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Derek Lowe The 2002 Model

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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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August 25, 2008

How Not To Do It: Water Aspirators

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Posted by Derek

You need access to vacuum if you’re going to work at the bench in chemistry. In fact, you need more than one kind. Reasonably hard vacuum (well, by our standards, which is laughable by the standards of the physicists) is down in the single Torr or below – that is, less than about 1% of normal air pressure. We use that for pulling out residues of water or organic solvents from our compounds. You can’t usually see it happening from the solid ones, but the syrupy liquids will foam up or blow a long series of thick bubbles when the vacuum is applied. The foam can be an irritating problem at times; some things will fill your flask with sticky bubbles and go right on up into the vacuum line if you’re not watching them.

The lesser vacuum lines are used for bulk evaporation of solvent (on your rotavap) and for filtering things off. We do an awful lot of both of those, too, and a full vacuum-pump pull is too vigorous for them in most cases. Evaporating down reactions is a constant task in an organic chemistry lab; I’d rather not think about how much of it I’ve done over the years. As for filtration, there are many cases where a solid product can be filtered out of the bulk liquid (which is good) or where some undesired solid by-product has to be filtered out before you can go on (not as good).

The low-tech way to get the sort of pull-it-though vacuum you need for these things is a water aspirator. You don’t see these as much any more, and you don’t see them at all in industry, since they necessarily pull solvent vapors into the water stream. But they work. An aspirator is basically a narrowing tube that hooks up to a hard-spraying water tap and has a sidearm fitting. The accelerating blast of water pulls the air in the tube along with it as it goes, creating a useful vacuum. If you wanted to make one rather more environmentally friendly, you’d keep a well-stocked dry ice condenser in line with it to trap out the solvent vapors before they go down the drain (which is what your rota-vap should have on it, anyway), but even with that, you’re always going to be turning the water flow into a waste stream. As I say, you don’t see them as much these days.

But we used them back when I was in grad school, that’s for sure, mostly for the rotavaps. If you wanted to keep things from splashing around back in your hood, you attached some rubber tubing to the other end of the thing and ran it further down the drain a bit.

Well, one day, one of the guys in the lab next door to me was shocked to see water blasting around in his hood. It was a real fountain, just geysering out full blast from what must have been a cracked water line or something in the back. He ran over and immediately shut off every tap – but to no avail. Roaring, showering water everywhere. Getting a look at the source, he realized, to his consternation, that the water was coming up out of the drain in the back of his hood. I remember standing there with him, staring at this in disbelief. It looked like a special effect. How on earth could you get water blasting up out of a drain pipe?

Suddenly it hit me. I ran around to the other side of the lab, where a new Japanese post-doc had taken up residence. “Masa”, I asked him, “Did you just put that rota-vap in your hood today?” “Yes, yes, just started it today”. There was a water aspirator flooshing away back in the back of his hood. “Did you put some rubber tubing on that thing?” “Tubing? Oh, yes” “How much?!” “Whoaaa. . .” He spread his arms to indicate the mighty extent of the rubber tubing he’d added.

Mighty, indeed. He’d run the stuff down his drain, through a horizontal pipe and right through a T joint, and back up out of the drain of the other guy’s hood, which backed on to his. So when he turned his water on full throttle, he immediately started irrigating his labmate’s space. We finally go thing turned off, and trimmed back the rubber tubing to a more reasonable length (like, not seven feet), and order was restored. For a while.

Note: if you want to see How Not To Do It to a really expensive vacuum rig, try here.

Comments (25) + TrackBacks (0) | Category: Graduate School | How Not to Do It | Life in the Drug Labs


1. NH_chem on August 25, 2008 9:40 AM writes...

Used to use GLASS water aspirators in grad school long before we worried about issues with the environment. I am sure a few solvents went into the water. Mostly pulled off the basics- EtOAc, DCM, Toluene, hexane, etc.

I vividly recall a water pressure spike that blew up my tubing to the size of a water ballon. And I was using vacuum tubing (not seven feet- more like 4 inches tops with hose clamps).

Worked great. Then industry had house vac followed by Teflon pumps (which are great- I prefer KNF. With a dry ice trap, you are good to go.

I could not imagine seeing a water aspirator today....anywhere!! Great story above.

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2. NH_chem on August 25, 2008 9:40 AM writes...

Used to use GLASS water aspirators in grad school long before we worried about issues with the environment. I am sure a few solvents went into the water. Mostly pulled off the basics- EtOAc, DCM, Toluene, hexane, etc.

I vividly recall a water pressure spike that blew up my tubing to the size of a water balloon. And I was using vacuum tubing (not seven feet- more like 4 inches tops with hose clamps).

Worked great. Then industry had house vac followed by Teflon pumps (which are great- I prefer KNF. With a dry ice trap, you are good to go.

I could not imagine seeing a water aspirator today....anywhere!! Great story above.

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3. Paiute Attack! on August 25, 2008 9:54 AM writes...

Water aspirators combined with rotovaps (Rotovap or Rotavap? Google decides: Rotovap: 24500 hits, Rotavap: 13400 hits.) on the open benchtop combined with a heavy flask containing way too much ethyl bromoacetate (Caution: Lachryamtor!) led me to have a first hand teargas experience one morning.

Used to have to allow hours to remove ethanol. Now in industry, time = money. Rotovap hooked up to a Welch with clean oil and a warm water bath gets rid of DMF over lunch.

And why are there so many units of pressure? Pa, bar, atm, Torr, psi? Can't we all agree to use just one?

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4. processchemist on August 25, 2008 10:23 AM writes...

Watered vacuum systems are still in use in industry (on kilolab-pilot plant are a good solution) but not the venturi type you're talking about (watered rotary vacuum pumps, typical void 10-20 torr): the survival of this hardware is granted by the low cost of this option (the cheapest one). Once upon a time industrial venturi type vacuum systems working with supersaturated steam were common (Wiegand), but now are less used in the western world (environmental problems: water/voc streams are easier to manage than steam/voc streams).
A water jet aspirator can still be used to build the cheapest scrubbing system I know about.

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5. Sili on August 25, 2008 10:37 AM writes...

I guess that makes Denmark a third world country ...

We did have house vac, but for everyday rotavapping and filtration it was water all the way. Of course, I was in an inorganic lab (and I sucked at benchword - prolly harder than the aspirators at times ...).

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6. Phil on August 25, 2008 10:58 AM writes...

In grad school here we compare how much pull we can get from our water aspirators. The russian post-doc can consistently get down to 7 torr, quite proud of it.

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7. SFMedChem on August 25, 2008 11:21 AM writes...

In the startup space my new company is using there are water aspirators supplied for rotavap use. They actually work fairly well, 100 mL DMF took around 2 hours to pull off last time I tried.

These appear to be self-contained units, however, so no danger of flooding the hoods of other unsuspecting chemists. They do tend to splash water around your *own* hood, though.

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8. on August 25, 2008 11:36 AM writes...


We can't agree on units because of the massive range of scale: you can work in very hard vacuum (about 10e-7 Pa) or betweeen diamond anvils (100e9 Pa). That's 16 orders of magnitude just in earthbound labs. Intergalactic space and neutron stars push the range further. Given this, any unit of measure will be either appropriate, or ridicuously small/huge.

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9. Jonathan on August 25, 2008 11:46 AM writes...

They might not be that common in Chemistry labs, but they still get a lot of use in the pharmacy school where I'm a postdoc.

Crappy 1980s building has no vacuum lines, so if you want to aspirate something in the lab then it's the easiest and cheapest way to do it.

Then again, this building has plastic (!) modular lab benches that someone evidently thought was a good idea when speccing the place. I don't know about you, but I don't think the benchtop is supposed to bow an inch or two in the middle...

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10. Matt on August 25, 2008 11:58 AM writes...

When I took O-Chem lab in college one of our tasks was vacuum distillation. I recall being in the lab well after everyone else had left because I was stuck with a faucet that must have been on a heavily-use stretch of piping. Everything would be going along nicely until someone a few floors up would turn off a faucet. Then I would suddenly get a drastic increase in water pressure and a concomitant drop in vacuum pressure which would cause all of my mixture to boil over into the collecting flask. I think I tried it for about three hours before admitting failure.

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11. andrew on August 25, 2008 12:03 PM writes...

My hood had a Schlenk line, but no house vac. A cheap plastic $20 aspirator from Fisher was useful when working with a Buchner funnel - the Schlenk line would have been totally excessive. Also, pulling large amounts of air into the trap would not be a prudent practice. I'd recommend having a small cheap aspirator in every hood. If it's just for filtrations, you don't waste too much water, and you don't get much organic solvent in the stream anyway.

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12. Hap on August 25, 2008 12:12 PM writes...

The last time I was in lab (1997) we had water aspirators all over, with individual vac. pumps for drying material and a dry-ice/vacuum pump rotovap for DMF, etc. No vacuum lines in sight, though I don't know if one of the more recent professorial hires had vacuum lines.

What's with the troll infestation (9, soon to be /dev/null)? Can you call an exterminator for those, do you have to call Animal Control, or can you just feed them bicarb until they detonate?

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13. Hap on August 25, 2008 12:24 PM writes...

Used to be 9. Sorry.

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14. andrew on August 25, 2008 12:27 PM writes...

I think asking a chemist how he uses a rotavap is like asking him how he packs a column... a hundred chemists will give a hundred answers.

I learned how to use it from a German; a very careful man, he always protects the equipment first and foremost. The bath temperature is usually set at 60C, and the rate of evaporation is controlled by the vacuum. Ether and DCM are evaporated simply with heat from the water bath. The pump is disconnected and the hose adapters (to the vacuum) provided by Heidolph are conveniently unscrewed to give pressure relief.

Other styles I have encountered include hot (70-80C) and fast (full vac), cold (30-40C) with vac (natural products guy), and as-fast-as-possible (full vac, adjust bath to fit). All perfectly justifiable, until the students get confused.

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15. andreew on August 25, 2008 12:31 PM writes...

SFMedChem: No Schlenk lines at your place? 100 mL of DMF should go off in half an hour or so at 60C with full vac on a Schlenk. It's volatile enough to go straight up without condensing in your hoses/line. I used to routinely distill off DMSO at 70-80C fairly quickly too.

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16. CMC guy on August 25, 2008 12:51 PM writes...

I worked at a Big Pharma that opened new labs with "hi and low house vac systems" and water aspirator were "illegal". These system varied depending on how many people were using so would have wide pressure swings so bumping was problematic. Of course after a few months the house vacs kept breaking down and would take days to repair so people got water aspirators as back ups. We always were forewarned of EH&S inspections so knew when to remove the devices to avoid getting written up. Eventually the small bench pumps became common and most people never used the built in systems.

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17. Don B. on August 25, 2008 1:30 PM writes...

"We use that for pulling out residues of water or organic solvents from our compounds".

I think that with oils, Dalton's Law of Partial Pressures" still applies & you never get the last of the solvent out below the boiling point of the oil.

Just a quibble.

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18. Jack Bauer on August 25, 2008 3:16 PM writes...

I always wondered how Chemists in hot places use DCM. Room temperature is enough to reflux, could you just stick your flask under a condenser and stir? What if it's 40C outside, wouldn't your 4L bottles just burst at the seems?

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19. Handles on August 25, 2008 6:51 PM writes...

Re labs in hot places, at my uni we had to keep the pentane in the fridge in summer. On the bright side, we rarely needed to melt the DMSO or t-butanol before use.

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20. SRC on August 25, 2008 9:39 PM writes...

wouldn't your 4L bottles just burst at the seems?

It would seam so.

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21. Jonadab the Unsightly One on August 25, 2008 9:48 PM writes...

About the different units for pressure, they're not all used for measuring pressure in the same kinds of contexts. psi, for instance, is used pretty much exclusively for the pressure in inflated objects; whereas, ambient atmospheric pressure is measured in kPa (if you intend to do any calculation) or inches of mercury (if you're just reporting the weather). "Atmospheres" of pressure are used in the same kinds of contexts as "gees" of acceleration, e.g., comparing different inhabited worlds in sci-fi. Have you ever run into a situation where you had one pressure specified in Torr and the other in psi and you had to convert in order to subtract or compare? Me neither. Distance in cm and inches, or in inches and feet for that matter, yeah, you run into that all the time. With pressure, not so much.

Jonathan, a little bowing in the middle would probably not be my main worry if the benches in a chem lab were plastic.

Sili, you can make Denmark *sound* an awful lot like a third-world country if you describe it just right, carefully avoiding any meaningful discussion of economic indicators. Let's see...

Denmark is an archipelago, consisting of over a thousand islands, with a total surface area of around 16,000 square miles, a mean elevation of about 100 feet above sea level, supporting a population between five and six million people. The size of the land area cannot be stated exactly since the ocean constantly erodes and adds material to the coastlines... The unit of currency is the kroner. One krone is worth about twenty cents US...

CMC guy, that's interesting, albeit not entirely surprising. Building-wide systems (for anything, not just vacuum) never quite work as well as they're supposed to do. A lot of buildings have perpetual problems just keeping the heating and cooling consistent from room to room, so it's not altogether surprising that the vacuum pressure of a house system would be inconsistent.

Bauer, if it's 40C, are you really going to be doing any actual work? Let's see, isn't body temp about 37C, and the degrees are about double normal size, so that's, what, six degrees above body temp, or somewhere around a hundred and four? Yeesh, let's hope it's not also humid. Anyway, you're either in a developed country, in which case you stay in the air conditioning when it's like that, or not, in which case you sit around doing nothing during the hot part of the day. Either way, you wouldn't be doing a whole lot chemistry work at 40C, methinks. At 40F, maybe (some would say that's a wee bit nippy; personally I'd be comfortable), but not at 40C.

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22. Jim Hu on August 26, 2008 1:27 AM writes...

We have some self-contained water aspirators - think ice chest with a motor circulating the water past a venturi. They work pretty well for gel dryers.

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23. Maks on August 26, 2008 8:50 AM writes...

To Jack Bauer: Did quite a few reactions in a fairly hot place (Israel). Without air condition working was simply not possible, we kept the low boiling non-flammable solvents in the fridge, ether I tried to avoid whenever possible and except for that the air condition had to keep the temperature all the time below 25 degree C. Frozen DMSO and t-BuOH was a fairy tale from another world in this lab......

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24. DOH! on September 5, 2008 10:22 AM writes...

You have to be careful with water aspirators to not turn off the flow of water before releasing the vacuum. When I was a freshman in college I got a job at a local biotech company as a lab assistant. In my first week I had purified a finished peptide by HPLC and was using a water-aspirator rotovap. The problem was that the system also used cold water for the trap, so I had two water lines running. I had the condenser line turned up way too high, as this is standard procedure for someone who doesn't know what he's doing (undergrads). So the condenser faucet starts flipping the rubber hose all around, and I panic and start turning off all the valves I can. Well, if you turn down the aspirator flow when you still have a vacuum in your flask, what happens is that the rotovap sucks in the now slow-moving water. As I looked on in horror, about a liter of nasty tap water crashed in and flooded my sample. I thought for sure I was going to be fired, as that peptide was worth more than I made in 6 months. I just started mopping up the water and then proceeded to clean any glassware I could get my hands on in an act of contrition. Somehow they didn't fire me, and that was pretty much the worst thing I did.

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25. PeteD on September 8, 2008 6:07 PM writes...

At our pharma Co, we use PIAB compressed-air-driven ejector vacuum pumps for our Rotary Evap. All you need is house compressed air (64-87psi) and are kinda expensive but use no electricity or water. Initially, we had no support from EU manuf. but local guy set it up for us and is now available as a complete set by Ace Glass. It has now been installed for all of our evaporators and if treated gently (no direct evaporation of highly reactive caustive chems) last for years with minor maintenance. Enjoy.

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