The Smell of Chemistry in the Morning

“May I present to you: the Smellmaster 9000.”

One of my professors once told me quite categorically that if you can smell someone’s chemistry, they are doing a bad job.  His point was that any chemist worth their salt would be doing stinky things in properly-maintained fumehoods, and never exposing themselves or their colleagues to whatever unholy stenches their reagents possessed.  To a certain extent, I agree with him.   I’ve never had to brave the foul miasmas of things like isonitriles and I never plan to, but if that eventuality arises you can be sure that I’ll do that in a fumehood.  Or possibly in a fumehood inside a fumehood.

But for most people who work in chemistry labs, the occasional waft of bizarre odours is not unusual.  Sometimes it’s even useful: a project I was doing a while back involved the consumption of phenylacetylene (which has quite a characteristic odour, somewhat similar to styrene), and doing a careful wafting test actually proved to be about as effective for determining a reaction’s completion as a TLC.  Not that everyone should smell-test all their reactions!  But the point is that working as a chemist tends to give you the peculiar ability to identify reagents by their smell, simply through familiarity caused by repeated low-concentration exposure.  The sharp fruitiness of ethyl acetate, the almond sweetness of benzaldehyde, the bitter nose-wrinkling sting of pyridine…there’s an entire world of pleasant and unpleasant smells in the world of organic chemistry, and just like everyone starts to accumulate their favourite and most-hated customers when working in retail, I have a suspicion that each chemist has their own personal list of best- and worst-smelling chemicals.  I’m sure we all remember high-school chemistry, and detecting the rancid butter stink of carboxylic acids down the hallway when people did their esterification lab, then getting to smell the artificial rum, banana, and mint flavours that resulted when they did the lab themselves.

Smells form very strong memories, and I thought it might be nice to share some of my own memorable olfactory experiences in chemistry, and see what others had to add to the conversation.

Note: I should emphasize that I did not go around shoving my nose in bottles of these chemicals, nor should you.  Please be careful with all chemistry you do, and always do it in a fumehood for your safety and that of your colleagues.

1. Pentafluorophenol.  I did some solution-phase peptide couplings a while back and had to weigh this stuff out on a regular basis.  Its physical properties leave something to be desired (so hygroscopic it appears to melt as you weigh it, highly volatile, and not exactly cheap), but its odour is something I don’t think I will ever forget in my life.  It smells almost like some non-existent overripe fruit, almost cloying in its sweetness, lingering for quite some time after being capped and removed from the weighing area.  It’s one of those smells that I wouldn’t say I enjoy, but it’s so intriguing that I also can’t say that I dislike it, either.

2.  Chloroacetyl chloride.  I love the smell of vinegar to begin with, but this stuff takes it to a whole other level.  Doing carbohydrate chemistry introduced me to this molecule and though I haven’t smelled it since it’s another absolutely unforgettable one.  It has a very similar smell to regular old acetic acid, but with this sort of appalling greasiness to it that I always found interesting and somewhat appealing.  Similar to this is trufluoroacetic acid, but not only is TFA more dangerous, its odour is so sharp at even low concentrations that it is on the whole quite unpleasant.

3. Methylindoles.  Very recently I had the regrettable task of doing some indole chemistry, and I am glad to have it behind me.  Though definitely not anywhere near the top of the all-time worst chemical smells, there is something about N-methyl, 1,3-dimethyl, and especially 2-methylindole that I cannot stand.  I had the incredibly poor judgement to open a vial of the 2-methylindole outside my fumehood and it’s safe to say that I will never make that mistake again.  Similar to that urinal-cake/mothball smell of naphthalene, yet infinitely more revolting, the smell of these compounds will linger for up to a couple hours if spilled or left open outside a fumehood (even after being cleaned up and/or capped).  The 3-methyl variety of indole, which I’ve also had the extreme displeasure of working with, is alternatively known as skatole, because it smells like…well, I think you get the idea.

4. Eugenol. Similar to the esterification lab, the extraction of this compound from cloves is a very common organic chemistry experiment in the Canadian university chemistry lab.  There’s nothing really surprising about it, because you’re extracting one of the nice-smelling compounds from an already nice-smelling spice, but I think it’s the transformation that makes this smell so interesting to me.  You go from cloves–a rich, heady smell that’s always made me think of a spicy chocolate Christmas tree–and when you isolate the eugenol the complexity vanishes, and you’re left with a single note (predictably).  The smell reminds you of cloves, but only in the way that esters remind you of their fruit counterparts.  The smell is completely one-dimensional, and though pleasant has none of the punch that freshly ground cloves do.  There’s just something about experiencing this one particular element of cloves’ smell, completely isolated, that I love.

So, fellow chemists, what olfactory adventures have your studies taken you on?  Can anyone come up with a plausible description for the legendary odour of isonitriles?  Does anyone have nuanced critiques on the qualities of sulfides and thioethers?  Have there been detailed qualitative studies on the nasal SAR of various benzaldehyde derivatives?  Or are there people out there with intimate knowledge of specific compounds whose odours they find irresistible?

Remember, knowledge is power.  And the nose knows.

6 Comments

  1. Try using low mw phosphines (PMe3, PEt3, etc) in a glovebox and not having the lab smell. Every time the antechamber is opened, that corner (okay half) of the lab smells of phosphines.

    We even had a setup so that we could evacuate the chamber and refill with clean lab air, but enough phosphine is left even after 3 cycles of that (I imagine we’re talking fairly low ppb levels at this point).

  2. You had a whiff of pyridine? Good luck with reproducing…

    I have the, ahem, pleasure of working with thiols regularly, and trimethylamine semi-regularly. The thiols have given the area around my fume hood a constant but slight odour, which is lovely, and no amount of bleaching seems to fix. (Incidentally, once you bleach hexanethiol it smells a bit like week-old cut grass)

    Trimethylamine is something else. I distil it from an aqueous solution – everything is sealed and contained in a fume hood, the solution is stored in my fume hood, and the liberated gas is kept at -78 in a Schlenk tube until use. The only outlet from the apparatus runs through a bleach solution. I perform the distillation with my hood on emergency mode (high air flow and irritating beeping). Despite these precautions, any time I do this the entire lab gets a fishy odour for the rest of the week.

  3. Thioureas. Pure flatulence.

  4. Mmm, eugenol. One of my favourite chemical smells <3 and better than vanillin or p-anisaldehyde, just because you don't get to smell it as often.

    I hate the smell of ethyl acetate, and always have. Baffles me how people actually enjoy that!

  5. I did some solution-phase peptide couplings a while back and had to weigh this stuff out on a regular basis. Its physical properties leave something to be desired (so hygroscopic it appears to melt as you weigh it, highly volatile, and not exactly cheap), but its odour is something I don’t think I will ever forget in my life. It smells almost like some non-existent overripe fruit, almost cloying in its sweetness, lingering for quite some time after being capped and removed from the weighing area. It’s one of those smells that I wouldn’t say I enjoy, but it’s so intriguing that I also can’t say that I dislike it, either.

  6. I keep hearing about the pure unforgettable vileness of isonitriles, and am intrigued. I know it’s difficult, but can someone give me some indication of what it smells like. Pretend you have to explain it, but try to leave the emotion (pure evil, from hell etc.) out of it so I can vicariously smell this substance!

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