About this Author
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

Chemistry and Drug Data: Drugbank
Chempedia Lab
Synthetic Pages
Organic Chemistry Portal
Not Voodoo

Chemistry and Pharma Blogs:
Org Prep Daily
The Haystack
A New Merck, Reviewed
Liberal Arts Chemistry
Electron Pusher
All Things Metathesis
C&E News Blogs
Chemiotics II
Chemical Space
Noel O'Blog
In Vivo Blog
Terra Sigilatta
BBSRC/Douglas Kell
Realizations in Biostatistics
ChemSpider Blog
Organic Chem - Education & Industry
Pharma Strategy Blog
No Name No Slogan
Practical Fragments
The Curious Wavefunction
Natural Product Man
Fragment Literature
Chemistry World Blog
Synthetic Nature
Chemistry Blog
Synthesizing Ideas
Eye on FDA
Chemical Forums
Symyx Blog
Sceptical Chymist
Lamentations on Chemistry
Computational Organic Chemistry
Mining Drugs
Henry Rzepa

Science Blogs and News:
Bad Science
The Loom
Uncertain Principles
Fierce Biotech
Blogs for Industry
Omics! Omics!
Young Female Scientist
Notional Slurry
Nobel Intent
SciTech Daily
Science Blog
Gene Expression (I)
Gene Expression (II)
Adventures in Ethics and Science
Transterrestrial Musings
Slashdot Science
Cosmic Variance
Biology News Net

Medical Blogs
DB's Medical Rants
Science-Based Medicine
Respectful Insolence
Diabetes Mine

Economics and Business
Marginal Revolution
The Volokh Conspiracy
Knowledge Problem

Politics / Current Events
Virginia Postrel
Belmont Club
Mickey Kaus

Belles Lettres
Uncouth Reflections
Arts and Letters Daily
In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline

In the Pipeline

« If You're Not Excited, Sit Down | Main | Enthalpy and Entropy Again »

October 25, 2010

Settle A Bet

Email This Entry

Posted by Derek

I had an email this morning asking me to settle a bet on lab technique. I'm not sure I know the answer myself, so I figured I'd throw the question out to the readership.

So here goes: in your vacuum cold trap, which I'll assume is cooled by dry ice (and not liquid nitrogen, for the most part), what solvent do you use: acetone or isopropanol? (If you use something else, feel free to add it to the list, but I think you'll be in a distinct minority). As for me, I used acetone back in grad school, but switched over to isopropanol years ago, because I didn't have to change it (or add to it) so often.

Comments (68) + TrackBacks (0) | Category: Life in the Drug Labs


1. The Disgruntled Chemist on October 25, 2010 10:49 AM writes...


Permalink to Comment

2. Brian on October 25, 2010 10:51 AM writes...

I am going to be the fence-sitter on this one. I have used either or and sometimes both. I always had the acetone washbottle in the hood, not always an isopropanol one.

Permalink to Comment

3. Stiv on October 25, 2010 10:53 AM writes...

Either or both - whichever is closer at hand when the trap needs filling...

Permalink to Comment

4. flavor on October 25, 2010 10:53 AM writes...

Haven't used dryice in a while for this but I used mainly IPA when i did. Or a 2:1 IPA:Aceton ratio.

Permalink to Comment

5. Mike on October 25, 2010 10:56 AM writes...

err.... always liquid nitrogen.

Permalink to Comment

6. mas3cf on October 25, 2010 11:03 AM writes...

IPA... lasts longer and has higher heat capacity

Permalink to Comment

7. GladToMoveToProcess on October 25, 2010 11:12 AM writes...

IPA, unless I'm condensing a LOT of stuff pretty rapidly. In that case, the lower viscosity of cold acetone seems to help the heat transfer.

Permalink to Comment

8. ChemistWannabe on October 25, 2010 11:17 AM writes...

I've always used acetone during undergrad...but now at the company where I'm working at, I'm not allowed to use either because of our safety I'm stuck with plain 'ol dried ice for now.

Permalink to Comment

9. vasili on October 25, 2010 11:29 AM writes...

No solvent.

It's greener!

Permalink to Comment

10. stop on October 25, 2010 11:29 AM writes...

i start with IPA and over the course of months i end up with 2:1 water:IPA. at which time i change the solution.

bad technique.

Permalink to Comment

11. Stephen on October 25, 2010 11:30 AM writes...

For my hi-vac trap, acetone in grad school, Isopropanol in my post-doc. I preferred the isopropanol for similar reasons.

Traps aside, what about cooling rotovap condensers? Economically, wouldn't it be cheaper to cool your condensers by running an ethylene glycol line through a chiller? Lowers business costs, and you can pick up good used chillers these days.

Permalink to Comment

12. RM on October 25, 2010 11:34 AM writes...

I don't do much vacuum-trapping currently, but when I was trained, everyone was using acetone. More recently, I've mostly noticed people using isopropanol or ethanol. Some people are appaerently ambivalent and use an acetone/isoproanol/ethanol top-it-off-with-whichever-is-handy mix.

Brian@2 I have used either ...

For a moment I read that as "I have used ether", and had a minor heart attack.

ChemistWannabe@8 at the company where I'm working at, I'm not allowed to use either because of our safety protocol

If you're not getting good performance with "dry" dry ice, there are several low flammability cryogenic liquids (Fluorinert type compounds) which might help. (I've used some in condenser-chilled cold traps, but not with dry ice.) They're comparatively pricey, though.

Permalink to Comment

13. J-bone on October 25, 2010 11:40 AM writes...

Acetone in both grad school and postdoc.

The rotovaps at my postdoc institute use the ethylene glycol cooler that Stephen is talking about, and they're FAR more convenient than having a cold finger that requires constant refilling/cooling (an extra headache here since the dry ice is down one floor).

Permalink to Comment

14. Leighton on October 25, 2010 11:43 AM writes...

I'll chime in with another vote for Isopropanol.

Permalink to Comment

15. sam on October 25, 2010 11:47 AM writes...

I always just siphon gas from a nearby car and use that for the cold trap. Diesel also works.

Permalink to Comment

16. Hap on October 25, 2010 11:48 AM writes...

For my vac line, I used LN2 in grad school. For the high-vac condenser, we used dry ice/isopropanol. I don't know what the difference in flammability is, but probably the lower volatility was the reason.

Permalink to Comment

17. GladToMoveToProcess on October 25, 2010 11:49 AM writes...

If the amount being condensed is small, I agree with #8 and #9 - dry ice by itself works fine. As to #11's question: for a lab-scale rotovap, a small circulating pump in a bucket of ice-water works well. In one job, we had a BIG rotovap (twin 20 Liter receivers, as I recall), with a dedicated glycol chiller and pump setup. Worked well also, but it sure took a while to get things cold when starting it up.

Permalink to Comment

18. Jimmy on October 25, 2010 11:52 AM writes...

Isopropanol. It doesn't evaporate as fast.

Permalink to Comment

19. notmedchem on October 25, 2010 11:53 AM writes...

IPA b/c it's gets nice and viscous. Which is especially necessary in the Florida heat.

Have also seen glycol/water chillers used instead.
Much more economical.

Permalink to Comment

20. Brian on October 25, 2010 12:04 PM writes...

@12 That's funny, except I haven't used diethyl ether in a while.

It's great when you have the funds for a circulator/chiller. When I was in San Diego, it was almost a necessity to use a chiller for reflux condensors and the like. Especially when the water comes out of the tap at 4 C.

Permalink to Comment

21. anon the II on October 25, 2010 12:08 PM writes...

Isopropanol is better. It doesn't evaporate as fast. It doesn't dry your skin out as bad if it spills on you. It smells better to me. It may be less volatile and therefore less flammable, but I did have a former coworker who managed to catch an isopropanol filled rotavap trap on fire. How the hell did that happened? Who knows?

I vastly prefer a dry ice trap to using those chilled recirculators. Evaporation is much faster, less solvent gets past, they take up much less valuable space and I'd debate the environmental impact. At least once a year, someone manages to pour all the glycol on the floor from a bad hose connection and chillers are expensive to run.

Permalink to Comment

22. HelicalZz on October 25, 2010 12:31 PM writes...

IPA. But with a bit of care when the trap is occasional. You eventually get a lot of water in there and ultimately something that will freeze, expand, and break some good glassware.


Permalink to Comment

23. coprolite on October 25, 2010 12:39 PM writes...

I was taught IPA, and that's straight out of Uttar Pradesh right there, it doesn't get much more real than that. Lucknow For Life.

Permalink to Comment

24. sparky on October 25, 2010 12:50 PM writes...

I've been out of the lab for ~5 years or so, but I always used acetone+dry ice in both the high-vac condenser and the rotovap. Always had large amounts of acetone on hand for washing glassware and rarely kept much isopropanol around, so I guess it was more a question of convenience than performance in my case...

Permalink to Comment

25. Nick K on October 25, 2010 1:03 PM writes...

I've always used ethanol with dry ice. Doesn't splash like acetone and smells lovely.

Permalink to Comment

26. startup on October 25, 2010 1:30 PM writes...

While I always use LN2 in my vacuum traps, I was trained to use acetone for -7x °C baths unless alkyllithiums are involves in which cases using IPA is a sensible safety precaution. With time I switched to IPA entirely, since it doesn't smell as much, and can be recycled in rotovap trap.

Permalink to Comment

27. anon the II on October 25, 2010 1:47 PM writes...

to # 24 sparky

Not to be mean, but with a nickname like "sparky", it's probably a good thing that you got out of the lab.

Permalink to Comment

28. anon on October 25, 2010 2:03 PM writes...

Acetone! IPA slowly picks up water as it sits after the dry ice is gone. The IPA/water mixtures really foam up when a subsequent charge of dry ice is added.

Permalink to Comment

29. JAB on October 25, 2010 2:19 PM writes...

IPA in preference, though water absorption by IPA is a problem. Acetone if I want the trap really cold. We use two dry ice traps on rotevaps, one built into the unit and one external. Used to use recirculators but also found them slow to chill, messy, and too big. For vacuum we use membrane pumps with vac controllers. Much better than aspirators or big vac pumps. And quieter...

Permalink to Comment

30. Ali on October 25, 2010 2:25 PM writes...


Permalink to Comment

31. Lacerta Bio on October 25, 2010 2:28 PM writes...

Back in my lab days, we all used acetone. But IPA or dry ice alone make a lot of sense to me.

Permalink to Comment

32. CMCguy on October 25, 2010 2:31 PM writes...

IPA- was suggested as having less inherent flammability and less toxic nature (liver in particular) plus I preferred the smell and did not dry out the skin as much when inevitably exposed. Would change out completely every 1-2 weeks because water content issues cited above.

LN2 was verboten in most places I worked unless special precautions as could trap O2 which when mixed with organics also trapped is an accident waiting to happen.

Permalink to Comment

33. dosser on October 25, 2010 2:35 PM writes...

IPA coz it does not evaporate as quickly or absorb water as much. But acetone forms a smoother slurry with dry ice.

Permalink to Comment

34. Annette on October 25, 2010 3:05 PM writes...

Acetone, because it is always in plentiful supply in our lab.

Permalink to Comment

35. weirdo on October 25, 2010 3:08 PM writes...

IPA, but change it out every two weeks.

Permalink to Comment

36. Ed on October 25, 2010 3:13 PM writes...

Acetone with dry ice was what we used in grad school to cool the trap.

Permalink to Comment

37. Synthetic Steve on October 25, 2010 3:33 PM writes...

Even from my undergrad days, I was taught to use LN2 in a high vacuum trap because one dry ice trap (with solvent) is insufficient. Two dry ice traps are supposed to be better than one dry ice trap, though. I always use an LN2 trap because I value my $3,000 high vacuum pump. I also heard that the vacuum pulls a little bit more when using an LN2 trap, but cannot verify that.

For my rotavaps, I use an ethylene glycol/water chiller to four degrees C, and an additional dry ice/isopropanol cold finger between that and the Welch (9 torr) self-cleaning diaphragm pump to catch the lower boiling solvents like ethyl ether, acetone, and methylene chloride. The ethylene glycol chiller is mysterious, though, in that the recirculating bath fills up and spills over every once in a while. Is water condensing in the chilling bath to cause the periodic floods? This flooding happened more when I had set the recirculating chiller at minus ten degrees C, which is why I suspect that water is the culprit.

Permalink to Comment

38. cientificorojo on October 25, 2010 3:54 PM writes...

I use isopropanol in graduate school. In undergrad, LN2.

Permalink to Comment

39. Anonymous on October 25, 2010 4:26 PM writes...

either before. Use nothing except dry ice the last ten years.

Heard about Biogen's layoffs. Any comments.

Permalink to Comment

40. Chemjobber on October 25, 2010 5:02 PM writes...

Acetone. Oops.

Permalink to Comment

41. pk on October 25, 2010 5:55 PM writes...

My O. chem professor uses isopropanol in his lab.

Permalink to Comment

42. Antique on October 25, 2010 6:18 PM writes...

Aside; for stack testing in the mid 70s we used acetone for organic stacks then took it home for the lab rats. It worked for what we were doing. I am sure the gvmt would have a better thought...

Permalink to Comment

43. PlatoMolloy on October 25, 2010 6:27 PM writes...

Which ever is closest. I prefer acetone because if you get a little ambitious in cooling it and it bubbles over there is less of a mess to clean up. IPA will just sit there while acetone evaporates.

Permalink to Comment

44. Dave_n on October 25, 2010 6:30 PM writes...

LN2 and isopentane. Holds nicely at -145 to -150, but then I used to do a lot of organometallic chemistry in another earlier life!

Permalink to Comment

45. Orthogon on October 25, 2010 6:41 PM writes...


Permalink to Comment

46. Anonymous on October 25, 2010 6:52 PM writes...

liquid nitrogen

Permalink to Comment

47. anonymous on October 25, 2010 7:04 PM writes...

I used acetone and dry ice as an undergrad, but in grad school I use liquid nitrogen.

Permalink to Comment

48. Nathan on October 25, 2010 7:11 PM writes...

LN2 during the day and CO2/isopropanol for pumping overnight

Permalink to Comment

49. Ron on October 25, 2010 7:41 PM writes...

I am a grad student in an organometallic chemistry lab, and I have never heard of anyone using a -78 C cooling trap for their vacuum line. I've always used liquid nitrogen for my traps. Now, for the rotovap, I prefer isopropyl alcohol to acetone even though it's a little difficult to replace the solvent when you need to.

Permalink to Comment

50. Frances on October 25, 2010 7:48 PM writes...

Isopropanol for me.

Permalink to Comment

51. milkshake on October 25, 2010 8:18 PM writes...

I clearly prefer acetone/dry ice both for rotovap and pump cold trap - it does not foam as badly as isopropanol/dry ice. I tent to dump the leftover acetone from the rotavap cold finger and replace it with fresh stuff - the consumption is negligible (compared to acetone consumed in glassware wash). Dry ice/acetone filled Dewar in cold trap lasts much longer (over 2 days without re-fill) than liquid N2 and one does not have to worry about liquid O2 condensation hazard.
I have used also refrigerated cold trap (-60C) in the past (and I liked it) and there I was using iPrOH because acetone would damage the silicone rubber parts of the cold trap flask.

Permalink to Comment

52. Eric Suh on October 25, 2010 11:26 PM writes...

In my o-chem days, we used acetone because it was there, but in my current (biology) lab, we use isopropanol, because acetone is hard to come by in biology labs. So, whichever is at hand.

Permalink to Comment

53. Andy on October 26, 2010 4:13 AM writes...

I use acetone - and was quite surprised to see that I appear to be in the minority. Also surprised to see that some people use no solvent. Does that work? I always assumed that most of the solvent would go into the pump with so little surface area.

Permalink to Comment

54. KinaseNerd on October 26, 2010 4:44 AM writes...

liquid nitrogen - since grad school - no need to change

Permalink to Comment

55. Sayuri on October 26, 2010 6:52 AM writes...

No solvent. Just a pack of dry ice and a lot of cotton and alu foil as thermal insulator.

Permalink to Comment

56. A Nonny Mouse on October 26, 2010 7:41 AM writes...

We use beer chillers for both the evaporators and the condensors in the fumehoods. At a cost of £250, they are considerably cheaper than the ones from lab suppliers.

Permalink to Comment

57. MonkeyNinja on October 26, 2010 8:05 AM writes...

@56 Can you post an example, I'm interested!

Permalink to Comment

58. Physicist on October 26, 2010 8:16 AM writes...

I use activated carbon in my cold trap. Of course, it's cooled by liquid helium...

Permalink to Comment

59. Pig Farmer on October 26, 2010 8:17 AM writes...

IPA, which also happens to be my favourite beer.

Permalink to Comment

60. barry on October 26, 2010 8:44 AM writes...

I used acetone/dry ice (mostly dry ice) in grad school and never changed

Permalink to Comment

61. ty on October 26, 2010 9:47 AM writes...

IPA, primarily for toxicity reasons.

Permalink to Comment

62. Mike on October 26, 2010 9:54 AM writes...

Isopropanol. My labmate uses ethanol - "even less toxic".

Permalink to Comment

63. okemist on October 26, 2010 10:33 AM writes...

I had mostly transitioned to IPA since the first company I worked at (which was all acetone). Now we use nothing but dry ice(like #7 & 8) capture 500 ml of water over night last week without losing a drop.

Permalink to Comment

64. HK on October 26, 2010 12:42 PM writes...

IPA for our rotovaps (we use immersion coolers), liq N2 for our Schlenk lines.

Permalink to Comment

65. pc on October 26, 2010 12:44 PM writes...

How low one can go with dry ice only?

Permalink to Comment

66. sepisp on October 27, 2010 2:29 AM writes...

Why would anyone put solvent in their vacuum pump-protecting cold trap? Liquid nitrogen-cooled walls are cold enough to solidify most things right away. Solvent, on the other hand, has the risk that if you accidentally pull a piece of our atmosphere into the trap, the solvent splashes and permits liquid to the pump. Prevention of which was kind of the point. Or are we talking about procedures where you remove a lot of solvent directly into the trap - that is to say, the trap isn't just a precaution to protect the pump.

Permalink to Comment

67. mirro on October 28, 2010 4:30 PM writes...


Permalink to Comment

68. Anonymous on November 6, 2010 9:18 AM writes...

I had used either IPA or acetone, like many of the posts, in my rotovap. However, I now use EtOAc in my trap. Why? It's just as effective as the other solvents but you can see how much water has condensed and when it's time to empty the trap.

Permalink to Comment


Remember Me?


Email this entry to:

Your email address:

Message (optional):

The Last Post
The GSK Layoffs Continue, By Proxy
The Move is Nigh
Another Alzheimer's IPO
Cutbacks at C&E News
Sanofi Pays to Get Back Into Oncology
An Irresponsible Statement About Curing Cancer
Oliver Sacks on Turning Back to Chemistry