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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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July 26, 2012

Amines and the Landscape of Chemical Stink

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Posted by Derek

I was using a tertiary amine the other day when the thought occurred to me: these things all smell the same. The amine smell is instantly recognizable, fishy and penetrating, in the same way that sulfur smells are also easy to pick out (rotten egg/skunk/burning rubber and worse). But as the triethylamine smell wafted along, I began to think that the sulfur stenches cover a wider range than the amine ones.

Is that so? Sulfur compounds certainly have the bigger reputation for strong smells, and it's well earned. But I still have the impression that various thiols or low-molecular sulfides are easier to distinguish from each other. They all have that sulfur reek to them, but in subtle and ever-varying ways. I sound like a wine critic. Amines, though, tend to be a big more one-note. Fish market, they say. Low tide. I'm not sure I could tell triethylamine from Hünig's base from piperidine in a blind snort test, not that I'm totally motivated to try.

There are exceptions. The piperazines often take on a musty, dirt-like smell that overrides the fishy one. (Note, however, that the classic "dirt" smell is largely produced by a compound that has no nitrogen atoms in it at all). And when they first encounter pyrrolidine, chemists (especially male ones) are generally taken aback. (Now that I think about it, does piperdine smell more like pyrrolidine or like the generic tertiary amines?) The straight-chain diamines should be singled out, too, for their famously stinky qualities. If you've never encountered them, the mere existence of compounds with names like putrescine and cadaverine should be warning enough.

We should probably leave pyridine out of the discussion, since as an aromatic ring it's in a different class. But it has to be noted that its odor is truly vile and alien, smelling (fortunately) like nothing on earth except pyridine. These examples are enough, though, to make me wonder if I'm short-changing the amines when I don't rate them as highly for range and versatility in the chemical odor department. Examples are welcome in the comments of amines that go beyond the Standard Mackeral. . .

Comments (56) + TrackBacks (0) | Category: Life in the Drug Labs


1. OldLabRat on July 26, 2012 9:15 AM writes...

I can distinguish morpholine and azetidine from piperidine, though they aren't odors I'd want to encounter again. How about fluorobenzyl amines? Or benzyl amine itself? Objectionable aromas and definitely distinctive from most simple aliphatic amines.

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2. Triflate on July 26, 2012 9:18 AM writes...

Collidine has a rather unique and persistent odour, easily discernible from pyridine.

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3. Colonel Boris on July 26, 2012 9:23 AM writes...

DABCO has a not completely unpleasant smell. I've worked with putrescine and cadaverine and couldn't smell them, although that was only a few months after I accidentally snorted hot THF vapour. Eleven years later and I still can't smell flowers...

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4. Hap on July 26, 2012 9:30 AM writes...

I haven't smelled it, but pyrrole is supposed to be unpleasant-smelling, as well, but distinct from the tertiary amines (though it really can't act like an amine because the lone pair on N is already occupied with making the ring aromatic).

Piperidine and pyrrolidine are secondary - do they have different odors than diethylamine, for example? (I have heard pyrrolidine does, but I don't know about piperidine.)

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5. Chemjobber on July 26, 2012 9:39 AM writes...

I'm grateful that other people have noted pyrrolidine's unique odor.

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6. H2NOTBS on July 26, 2012 9:40 AM writes...

My lab in grad school used tons of O-TBS-hydroxylamine which is a special combo of grassy/earthy aroma from the TBS group and decaying fish from the amine portion. We had debates in the lab since some people enjoyed the smell while others thought it was vomit inducing.

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7. q on July 26, 2012 10:14 AM writes...

does pyridine do anything to the male reproductive system?I hv read conflicting reports...

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8. Pig Farmer on July 26, 2012 10:24 AM writes...

Phenylhydrazine, as I remember, has a hint of nitrogen dioxide about it (maybe it's an oxidation impurity that causes that). I actually find the smell of nitrogen dioxide in low concentrations quite pleasant, a bit halogen-like.
Pyrrolidine and cadaverine smell about the same to me, which is to say a distinctly -ahem- masculine aroma. I've smelt rotting flesh before, and it was all I could do not to throw up on the spot. I've worked with 2-thiophenemethanethiol before, and at high concentrations it is revolting, but at lower concentrations (again probably with oxidation-related impurities) smells a bit like freshly-ground coffee.

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9. Hap on July 26, 2012 10:27 AM writes...

2-furanmethanethiol's used as a flavoring agent (I think for coffee) - a woman I know who was doing analytical work was exposed to a lot of it. It's not really good for you, at least in large quantities.

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10. SGP on July 26, 2012 10:37 AM writes...

I've worked with putrescine, it's not pleasant. To me, pyrrole has a very similar odour.

I've made a few acid hydrazides too. Very different from amines, but still not very nice, but a good indication of a successful reaction - much like making aldehydes.

I would like to point out that I don't intentionally sniff my reaction mixtures as a means of following reaction progress.

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11. Rock on July 26, 2012 10:37 AM writes...

To answer your original question: yes, I think you are short-changing the amines. Thiols may appear to be more distinguishable because most of us tend to limit our exposure to them as much as possible. The ones we do use tend to be fairly diverse in structure. Thiophenol vs methyl mercaptan or 1,2-ethylene dithiol for example. Can you say for sure that you would be able to tell apart t-butyl, isobutyl, cyclopentyl, or cyclohexyl mercaptan?

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12. petros on July 26, 2012 10:39 AM writes...

Skatole is used, at low concentrations, in fragrances! But it is an indole rather than an aliphatic amine

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13. newnickname on July 26, 2012 10:48 AM writes...

@7: According to 'Solvents in Common Use: Health Risks to Workers' (Royal Society of Chemistry, 1988), it is a myth that pyridine causes male sterility. Pyridine does not affect men's reproductive powers in any way. Of course, there might be new data since 1988. I LIKE the smell of pyridine but I try to avoid it.

While I'm here ... I USED to know the answers but couldn't find them in a quick search of the web.

What is the major chemical that causes the recognizable odor of freshly mown hay?

Likewise, what is the odor of freshly mown grass?


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14. ScientistSailor on July 26, 2012 11:02 AM writes...

Notice how similar functional groups have similar smells? Ever wonder how molecules with vastly different shapes have have nearly identical smells? What instrument would a chemist use to detect specific functional groups? IR maybe? For an alternate theory of how olfactory receptors work read Emperor of Scent by Chandler Burr or watch the TED talk here:

Here's the punchline: decaborane (B10H30) smells like garlic...

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15. Chemjobber on July 26, 2012 11:11 AM writes...

Freshly mown hay? Isn't that phosgene?

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16. Derek Lowe on July 26, 2012 11:17 AM writes...

Freshly cut grass smell is largely due to coumarin, I think. See here:

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17. MatSci on July 26, 2012 11:18 AM writes...

My wife worked with a leaky cylinder of triethylamine during grad school. She reeked of rotting fish every day and I made her shower as soon as she got home. OTOH, all she wanted to do was eat seafood.

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18. Organometallica on July 26, 2012 11:30 AM writes...

One thing that I've noticed is that sulfur compounds and amines smell worse/different when mixed together (as in the workup of any DMSO based alcohol oxidation), than when you smell them separately. In the mix, the dimethyl sulfide overpowers the amine smell to me, but it definitely smells different than pure dimethyl sulfide.

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19. Dr. Z on July 26, 2012 11:45 AM writes...

Phosgene also smells like freshly mown grass. And I don't mean that the smell of freshly mown grass is due to phosgene.

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20. agsone on July 26, 2012 11:57 AM writes...

I've detected a bottle of pyridine being moved between hoods ten yards away but have barely noticed cadaverine while working with it myself.

N-methylmorpholine has a definite bouquet of ripe tuna.

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21. AndrewD on July 26, 2012 11:59 AM writes...

Dr Z @19, I have found the smell of phosgene to be akin to Emulsion Paint (at least UK versions of Emulsion Paint}. This did give rise to sensations of panic when the labs were painted whilst I was using kilogram quantities of phosgene!

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22. JH on July 26, 2012 12:07 PM writes...

I once mistook a bottle of N-methylpyrrolidine for N-methylpyrrolidone and tried to use it to dissolve some polymers. The smell is surprisingly strong for an amine. Even co-workers outside the lab noticed it.

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23. Pig Farmer on July 26, 2012 12:10 PM writes...

Did a quick search on google and found this:

Apparently the freshly cut grass odor is caused by "green leaf volatiles" such as cis-3-hexen-1-ol

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24. BCP on July 26, 2012 12:15 PM writes...

@newnickname I always associated the fresh cut grass aroma to anisaldehyde

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25. Fred on July 26, 2012 12:55 PM writes...

"Skatole is used, at low concentrations, in fragrances! But it is an indole rather than an aliphatic amine"

Interesting! Indole itself stinks to high heaven, IMHO. Reminiscent of burning rubber to my nose.

BTW, re amines: aldehydes and acid chlorides tend to be easily "ID'ed" as aldehydes and acid chlorides, as well.

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26. DannoH on July 26, 2012 1:08 PM writes...

I love the topic of the smell of thiols and amines. Having had a close encounter with a large quantity of thiodiglycol and its chlorinated derivatives (15 years ago), nothing smells right to this day. My favorite is freshly ran over skunk; smells like someone peeling oranges, which is not entirely unpleasant.

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27. Derek Freyberg on July 26, 2012 1:26 PM writes...

I seem to recall reading, many (30+) years ago, that the stink of skatole (purportedly the odoriferous compound in feces) was not skatole itself, but impurities, and that highly purified skatole didn't stink. Assuming this is so, I wonder how many of the nasty-smelling compounds under discussion here are actually themselves truly nasty-smelling, or just contaminated with something more foul.

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28. Karel Capek on July 26, 2012 2:43 PM writes...

Please don't give the amines short shrift.
Methyl anthranilate -- oh, such a nice grapey efflorescence.
From wikipedia:
"At full concentration, it has a fruity grape smell; at 25 ppm it has a sweet fruity concord grape like smell with a musty and berry nuance."

And it is food grade! Come on, let's feel some love for amines. Drink the Kool Aid!

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29. Hap on July 26, 2012 2:47 PM writes...

26: I thought that run-over skunk smelled to me like really strong lemonade (with the pulp and everything), but my wife does not concur. I'm not really thinking I want to experience skunk odor in other arenas, though.

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30. Sunny&Warm on July 26, 2012 3:28 PM writes...

To put a point on the comments of #4&8. I once had a particularly attractive female coworker who upon smelling N-methylpyrrolidine for the first time couldn't help herself from exclaiming "that stuff smells like cum!". This resulted in much ammusement and titilation for the rest of the department.

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31. Anonymous on July 26, 2012 3:29 PM writes...

group is bad anyway, phosphines or arsines aren't any better smellwise than amines.

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32. Hap on July 26, 2012 3:36 PM writes...

Yeah, but we can smell amines without them either erupting into flame or killing us. Or both.

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33. Dr. Z on July 26, 2012 3:42 PM writes...

AndrewD @21, I personally never had the chance to smell it (fortunately!) but in the safety trainig for our site, this is what they say it smells like.

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34. flavor on July 26, 2012 4:08 PM writes...

@newnickname and derek. When you mean fresh cut grass while it is still green and young and not yellow the smell is hexanal. Coumarin is indeed more hay-like.

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35. newnickname on July 26, 2012 4:54 PM writes...

Thanks for the grass and hay odorants references.

@9: Another coffee flavor / odor chemical is 3-methoxy-2-methyl-2-cyclopentene-1-one [3883-56-5]. I had to make a batch of that for some old project. And I don't like coffee or the STRONG smell of coffee.

One of RB Woodward's earliest papers is on "The Staling of Coffee. II" Prescott, S. C.; Emerson, R. L.; Woodward, R. B.; Heggie, R. Food Research, 1937, 2, 165-181. "Staling in roasted coffee cannot be attributed wholly to oxidation and consequent rancidity of the fats. The fats are not responsible for either the flavor or aroma. Roasted coffee contains about 3% chlorogenic acid, a compd. which gives off CO2 on heating to form p-vinyl guaiacol. Guaiacol is also easily oxidized. There is some assocn. between guaiacol and its derivs. and coffee odor. Terpenes are also responsible for some of the taste and odor. Furfuryl alc. is present in roasted coffee but not in aq. coffee exts. which have been prepd. from aged roasted coffee. When freshly distd., it is sol. Attention is directed to the work of Staudinger and Reichstein (C. A. 24, 2213) who attribute the flavor and aroma to S-contg. compds. of the heterocyclic mercaptan series of the general formula ASH or derivs. thereof. A list of org. compds. isolated from roasted coffee is given."

As I recall, they make reference to a long chain C30 polyene and correlate it to the formation of steroids in aged coffee beans. Without any proof, I like to speculate that it might have been squalene and that would be another very early Woodwardian insight into the possible biogenesis of steroids from squalene.

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36. Anonymous on July 26, 2012 8:01 PM writes...

As a somewhat naive intern at Eastman Kodak in 1980, I worked for a synthetic chemist who did not go a week without using phosgene to couple one part of a dye to another part. The first time he handed me the bottle of phosgene (12% soln in toluene), he explained that “if you detect the odor of freshly-cut grass, you are as good as dead. So just hold your breath when you open the bottle to weight out XX grams.” I plaintively asked if there was something like a gas mask that I could wear, just like the World War I soldiers who might have come across this one-time war gas. The boss laughed and said no.
The first time I used the phosgene I managed to hold my breath (barely). The second time, I did detect the faint odor of grass. I thought I was going to die.
But I didn’t. Apparently you can breathe a tiny bit in and live to tell others about it.

The next year I went to work at Dow. My first week in the lab, I was handed a respirator and told I was to wear it when working with any inhalation hazard. I turned to my new boss and said, “You mean they still make gas masks? Does this mean I won’t have to hold my breath?” He looked at me like I was an idiot.

I never worked with phosgene again. For a war gas, it does have a rather pleasant scent, however.

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37. RL on July 26, 2012 8:03 PM writes...

As a somewhat naive intern at Eastman Kodak in 1980, I worked for a synthetic chemist who did not go a week without using phosgene to couple one part of a dye to another part. The first time he handed me the bottle of phosgene (12% soln in toluene), he explained that "if you detect the odor of freshly-cut grass, you are as good as dead. So just hold your breath when you open the bottle to weight out XX grams." I plaintively asked if there was something like a gas mask that I could wear, just like the World War I soldiers who might have come across this one-time war gas. The boss laughed and said no.
The first time I used the phosgene I managed to hold my breath (barely). The second time, I did detect the faint odor of grass. I thought I was going to die.
But I didn't. Apparently you can breathe a tiny bit in and live to tell others about it.

The next year I went to work at Dow. My first week in the lab, I was handed a respirator and told I was to wear it when working with any inhalation hazard. I turned to my new boss and said, "You mean they still make gas masks? Does this mean I won't have to hold my breath?" He looked at me like I was an idiot.

I never worked with phosgene again. For a war gas, it does have a rather pleasant scent, however.

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38. anon on July 26, 2012 8:26 PM writes...

I once tried to activate 75 g of isobutyric acid with HBTU using 3 eq of pyrrolidine as a base. My plan was to make a thioester, all under a personal atmosphere of diethyl ether. Unfortunately, I passed out during the addition of benzylthiol to the reactions mixture and was never able to isolate the final product.

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39. schinderhannes on July 27, 2012 2:35 AM writes...

Its funny how you Americans sometime talk "around" things out of some strange uptightness.....

You could have made things a lot easier by mentioning that there is an aliphatic polyamine named spermine LOL

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40. srg on July 27, 2012 3:18 AM writes...

When working for a CRO in the UK, I once had to prepare a tris-tosylate (via the tris azide!!!) from 1,1,1-tris-(aminomethyl)ethane (or isle of man amine thanks to its three amine legs). The "manliness" of the smell of this compound was utterly shocking. Containment of the few grams of material was bottle, sealed in polyethylene bag (x2) in a sealable polypropylene container itself sealed in a bag.

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41. anonymous on July 27, 2012 5:05 AM writes...

...and of course, let's not forget spermidine (tee hee hee) !

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42. Cymantrene on July 27, 2012 7:12 AM writes...

Recently i work with polyunsaturated fatty acid derivatives. They all smell the same, just like cod liver suspended in linseed oil. It does not matter, what group is at the alpha-end, carboyxilic acid, alcohol, silylated alcohol, ester, whatever), the isolated double bonds rule the smell.

Anyway, i accustomed to the smell of some bad molecules: smell of cyclopentadiene, thioanisol or isonitriles simply means the smell of a properly working lab for me. What i can't stand is benzylalcohol. Not that bad at first, but it sticks in the mouth for hours. Horrible.

Skatole has a smell of jasmine in proper dilution. I smelled some cheap rinse, they were labelled to have jasmine fragrance, and using them on clouds really gave the smell of jasmine. However, the smell of the rinse concentrate was a borderline between faeces and jasmine.

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43. GladToMoveToProcess on July 27, 2012 7:50 AM writes...

Re #13, 42 and others: I once met someone who claimed there are two kinds of people: those who like the smell of 1-butanol but hate pyridine, and those with the opposite reactions. (I'm definitely in the "like pyridine, hate butanol" camp - butanol nearly sickens me.) I've tested this hypothesis with many students, and it seems to hold, with about 3/4 in the "like butanol" camp. Anyone else noticed this?

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44. MatthewK on July 27, 2012 8:14 AM writes...

You realise of course that how something smells is not intrinsic to the substance itself, but just an indication of how it stimulates the particular receptors we have in our olfactory bulbs. Just like we see a tiny sliver of the e-m spectrum, we detect a few qualities of chemical structure with a few hundred chemosensitive receptor structures. Mice, for example, have about three times as many olfactory flavours available to them.
So the smelliness or the variety of smells in a group of compounds is a more-or-less coincidental match between their structures and the things that smell evolved to detect, such as palatability, putrescence, etc. - information we need to survive. It's nothing fundamental.

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45. Organometallica on July 27, 2012 8:36 AM writes...

This talk of phosgene reminded me of this poster I saw on wikipedia for warning soldiers in World War II about phosgene.

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46. Organometallica on July 27, 2012 8:42 AM writes...

All this talk of phosgene smelling like cut grass reminded me of this poster I saw on wikipedia that was for warning soldiers in World War II about the signs of phosgene.

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47. John Spevacek on July 27, 2012 11:14 AM writes...

I am always amazed though by how amine can cancel a thiol.

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48. KOH on July 27, 2012 11:33 AM writes...

Piperidine is definitely more like pyrrolidine than the other alkyl amines. I am a male chemist with a (rather embarrasing) specific asnosmia for that distinctly male odor; I smell neither piperidine nor pyrrolidine. I literally smell nothing when presented with these (or similar) odors. Triethylamine, Hünig's base, et al., on the other hand, are all giant fishbombs to my nose.

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49. The Iron Chemist on July 27, 2012 1:08 PM writes...

2-Pyridinethiol is surprisingly not stinky.

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50. ScientistSailor on July 28, 2012 7:24 PM writes...

@44 Your first sentence is self-contradictory. How a molecule stimulates the olfactory receptors IS an inherent property of that molecule. That's why when you say this smells like fresh-cut grass, I, and everyone else, knows exactly what you are talking about.

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51. Bob Honclbrif on July 30, 2012 2:50 PM writes...

First time I used that stuff I was bracing myself for the hell-child of two terrible stinks, but it only smells faintly of garlic. The explanation I've heard is that mercaptopyridine exists mainly as the thiopyridone tautomer.

In other news, I've never thought that putrescine was really that deserving of its name. It smells a little semen-y, but not of concentrated death and decay. Also, smokes like a mofo when you try to pipet or pour the liquid.

Near my building there used to be some flowering trees (hawthorn I think) that absolutely reeked of polyamines when in bloom. Probably why they were cut down as part of a renovation project, even though they were nowhere near where the renovating was happening.

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52. LambdaE on July 30, 2012 8:08 PM writes...

The only amine (that I can think of) I have smelled is 1,6-diaminohexane, and it's not that bad. It doesn't remind me of fish at all, rather a peppery odor, and not a very strong one. It's also a crystalline solid unlike many of the amines previously mentioned.

I'll have to make some pyridine soon. A very useful compound, but I also have to smell it - to see if I'm in the "hate" or "love pyridine" camp!

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53. anonymous1 on July 31, 2012 1:45 AM writes...

@43: I hate both pyridine and butanol. There's something about the C4 compounds that really stinks: n-butylamine, n-butyraldehyde, n-butanol, and of course, n-butyric acid. All just a little more pungent than nearby strait-chain relatives. (But of course some of the branched chain acids really stink.) Pyrrolidine doesn't smell much like an amine to me. I kind of like the smell of skunk on a summer evening, as long as it's not too strong--a nice rural odor. And on the subject of skunk, there are some allylic chlorides that smell like sulfides to me. As for the combination of sulfides and amines: I always thought that the particular odor of a swern oxidation came not only from the dimethylsulfide and triethylamine, but also chloromethyl methyl sulfide that can form as a byproduct. Also, I once scaled up a Swern oxidation with a volatile aldehyde product. During process optimization, we tried using trimethylamine (gas cylinder) instead of triethylamine, with the idea that we could remove it more easily. Boy, did that stink, far worse than TEA, and by the way, the Swern didn't work as well with it. I will end by saying that two chemicals that truly nauseate me are ethyl isocyanoacetate (and really any isonitrile) and the compound that you get when you mix acetone with ethanethiol (probably the dithioketal of acetone). It smells like concentrated essence of cat urine.

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54. anonymous on July 31, 2012 1:06 PM writes...

Ah, pyridine.
I worked in a synthetic lab once and remember that for me, pyridine had three distinct smell/concentration regimes.
In great dilution, it had a pleasant vanilla whiffiness about it. 2,2'-dipyridyl has that smell in spades ... it smells gloriously like Christmas cookies to me. In fact I sto *ahem* relocated the dipyridyl bottle from the stockroom so that i could crack the cap and take a nostalgic sniff once in a while.
At mid-concentration, pyridine assumed the full foul round "alien dead meat" smell that is considered characteristic.
At really high concentrations, it had the sharp splvent stink of tetrahydrofuran ... in fact I can't tell a massive faceful of either solvent apart.
In terms of odors I learned to hate: tosyl chloride. When i started with it, I hardly noticed it. After a couple of years, i found it so retchingly offensive I had to weigh even tiny portions in a hood, with a big alcohol/ammonia squeeze bottle handy.

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55. anon on August 1, 2012 8:46 AM writes...

The vibrational theory of olfaction has yet to be experimentally proven. Hence, I don't buy it at all.

@44 The exact same argument can be made about drugs.... so what is your point?

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56. Nitric Acid on January 10, 2013 3:34 PM writes...

I've always heard about phosgene smelling like "new-mown hay", which is (of course) a thing I've never actually smelled in my life. While disposing of an old chloroform still, however, I detected an unpleasant odor, and though, "Ew! This smells like the bottom of an old lawn mower!"

Then it clicked.

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