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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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May 7, 2010

Things I Won't Work With: Small, Smelly Isocyanides

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Posted by Derek

Everyone's heard of cyanide, whether they've spent any time in a chemistry classroom or not. And if you form a covalent bond to the carbon of that CN group, you've got a nitrile, and those are familiar compounds to any organic chemist. But what if you flip the group around and bond it via the nitrogen? That gives you a weird situation, where the nitrogen has a formal positive charge and the carbon is left with a formal negative one, which looks somehow unnatural. But that's an isonitrile (isocyanide) for you.

They're actually quite useful, although I'd guess that the majority of chemists have never encountered one. But if they have, they've remembered it, because isonitriles are not shy about announcing their alien character. Our noses can immediately tell the difference between garden variety nitriles and their evil twins. The former often have no smell at all, or run to a faint spicyness. The latter smell like. . . like. . .well, I've never actually been downwind of the Abominable Snowman's armpit or been had my eyeglasses fogged up by a Komodo dragon with stomach trouble, but those are the examples that come to mind.

Fragrance expert Luca Turin has described isonitriles as "the Godzilla of scent", and that's accurate, if you also try to imagine Godzilla's gym socks. "Penetrating" and "repulsive" are good words to describe your typical isocyanide. It feels like the odor is aggressively storming your nasal passages, and it really makes you want to be somewhere else very quickly. This abstract gets the point across well. Problem is, it can be one of those smells that stays with you ("I like it in here. Stop bothering me."), so going somewhere else - although a recommended first step - is not always enough to do the trick. As a paper on the synthesis of these fine compounds puts it:

It should also be noticed that due to the extremely distressing odour of isocyanides the application of the usual techniques of purification is especially difficult since the exposure to isocyanide vapours, even at very low levels, must be rigorously avoided.

Good advice! But hard to put into practice if you use the things at all, since it doesn't take much. Even the not-so-volatile isonitriles get up on the table and shout at you, but the low-molecular-weight ones are truly hard to take. And the pride of that bunch seems to be the n-butyl, which should come as no surprise. Straight-chain butyl compounds are well known to be just a poor match for human sensibilities. Butyl alcohol is stinky, butylamine foul, butyraldehyde reeks, butyric acid is famously disgusting, and butyl mercaptan is a standout even in the vile crowd of thiols.

So butyl isocyanide is, well, something to experience. I've never had the pleasure, and will take pains not to. I can do no better than to quote the 1937 observations of one of the first groups to figure out how to prepare this noble reagent in quantity:

Butyl isocyanide proved to be so disagreeable to manipulate that none of its physical constants except boiling point were determined. Even when a hood with an extra forced draft was used, the odor pervaded the laboratory and adjoining rooms, deadening the sense of smell and producing in the operator, and in others, severe headaches and nausea which usually persisted for several days.

Sounds great. Many of you may have had similar experiences at some point, but it usually takes more than just spilling a drop of stuff on the floor to bring them on. Here's the whole thing, in a bottle! Available wherever fine chemicals are sold, actually. Don't just live an average, boring life: go wild - go isocyanide!

Comments (55) + TrackBacks (0) | Category: Things I Won't Work With


COMMENTS

1. Ed on May 7, 2010 8:03 AM writes...

If you compare the stinkiness of butylamine and 1,4-diaminobutane, I wonder how awful 1,4-bis(isocyano)butane must be!

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2. You're Pfizered on May 7, 2010 8:29 AM writes...

Anyone who ever had the pleasure to run an Ugi (http://en.wikipedia.org/wiki/Ugi_reaction) will know the joy that is isocyanides.

If you stick with the higher molecular weight ones they'll stink, but don't permeate much out of a fume hood. That said we still kept these guys double bagged inside our hoods while making our cores.

Brings back some memories for me, that's for sure. Well, maybe flashbacks would be a better description.

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3. RB Woodweird on May 7, 2010 9:10 AM writes...

"the odor pervaded the laboratory and adjoining rooms, deadening the sense of smell and producing in the operator, and in others, severe headaches and nausea"

Reminds me of my PI. You could often smell him coming down the hall.

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4. Hap on May 7, 2010 9:23 AM writes...

An old organic chemistry text I had described the difference in product when Sn2 reactions were performed with silver and sodium cyanides, the former giving (large amounts of) isocyanides while the latter giving cyanides. "Nauseating" was the adjective I remember.

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5. Maks on May 7, 2010 9:28 AM writes...

When I was a student I worked for a company which was famous for doing all kind of Ugi-like reactions. The isonitriles were stored in a seperate fridge which had its own chemical hood. Yes, the smell is horrible, it is a chemical smell in the sense that it doesn't remind you of anything natural, we all know what butylamine and butyric acid reminds us of, but the smell of isonitriles doesn't have any natural counterpart.

A small story from the same company: One of the biologist went to a theater show after work and left here evening dress in one of the lockers near the chemical department. Unfortunately it was the day of a large scale synthesis (several grams of Ugi product). In the theater they told her politely too leave after several people complained about the unbearable smell.

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6. LeeH on May 7, 2010 9:54 AM writes...

In a previous life I was making aromatic isonitriles for the production of Tc1+ isonitriles as imaging agents. I was unaware of the horrible smell. I made the mistake of making phenyl isonitrile from 10 grams of aniline. The smell stayed with me for days. From then on, I used phase-transfer chemistry to produce small amounts of compound - this minimized the handling of product.

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7. Dark-Star on May 7, 2010 10:12 AM writes...

Nice to see an update to the "things I won't work with" line at long last! I and other non-chemists thoroughly enjoy these pieces.

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8. Brendan on May 7, 2010 10:12 AM writes...

Maybe I need to redraw this then:

http://chemscrapes.blogspot.com/2009/02/pooeeee-was-that-you.html

apologies for the shamless self-promotion.

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9. darwin on May 7, 2010 10:28 AM writes...

I am not a chemist, but the sophomoric humor of opening B-mercaptoethanol near labmates never got old.

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10. anon the II on May 7, 2010 10:46 AM writes...

To Brendan:

I have to say that if posting the same thing seven times doesn't amount to "shamless self-promotion", nothing does.

shamless?

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11. Brendan on May 7, 2010 10:57 AM writes...

Agreed - the 7 (or more) postings was completely innocent and I asked to have the excess removed.

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12. Charlie Murphy on May 7, 2010 11:36 AM writes...

In the heyday of Combi-Chem, I ran a few libraries with Isocyanides. But, the only way to ensure they weren't degraded was to collect FT-IT spectra on the starting materials. Imagine my joy, sitting in the analytical lab preparing isocyanide films onto ZnSe...40 spectra later, I could taste the stuff!

Thankfully, the FT-IR was in a fume hood.

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13. J-bone on May 7, 2010 11:45 AM writes...

One of the grad students in my lab used to think it was funny to rotovap BMS because we'd all complain so much about it. He'd retort "Oh, I use it so much I don't even notice the smell anymore." Coincidentally, this particular grad student had fragrant BO and we were forced to buy an air freshener for our office to cover up the scent of him. On particularly warm days the battle between his armpits and the flowery concoction in that air freshener could have killed one of those mining canaries.

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14. J-bone on May 7, 2010 11:52 AM writes...

One of the grad students I worked with thought it was funny to rotovap BMS and dispose of it in the common waste bottle rather than a separate one in the hood because we'd complain about the smell. He'd retort "Oh, I work with the stuff so much I don't even notice the smell anymore."

Coincidentally, this particular grad student also had fragrant BO and we were forced to buy an air freshener for the office to cover up the smell of him. On particularly warm days the battle between his armpits and the flowery concoction in that air freshener could have killed one of those mining canaries.

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15. Hap on May 7, 2010 12:00 PM writes...

Oh, his future employers are going to love him. After sixty hours a week in a lab, I'd be looking out for garrottes if I were he.

One of the post-docs in another lab didn't bother to bathe but every week or so - the question would be whether that, his self-absorbedness, or his ability to leave thionyl chloride on the rotovap (no, not in a hood) was his least endearing trait.

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16. Hap on May 7, 2010 12:08 PM writes...

Oh, his future employers are going to love him. After sixty hours a week in a lab, I'd be looking out for garrottes if I were he.

One of the post-docs in another lab didn't bother to bathe but every week or so - the question would be whether that, his self-absorbedness, or his ability to leave thionyl chloride on the rotovap (no, not in a hood) was his least endearing trait.

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17. CanChem on May 7, 2010 12:29 PM writes...

We had a PhD from Pakistan on our floor who smelt like showering was blasphemous, yet got ready for prayers every day by washing his feet in the only non-lab sink on the floor. I never thought you could get dirtier by washing your hands till the day I was next in there after him. Really a treat of a person to share facilities with. His other notorious maneuver was pour his excess benzenethiol down the drain. Can't say I miss that either.

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18. Sili on May 7, 2010 4:08 PM writes...

Oddly enough I don't actually recall whether I made an isonitrile ore not, but it was one of the tests we had to do in one of the analytical org chem courses to detect primary amines.

This seems like another good time to flog Excuse me, sir, would you like to but a kilo of isopropyl bromide. The author made something like 200 ml methylisocyanide for an academic lab. He reports hearing angels sing before having to reconvalesce for months (I think).

First thing the post doc did upon receiving the compound was drop one of the bottles on the floor.

Permalink to Comment

19. Hap on May 7, 2010 4:38 PM writes...

14: I'm thinking you all needed to watch MASH more. On one of the episodes, two of the main characters refused to bathe until their roomie was purged of his French horn. They were publicly hosed down with soap and water (with the mentioned horn being flattened by a Jeep).

I think that might be an effective way to send the message that one needs to bathe more often, particularly if performed in, say, January in Urbana-Champaign. It's not like anyone in grad school expects social decency anyway (otherwise the putz would have learned to shower).

Permalink to Comment

20. Karl on May 7, 2010 4:43 PM writes...

#18: I thought it was methyl iodide. I'll have to go back and look. "Excuse me..." is an excellent read, made even better by the incredulous looks one gets when asked what one is laughing at!

Permalink to Comment

21. Slurpy on May 7, 2010 5:10 PM writes...

My former undergrad research group has been synthesizing phenylisocyanides for several years now. They are pretty horrible things normally, but at one point one of the reactions went awry, and we had to evacuate the lab, we were all choking so badly. Perhaps the student inadvertently made one of the lighter-MW species. . .

Permalink to Comment

22. widget on May 7, 2010 5:55 PM writes...

Derek--this is a another chapter for your book! Very funny post! Apropos of that,we had a post-doc in the lab years ago who took a bottle of B-mercaptoethanol from the freezer and proceeded to microwave it to thaw it out.. wow--cleared the lab.

Permalink to Comment

23. Sili on May 7, 2010 6:21 PM writes...

Karl, thinking about it I think you're right that it was indeed MeI that poisoned him, but I still think it was in the process of preparing MeNC - which them was promptly spilt by the customer.

Permalink to Comment

24. Alkaloid on May 7, 2010 6:34 PM writes...

I discovered the hard way, while making 20 g of an isocyanide, that POCl3 doesn't hydrolyze at 0 deg C. My sep funnel turned into a geyser, and I just held on for dear life as it sprayed into my hood. I had the sash low enough that it only got on my arms...

Permalink to Comment

25. Bob on May 7, 2010 9:02 PM writes...

When I was working in industry the other group in the lab were doing Ugi reactions (lots of them and on multi-gram scale). They were pretty good at keeping everything in the fume hood but the outside exhaust was aimed at the air intake of the administration offices across the road. Needless to say accounts didn't like that and the group had to work nights.

I would love to go all CSI and find out what compounds the accounts office is contaminated with.

Permalink to Comment

26. CanChem on May 7, 2010 9:14 PM writes...

@24 - ah yes, POCl3... it was a problem often enough where I work that we all had to sit through an exceedingly long and dull training session on quenching.
@19 - that was a classic episode, especially the replacement "instrument" offered as a goodwill gesture. With a sufficiently multinational workforce at work that this could be a problem they've circumvented this by more of the same training, demonstrating the incredible technology of the toothbrush etc...

Permalink to Comment

27. Revin on May 8, 2010 3:36 AM writes...

I work in the oil industry... Sorry reddit. We use barrels of Butyl mercaptan to make natural gas have that rotten eggs smell (Pure natural gas is odorless). You can literally smell a few drops of it from over a mile away. The concentrated smell will make you very sick, trust me. One drop on your clothes, and no dates for a month. Not that I need dates, I have reddit NSFW.

Permalink to Comment

28. GladToMoveToProcess on May 8, 2010 8:07 AM writes...

Ah yes, Ugi reactions - we called them Ugh-i's.

This caused me to look up an article I read decades ago on synthesis of vinyl isocyanide (JACS, 1968, 90, 3761): "The atrocious odor is followed by a bitter aftertaste." The synthesis was via the explosive isocyanoethylbenzene-sulfonate ("moderately forceful detonation to a black cloud of sticky tar.") Also, from the experimental: "no evidence of explosive character, but heat initiated explosions of methyl and ethyl isocyanide have been recorded." Happily, I've never worked with the butyl!

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29. Joe on May 8, 2010 2:28 PM writes...

Gergel's book Excuse Me Sir, Would You Like to Buy a Kilo of Isopropyl Bromide? is out of print now but there is a PDF copy available at http://library.sciencemadness.org/library/books/gergel_isopropyl_bromide.pdf.

Ignition! by John Clark is also available from the same place.

Permalink to Comment

30. Brooks Moses on May 9, 2010 1:54 AM writes...

Joe @29: Thanks for those links! I've just spent a quite pleasant entire day reading the two books.

Out of curiousity, I did a web search to see whether I could find what had become of Gergel's Columbia Organic Chemical company, and was not at all surprised to find that the main thing left was the EPA cleanup of the old plant site.

Permalink to Comment

31. Sili on May 9, 2010 2:23 AM writes...

EPA cleanup of the old plant site.
So only the first one burnt down?

Heh. I guess he got out in time to keep the externalities external.

Permalink to Comment

32. B Mused on May 10, 2010 3:08 AM writes...

Never, never, never get a project student to do an Ugi reaction, their lab book ends up smelling, they end up smelling, the lab ends up smelling, your office ends up smelling. It does make you think about all those nasties that don't smell and get walked from lab to lab and back again, perhaps best not to think about that actually.

Permalink to Comment

33. China Bonding on May 10, 2010 3:28 AM writes...

I used to work with these in grad school and my first job all the time. Took pride in going up to my lab mates and say..

"Do you smell something?"
"No"
"EXACTLY!!!"

but it took about two years and one lab evacuation to get here. ha!

On several days i was riding my bike home late at
night past the arboretum and I swore I smelled isonitrile from flowers.

Permalink to Comment

34. Harry on May 10, 2010 9:07 AM writes...

The remarks about Butyl Mercaptan brings back a (thankfully) mostly forgotten memory.

The palce i worjked while going to school (and for several years after graduation made as well as used mercaptans in fairly large quantities.

One blustery summer day some employees were tidying up a pile of old (supposedly empty) drums.

One of them turned out to be a (very rusted)drum of butyl mercaptan that had about an inch left in the bottom. When it was moved, the bottom fell out and dumped the butyl mercaptan on the ground.

The stench was pretty incredible, even for those used to woking with the stuff. The wind was gusting up to 40 mph, blowing the smell for miles.

We finally cleaned it up with copious amounts of soapy potassium permanganate soloution, but not before the DEP folks were geting reports of natural gas leaks as far as 12 miles away.

A couple of them showed up at the gate shortly after we reported the spill. The plant manager asked then if they wanted to watch the cleanup. They politely declined and left the scene.

Ah yes, good times...good times.

Permalink to Comment

35. Dark-Star on May 10, 2010 11:29 AM writes...

Joe @29 - Thank you beyond words for that link...I've been looking all over online and RL bookstores for a copy of Ignition!.

Permalink to Comment

36. Sili on May 10, 2010 12:25 PM writes...

Joe @29 - Thank you beyond words for that link...I've been looking all over online and RL bookstores for a copy of Ignition!.
I got it via interlibrary loan.

Though I don't recall where they found it.

Permalink to Comment

37. Matt on May 10, 2010 1:00 PM writes...

@Sili: I got Ignition! and Excuse Me... via interlibrary loan also, then scanned them to share. I had read Ignition! repeatedly as a child, but this blog is where I first heard about Gergel.

I'm glad you enjoyed them :-)

Permalink to Comment

38. Harry on May 10, 2010 3:42 PM writes...

I've known Max Gergel and some of the other folks mentioned in the book for years. Many of them have already passed on and the rest will all too soon.

Not many characters like Max left in an industry gone bland and stale.

Also: Joe @ #29- thanks so very much for the link! I'd tried to find both Max's book and Ignition! for quite a while. Got them saved to my thumb drive reference library for later enjoyment.

Permalink to Comment

39. Dark-Star on May 10, 2010 9:47 PM writes...

Harry, are ANY of them still around? I'm alternately laughing myself silly and being utterly fascinated by reading about their experiences in the early heydays of rocketry, and would thoroughly enjoy to meet one of them, or even just carry on an email conversation.

Permalink to Comment

40. GladToMoveToProcess on May 11, 2010 5:26 AM writes...

Joe@29: Thanks so much for the link. I read it back in the '80s, but had forgotten how funny it was. I met Max Gergel in 1993, when we both were visiting a closed plant to see if there was anything we could salvage from the old equipment. Sadly, didn't have time to hear many of his stories.

Harry@34: Fresh from my postdoc, I was teaching sophomore organic in a big lecture hall in another building. To demo what mercaptans smelled like, I opened a bottle of tert-butyl mercaptan, knowing that the air movement in the hall was away from the lecture bench. It was great to watch the wave of disgust move up through the class. Of course, I hadn't thought that the smell would leave the hall, and had to run all over the building assuring everyone that there wasn't a gas leak. When I got back to the chem building, there was a note in my box insisting that I see the chairman; he suggested quite strongly that I never, EVER do that demo again....

Permalink to Comment

41. Jean-Claude Bradley on May 11, 2010 8:46 AM writes...

We routinely run lots of Ugi reactions in my lab. My students have indeed reported that n-butyl isocyanide is the worst.

Permalink to Comment

42. Hap on May 11, 2010 9:11 AM writes...

#29/#37: Thank you for the links. I didn't have any idea where I would be able to read them (Ignition and Would you like...).

Permalink to Comment

43. Anonymous on May 12, 2010 9:33 PM writes...

You honestly think this will work...you must be tarded.

Permalink to Comment

44. Anonymous on May 12, 2010 9:33 PM writes...

You honestly think this will work...you must be tarded.

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45. Zoe Brain on May 13, 2010 12:02 AM writes...

Our building is downwind from the Research School of Chemistry. Whose fume hoods open on to their roof, and from there, straight into our HVAC system.

Yes, we know what butyl isocyanide smells like. It was three days before we could enter the building again.

Permalink to Comment

46. GladToMoveToProcess on May 13, 2010 6:34 AM writes...

#45: Back in grad school, someone in another group did a large Moffatt oxidation. This burped out 5 or so moles of dimethyl sulfide, which the hood handled fine. In the near dead calm of a warm, humid midwestern summer night, the cloud slithered across the roof, down the side of the building, and across the lawn into the air intake for the accelerator nearby. Fearing a gas leak, the physicists shut down the beam - evidently a Big Deal for them. They weren't amused.

Permalink to Comment

47. Hap on May 14, 2010 2:42 PM writes...

For those of us who have missed partaking in the pleasure of isocyanides, I am trying to obtain an estimate in terms I have experienced - are their odors better or worse than the that of an 18-month old's diaper pail (full or empty - apparently the plastic has become imbued with the odor so it really doesn't matter other than in how easily the pail closes to deny access to the odor)?

Permalink to Comment

48. Patrick on May 23, 2010 2:12 PM writes...

My O. Chem prof wafted a bottle of one once with a student to see what they were like. The student then described it has "Smelling like death" and also said "Get it out of my nose!" Like others have mentioned there is no point of reference for them.

Permalink to Comment

49. Janine on June 15, 2010 4:31 AM writes...

Oh, my God. I just came across this after finding out that the mavelolent, mephitic miasma which recently penetrated my room so badly that I had to move to a new place was caused by my coworker, who's a biochem major, sticking isonitrile in my AC vent as the mother of all pranks. I had to throw away a lot of my things because the stench just would not get out, and the rest I washed again and again... I could not sleep for two nights - literally, not even a two-minute nap - because of the unbearable nausea.

Here's what I had to say about it when it happened:

"What the fuck is that gagging stench periodically blowing from the AC? The nausea has kept me awake all night. Am I developing parosmia or losing my mind? That shit smells the way I imagine a congealed mound of ebola or a rotting alien would. Is there an AC repairman in the house?!"

So your Yeti armpit and Komodo dragon diarrhea comparisons made me laugh. Can anyone really describe this stench?!

Permalink to Comment

50. Janine on June 15, 2010 7:37 AM writes...

And to hap: the smell is INCOMPARABLY worse than any amount of baby dung you could conjure. I'd rather LIVE in a diaper pail than smell this horror for a single minute. Actually, it might improve your relationship with your infant if you took a whiff of this stuff, because you'd actually grow to enjoy the smell of feces by comparison.

Permalink to Comment

51. Pravin Patil on November 26, 2010 6:53 PM writes...

Hi Friends,
It's true that tBuNC bad smell!

But day when I synthesis it no one complaint about any smell in lab, most of time I synthesised in 65-80 gm scales.
if you know it's bad smell - work in good ventilation area good fume hoods, and don't contaminate anything and wash everything with acidic ethanol after reactions so that un-distilled or any traces of isonitrile present in your any reactor is kill by acid and no smell.!

Permalink to Comment

52. Ken Stein on December 8, 2011 11:55 AM writes...

huh.

is it a bad sign that all I can think is 'I wonder if one could synthesize butyl thioisocyanide'?

It is a good thing I am not a chemist, I think.

Permalink to Comment

53. chervarium on January 28, 2012 8:42 AM writes...

I actually plan to convert 5ml of Ph-NH3 to Ph-NC just for the fun of it and watch / film the reactions of the others :). I vividly remember the smell from a microlitre scale reaction (literally pushed 1ml of conc. HCl in methanol into the reaction flask).

Permalink to Comment

54. Atanas Bachvaroff on November 26, 2013 6:43 PM writes...

'M just about to conduct two reactions of conversion of 1-butylamine and 1-propylamine into their respective isocyanides cousins... Dare you, no fume hood :).

Permalink to Comment

55. Garth on February 2, 2014 2:54 AM writes...

Oh good Lord, you've reminded me of the time we worked with butyl mercaptan in undergrad experimental chemistry.

That amazingly vile smell is burned into my memory. We had it inside a glove bag in a fume hood, and still the smell upon entering the lab was enough to knock down a horse!

I had to throw away the folder I used for notes that term, as it reeked unbearably.

Suffice to say that if isoncyanides smell worse than that, I want nothing to do with them.

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