electrochemical etching setup.

Luckily everything was in a hood, but I believe that is when I decided that I would leave the chemistry to others and merely use their expertise in conjunction with proteins.

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8. RTW on January 23, 2009 12:18 PM writes...

A major part of these problems could have been ameliorated if the PI, and or other responsible person in the LAB supervised people unfamiliar with using these reagents initially. t-BuLi is perhaps the worse organometallic to use in the lab. Someone that had never used it specifically before would be well advised to have someone watch them when handling the stuff, just to have an extra set of eyes, and hand should something go wrong. This makes for a positive experience and perhaps establishes proper respect for the reagent up front.

Secondly I also vote for the plastic disposable syringe, but I would perhaps used smaller easier to handle quantities. Say 3 times 20 or even 6 times 10. It would have been safer to only extract smaller amounts from the bottle.

I was fortunate in my undergraduate research days to use these materials, and also had a full professor that would come observe and teach proper laboratory technique. Unfortunately another fellow down the hall wasn't as lucky and managed to blow his professors lab and himself up. He survived but just barely. Issue was one of experience, and supervision. Handling of far too large of quantities at one time.

Fortunately the people that responded didn't panic or it could have been much worse.

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9. Kent G. Budge on January 23, 2009 12:48 PM writes...

A physical chemist friend once had a large cylinder of liquid nitrogen fall over when he was working alone late at night. His instinct was to catch the cylinder before it hit the concrete floor.

Unfortunately, the stopcock was open and a steady trickle of liquid nitrogen ran across the back of his hand as he struggled to pull the cylinder back into an upright position. Left an *impressive* scar.

Liquid nitrogen. What could be more innocuous?

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10. Hap on January 23, 2009 12:48 PM writes...

Is TMSCHN2 used because it doesn't require previous prepn. or becaue it is less volatile and explosive than CH2N2 (or both)? For some reason, I didn't think TMSdiazomethane was hazardous, which would be a bigger oops if there were the possibility of working with it.

Perhaps you might ask the person who communicated the story to you to write a sanitized (of propietary knowledge version) for CEN or someplace else that gets safety news.

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11. milkshake on January 23, 2009 12:52 PM writes...

I use plastic syringes for alkyl lithiums without problem, the 20mL, 5mL and 3mL sizes work particularly well. The big 50mL syringes however are useless and should be avoided, larger quantities are best transfered by canula or in multiplies of 20. You want to be careful not to pull the plunger all the way out and having stuff suddenly pouring out on you hand and sleeve.

At my first company we had a dude who incinerated his whole hood with tBuLi - he decided to reflux (!!) his material in excess of neat tBuLi, about 100mL of it.

Also small fires can be put out when you dump your dry ice bucket on them - lot less messy than powder fire extinguisher, and no safety incident paperwork to fill afterwards

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12. imarx on January 23, 2009 12:57 PM writes...

Does anyone know of a resource (perhaps online) for practical warnings wrt the usage of chemicals? I've always been frustrated with the uselessness of MSDS (which makes sodium chloride sound like a hazardous substance) and the warning labels on the bottles aren't much more helpful. I wish there were some compendium of practical knowledge about how to deal with particular chemicals. For example, a colleague recently informed me that osmium tetraoxide is really bad for your eyes. I'd never have known that if he hadn't told me. Derek's TMS-diazomethane story is another example of useful knowledge that you wouldn't necessarily get from reading the label on the bottle.

Is there someplace where people can separate out the really really bad stuff from the "fine as long as you don't eat it" stuff and provide specific tips on safe handling?

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13. Bethany Halford on January 23, 2009 1:12 PM writes...

Probably not as comprehensive as what you're after, imarx, but C&EN does keep an archive of the chemical safety letters it has received since 1993.

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14. Hap on January 23, 2009 1:28 PM writes...

Being volatile is usually a problem - OsO4 is a good oxidant, but its problems with eyes stem from its volatility at ambient temperature (it has a a high vapor pressure, and so it gets into your eyes and oxidizes them, giving Os metal in the eyes - Os metal when exposed to air gives OsO4 in significant quantities). The war gas/pseudo war gases (methylating agents, phosgene, diazomethane/TMSdiazomethane, etc.) are volatile enough to get into your lungs, and those in particular give no sign of having done so...until you can't breathe.

Fluka's catalog general gives summaries of the hazards of the chemicals, and I assume others do as well. I think CEN has searchable safety messages (letters to the editor on safety incidents).

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15. Jose on January 23, 2009 1:36 PM writes...

The best source of real safety data is the NIOSH pocket guide (online)- actually separates extreme nasties (dimethyl sulfate, HMPA, etc) from the humdrum.

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16. bill on January 23, 2009 1:38 PM writes...


While I understand your concern about refluxing in t-buli.

If you look up the synthesis of (t-bu)3SiH you will see that it calls for taking (t-bu)2SiF2 and adding t-buli in excess. Then you distill out the pentane the t-buli comes in and add a high boiling solvent (?decane? I'm not sure) and refluxing for 24 hours or so.

So, while it may not have been appropriate for you colleague's reaction, it does have precedent.

Though following this blog, there are many things with precedent I would not want to work with.

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17. Ralos on January 23, 2009 1:43 PM writes...

Very sad to hear this news.

During my PhD, my advisor had a strict protocal when using alkyl lithium or other nasty reagents. As previously posted, protective equipment, safety glass, gloves, and face shield were mandatory. But, an added rule was to have a person standing behind you with a Fire Extinguisher and someone else responsible near by to lend aid when using something as dangerous as t-BuLi. For t-BuLi, our group kept to smaller glass syringes (~10 to 20 mL max) which provided the greatest control.

In my postdoc, my prof added pre-task analyses for safety before using anything considered dangerous even in a small reaction to ensure his students and postdocs would know what to expect.

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18. bearing on January 23, 2009 2:26 PM writes...

Another thing that might help, as silly and as superficial as it may sound, is a curtain around the safety shower.

I have worked in two environments -- one student organic chemistry lab, and one chemical plant -- where individuals were injured because, their clothing soaked by a chemical spill, they lost valuable seconds and minutes to go somewhere they could remove the clothing in privacy.

One was a male student who went down the hall to the bathroom to remove his jeans after spilling concentrated sulfuric acid on himself, the other was a female technician who got sprayed over her entire body -- I don't remember the chemical, sorry, but she spent time in the hospital afterward. In both cases there was a shower literally steps away.

Human nature won't change, and "strip naked in front of a mixed group of co-workers" will always be something people are resistant to do.

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19. training on January 23, 2009 2:37 PM writes...

Under no circurstance, Should the PI allow (encourage?) a fresh graduate student to conduct such a reaction without proper training.

Even worse, the PI should not encourage (force?) graduate student to work during the holiday without adequate supervision.

Folks, we all know the reality in graduate school.
Instead of sitting here talking about "chemistry", let's do something the help those innocent young kids. Let's dig out the deep reasons behind this kinds of accidents.

God bless chemists.

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20. nitric oxide 99 on January 23, 2009 2:48 PM writes...

This post has got me thinking about something I'm planning in the coming week - a Strecker-like reaction requiring about 100 mmol of HCN. The original German paper I'm following calls for addition of "wasserfreie Blausaure" - pure HCN (which I guess is blue colored in liquid form?).

I'm hoping I can get away with generating the HCN in situ by addition of AcOH to KCN.

Obviously I'll be working in the hood with sash down and flushing thoroughly with N2 after the reaction's complete. Anything else I should consider to stay safe?

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21. MikeEast on January 23, 2009 3:01 PM writes...

My heart sank reading this post. Probably because as a 22-year-old chemist I also did not comprehend the potential dangers in all of the bottles and jars around me.

There but for the grace of God go I.

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22. pharmaresearcher on January 23, 2009 3:32 PM writes...

I would suggest cannulating pyrophorics into a septumed graduated cylinder when dealing with large volumes then recannulating into the reaction there is little hand strength involved and if the cannula clogs you don't have to worry about alot of BuLi you can't quench.

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23. Me on January 23, 2009 3:41 PM writes...

t-Butyl Lithium is less dangerous than trimethyl-Aluminum.

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24. Swapna on January 23, 2009 3:43 PM writes...

Heard about this through a colleague. Tragic indeed. It's almost "mandatory" for graduate students to work on weekends and holidays here, but none of us ever does it alone. There's at least one other person in the same lab. or the next.

I always set up any reaction involving alkyllithiums on weekdays when the response time from folks around will be reasonably higher if I screamed bloody murder.

More importantly, proper training is key, be it by the PI or a senior graduate student/post-doc. Setting a good example for the young'uns has to exist.

Derek, you really touched upon an important point there with learning to recognize the potential hazards associated with conducting any reaction. If you run through the drill before you start the reaction, it is indeed true that the response to an accident is better and well-judged.


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25. jkp on January 23, 2009 3:47 PM writes...


NotVodoo has an attempt at practical "peer reviewed" safety precautions (see Reagents). Their idea could definitely use some refining, but I think it's a step in the right direction.

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26. Sili on January 23, 2009 3:56 PM writes...

"wasserfreie Blausaure" - pure HCN (which I guess is blue colored in liquid form?).
No. It's called "Blausäure", because it was first synthesised from "Berlinerblau" - Prussian blue.

And yet again I realise that I'll never get to work as a chemist. I really did waste my years at uni, not picking up any good lab habits.

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27. Hap on January 23, 2009 4:22 PM writes...

I assume most places have mandatory safety training for working with HCN - where I was at undergrad, training was mandatory if you intended to work with fluorine, nickel tetracarbonyl, hydrogen cyanide, and one other (that I can't remember). There's kits for immediate treatment of HCN toxicity as well (before you go to the hospital) as well. I think anhydrous HCN also has other hazards (it likes to polymerize, I think).

Is there another way to do your reaction, not involving a couple of grams of concd. HCN?

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28. InfMP on January 23, 2009 4:31 PM writes...

Well, to elaborate on the TMSCHN2 story, it happened in the province in canada where i am from...
A worker at a pharm company in windsor died in the hospital long after the work day was done. His lungs were dissolving and he told people the chemical he was working with. So much for the "safe" CH2N2
CBC reported the story if you google. (they are like ABC or CBS in Canada).

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29. Mass on January 23, 2009 5:38 PM writes...

Regarding HCN alternative: Use acetone hydrin as an alternative to HCN.

Regarding plastic syringe: You do not have to deal with the clogged ones ...You can dispose them of. Does any one know which make is good and inexpensive? I have decided to shift to them for good.

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30. milkshake on January 23, 2009 7:00 PM writes...

Strecker: I used to do a 30-gram-scale Strecker by adding solid zinc cyanide into ice-cooled mixture of my aniline and N-alkyl piperidone in 80% acetic acid. It worked very well and the HCN release was negligible.

I also did a variant of Strecker by mixing the cyanohydrine of my ketone with an excess (4 equivs) of morpholine and heating the mix to 60C for few hours.

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31. S on January 23, 2009 8:13 PM writes...

This is really strange... I'm an undergrad, just started working in a research lab today. I read this article before going into lab, and was told that I would be using trimethylsilyldiazomethane in my first reaction... I didn't put it together that this was the same compound. Strange. And kind of creepy.

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32. DLIB on January 23, 2009 9:22 PM writes...

bearing: Not a silly idea at all...

I know a lady who has burns all over her legs from Piranha because she was to embarrassed to get into the safety shower. They now have curtains

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33. Chemist of Sorts on January 23, 2009 9:32 PM writes...

Tragic but unfortunately a result of academic culture. Most grad students are trained by senior students/post docs who don't always take care to do it right. They often have other things to do and, anyway, the atmosphere is that you learn as you go along. In my experience, academic advisors have minimal contact with students in regard to technique.

The majority of the responsibility for this has to lie with the PI. Safety is the most important aspect of lab life. As a PI myself (industrial), I will not allow anybody working for me to do anything that I don't feel confident they can do safely and correctly. If this means that I add a reagent to an associate's reaction while they watch, so be it. I have done this in the past and would do it again if I have any misgivings about someone's experience and skill. PIs must be aware of whats going on in their labs, and adjust accordingly. Anything less is negligence.

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34. Chemjobber on January 23, 2009 10:15 PM writes...

@Nitric: I like Milkshake's suggestion the best, but if you want to read an interesting view of HCN from Derek himself, here's the link:

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35. frozenraisin on January 23, 2009 10:16 PM writes...

With regards to using HCN, I think the following should be considered a necessity:

1) A functioning HCN detector
2) A coworker nearby (but not too nearby) who is familiar with the HCN detox procedure including the adrenaline injection
3) A clean air line for breathing should be available in an industrial setting, e.g. kilo lab.

Also keep in mind that the first symptoms of HCN poisoning is identical to a panic attack.

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36. BCP on January 23, 2009 11:41 PM writes...

Another vote for using cannulation for tBuLi. Big syringes are a no-no.

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37. Krillin on January 24, 2009 12:46 AM writes...

When I worked at a military lab, lab coats were only worn during visits from the brass. Actually working in them would incur the risk of getting them dirty and causing the lab to fail a cleanliness inspection.

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38. processchemist on January 24, 2009 3:53 AM writes...

I have, helas, a wide experience with t-butyl lithium on bench - Kg scale. I think that low pressure cylinders you use with reactors are much safer than bottles with septa - IF USED BY WELL TRAINED OPERATORS - and so 5 or 20 Kg of t-BuLi are "safer" than 320 ml.
For small quantities my preference goes to glass syringes up to 20 ml. Also cannulation of multiple bottles, with t-BuLi, has safety problems (when you change bottle).
Obviously you must be sure of the absence of overpressure in the bottle - this is the safest way to deal with it. To use plastic syringes with a tight plug, in my opinion, is not so safe: you can have an excessive pressure in the bottle without being aware of it.

For beginnes aldrich tec bull about air sensitive rectives is one of the best documents I've seen around.

Strecker: I'm dealing currently with some. I see that work up, more than reaction, has safety issues. Working on the 10-50g scale with a 10% excess of cyanide without a tight pH control it's not advisable.

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39. lassa on January 24, 2009 10:07 AM writes...

Thought I'd throw in my two pence having done a number of multigram scale Streckers. I found the best way to generate the HCN was using a stock aqueous solution of KCN (easily handled solid), and stock solution of acid (I think I was using HOAc at the time). I never observed any gases, never smelled any almonds, and after a basic workup everything went to the toxic waste people, no problems.

As far as the t-BuLi use, I never liked cannulation. Too often I've seen people with plugged cannulas just keep upping the pressure on the bottle/flask they're pushing out of. I always think it looks like an incident waiting to happen. Count this as another vote for *threaded* 20 mL disposable syringes. (Never try to reuse one either, as they always seem to leak on the 2nd try.) Use as many as it takes to get where you're going.

Condolences to anyone who's been injured, or lost someone due to this kind of incident. Truly regrettable.

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40. Lab Coats on January 24, 2009 10:33 AM writes...

What is the current consensus on the preferred material for lab coats: 100% cotton or cotton/polyester blend? I would prefer 100% cotton because it will not melt like synthetics, but they are hard to find.

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41. Retread on January 24, 2009 2:18 PM writes...

Always tragic to see a young life terminated, particularly when from something preventable. As an M. D. I saw plenty -- drug overdoses, alcohol related automobile accidents, barroom fights, AIDS etc. etc.

This brings up the following poinst. You all know how to behave safely in a lab. What out of the lab risky behavior do you indulge in? How many of you smoke, how many drink to excess, use narcotics, cocaine etc. etc. Time to reflect on what happened and stop doing these things.

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42. Anonymous on January 24, 2009 2:43 PM writes...

is it just me or is "Retread" a total douche?

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43. AliG on January 24, 2009 4:41 PM writes...

I once needed to use HCN on decent scale. I found it convenient to prepare a solution of it by dripping sulfuric acid onto NaCN and condesening into a solvent of choice (toluene for me). You can preweigh a flask with solvent in it and condense the HCN into the solution cooled in a dry-ice bath. Afterwards, you re-weigh the flask and you know the concentration of HCN. You never have to deal with pure liquid HCN. Also you can buy cyanide antidote kits, but someone with medical training will have to order it.

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44. The Inorganic Gardener on January 24, 2009 7:27 PM writes...

Alas in the UK, the cyanide antidote kits are becoming a thing of the past. I work with cyanide regularly (cyanoloysis of higher polythionates) and even though I get through kgs of KCN a month, I've never let myself get blasé about the stuff. Always supercareful and very strict with myself about procedure etc. The antidote kits are, as far as my departmental H&S guy is aware, no longer recommended in the UK due to the number of misadministrations etc which have caused more harm than good. The only thing we have an antidote kit for is diisopropylfluorophosphate - one to avoid if you can help it!

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45. milkshake on January 24, 2009 11:05 PM writes...

Young synthetic chemist's life is not tragically terminated - its "quenched prematurely" .

HCN generation: For small-scale reactions it is better to use TMSCN (with gloves) in the presence of 1.2 equivs of isopropanol or methanol at OC, it desylilates promptly even at low tempetature.

TMSCN is somewhat expensive though, and just as toxic on molar basis if you spill it on yourself or ingest it.

Cyanide aantidote is not adrenaline injection as mentioned here (someone must have watched too much Pulp Fiction lately) but n-amyl nitrite "poppers".
Amyl nitrite does not work too well though and a better antidote is an IV injection of a sub-lethal dose of sodium nitrite, about 300mg, followed by injection of several grams of sodium thiosulfite.

Obviously you don't want to improvise this risky IV antidote rescue in the lab (there are commercial antidote kits available) but having some volatile nitrite at hand is probably a good idea when working with a source of HCN. The downside is that the nitrite inhalation by itself can make you feel pretty sick for the rest of the day as I have once found out during a careless work with TMSCN

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46. Krillin on January 24, 2009 11:47 PM writes...

Some day we'll have a cyanide antidote that works prophylactically.

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