Org Prep Daily

January 14, 2007

Setting up a vacuum manifold

Filed under: procedures — milkshake @ 11:31 pm

This is a pretty familiar subject that everybody in an organic lab has already dealt with. I have few notes on things that worked for me:


Dual-bank manifold (5-fold) with bore glass stopcocks from Chemglass (their new version of it) and the same kind of manifold from Aldrich are both very good for the common organic applications.

I really dislike the manifolds with Teflon highvac stopcocks: their teflon fingers wear out quickly and it is easy to break the manifold if you over-tighten them.

For greasing the glass stopcocks Apiezon grease brands are vastly superior to other hydrocarbon-based lubricants. Apiezon M is somewhat less overpriced than other Apiezons (costs about $60/100g) but it still works better than any other grease brand that I tried. Silicon grease and perfluorinated grease are unsuitable for manifold stopcocks – they cause leaks in the joints.

Vacuum meter

Vacuum meter should be hooked up directly to the manifold, before the cold trap. There are digital vacuum meters on the market but the classical Welsh vacuum gauge is affordable ($600) and robust on continuous use. It is even precise enough to be used for highvac distillation. The Fisher catalog # for this vacuum meter is 11278 (“vacuum gauge 115V 60Hz”).

Bubbler gas outlet/valve

It is good to have a mineral-oil bubbler with a ball that plugs it and prevents a back-suction of oil when vacuum is applied during vacuum/gas back flush on a dual bank manifold. I think it is called Firestone valve after the guy who invented it, even better is if the bubbler valve has an additional shut-of stopcock. One should use the more viscous heavy mineral oil for the bubbler and position the bubbler such that an accidentally sucked-in mineral oil wouldn’t make it into the manifold (one can add a small empty trap flask between the bubbler and manifold). It is a nasty mess if one has to take the manifold apart and clean the oil out.

Cold trap

Many people in academia prefer dry ice trap but adding dry ice and frequently emptying the cold trap is a chore. I like the refrigerated cold traps because they run without much attention and need only infrequent cleaning. They make continually-operating vacuum line very easy to set up and operate. Running the oil pump continually is good for the health of the pump also – if one changes the oil on monthly basis. There is couple of refrigerated vapor trap models on the market, for example from FTS and Thermo-Savant. The cheaper -60C two- or four-liter flask models (about $1500 – 1800) are in my opinion sufficient if one is reasonably careful – evaporating large quantities of super volatile stuff like dichloromethane into the highvac system is bad idea with any setup. (Few mL of highly volatile solvent will pump itself out from the system without any harm over a short time period – if the pump is running continuously).

Isopropanol works fine for the cryo bath in refrigerated vapor traps (the recommended super-expensive silicon cooling-transfer liquid is waste of money).

Thermo Savant has disorganized customer service and long delivery times, also the black rubber caps on the glass insert trap tend to rot and crack after a year or so – one should buy a replacement cap with. (Alternatively, Savant also offers an all-glass insert flask that is much better in my opinion than their standard-issue insert with the rubber cap).

FTS Titan trap is exceptionaly good – but also too large and too expensive; FTS now sells smaller and less expensive models also but I dont have any experience with them.

No cold trap will remove HCl gas. HCl is one of the worst metal-corroding acids – getting HCl into pump will predictably cause it to seize over time; the repair is expensive and the pump is never good ever after. Using an additional KOH pellet or soda lime trap is a good idea if one has to vacuum-dry compounds like acyl chlorides.

Oil pump

Manifold pump should be a two-stage oil pump (with ultimate vacuum below 4 mTorr) and should have the pumping speed well above 120 liters per minute. The pumping speed is the most important parameter and it is a common mistake to buy a manifold pump that is too underpowered for the job.

Old-timers prefer belt-driven pumps for continuous use because the belt-driven pumps tend to withstand more abuse. My complaint about belt driven pumps is that they are too big (for a pump with a decent pumping speed) to be placed under the hood and they tend to generate more heat than direct drive pumps (I don’t know if this is the efficiency thing or a ventilation problem – but I remember having a hood surface seriously hot from a big belt pump that was running underneath). In my opinion direct-drive pumps are now sturdy enough to be run continuously as manifold pumps. I particularly like direct drive Welsh-made Fisher Maxima M12C pump – it has a great pumping speed (230L/min) and the price is reasonable ($1600), the pump is quiet, not too hot to run in a narrow cabinet under the hood (if the backside of the cabinet is removed) and it seems quite reliable and resistant to abuse.

(However I wouldn’t recommend a similar but smaller Maxima M8C pump – because of their lousy lifespan. Almost all the M8Cs that we bough from Fisher have died within 2 years, despite frequent service and warranty repairs. Oil that was slowly seeping from underneath the pump (from a loose seal along the shaft) – a recuring problem that we had with almost all our M8Cs – was a particularly annoying problem.)

If you have both belt-driven and direct-drive pumps in the lab please note that these pumps use different oils which are not interchangeable. Direct-drive pumps operate at more than double rpms of the belt-driven pumps so they use less-viscous oil.

After the oil change, the pump with new oil can take an hour or so to warm up and pump itself out, before achieving its best vacuum.

Vacuum tubing

Tygon thick-walled vacuum tubing is expensive but it is very good for connecting the manifold to the trap and pump. The tubing should be as wide as possible and the connection between the cold trap and manifold should be as short as possible. Rubber tubing has high gas permeability and poor chemical stability so it should be avoided. Butyl rubber is an excellent alternative but it is not transparent like Tygon.

Tygon brand and a common brand vinyl tubing is not good for connecting the manifold stopcocks to the flask or apparatus – one always has to watch out for plasticizers leaching out from the tubing due to traces of organic solventsand getting into the reaction flask. I use the highly flexible natural rubber tubing or – for the really highvac connection to apparatus – the butyl rubber tubing.

For disconnecting the hoses, it is preferable to use a new razor blade rather than sizers when cutting the tubing off the manifold. It is generally a bad idea to try prying the tubing off by force – the glass manifold connectors break off easily.

Leaks and performance

When checking for leaks, one has to start at the pump and keep working his way up to the manifold. If one cannot get below 300 mTorr on a closed manifold, something is leaky along the system (a stopcock for example) – or the pump is going bad. With a good pump setup and a tolerable degree of abuse, 50 mTorr is a good idle vacuum in a common organic chemistry 5-fold dual bank manifold setup.

Update: I have been very fond of  M12C direct drive pumps that we bought initially but I must admit that several of these pumps, especially those pumps we received later in 2007 and in 2008 from Welsh developed a serious oil leak problem, one that seems to be related to faulty seal along the main shaft. This is rather annoying bug, and the Welsh engineer was less-than-helpful and tried to blame the problem on users so that he would not have to deal with that many warranty repairs. I got tired of his excuses and flakiness, and taken together with ridiculously long delivery times (some of these pumps were delivered more than half year after the promised date!) I cannot really recommend Welsh direct drive pumps anymore. If you have the money for it, Leybold pumps have much better reputation for reliability.

Update 2: I also got eventually used to the highvac manifold with teflon fingers – I guess this is what one needs to use with diffusion pump (and liquid nitrogen cooled cold traps) for 5 – 15 mTorr vacuum work needed in polymer chemistry. A bit of overkill for medchem though


  1. Fantastic post. I’m curious to know more about why perflorinated greases (like Krytox) don’t work so well. I use that stuff for everything; I like the idea that it won’t infiltrate organic solvents and products as easily as other lubricants. Maybe I should go back.

    Comment by Paul — January 15, 2007 @ 12:14 am

  2. I don’t know why this is so – but I suspect that with Krytox it is the same problem as with the silicon grease – it is gelatinous and doesn’t spread evenly throughout, and the film tends to stiffen when it sits idle for awhile – and then the film tears if you rotate the stopcock so you get some tiny hair-like leak chanels forming in the greased joint.

    Silicone grease works great on lyophilizers (where one would not want to use hydrocarbon-based grease on rubber seals as this would gradualy damage them) – but there are no moving surfaces on lyo, like with stopcocks.

    Comment by milkshake — January 15, 2007 @ 12:35 am

  3. Great setup if you have enough money like you are working in industry. I just wonder how many academic groups can afford it. When I was doing my phd, I didn’t not even have a manifold.

    Comment by diketene — January 16, 2007 @ 10:24 pm

  4. In academia a glassblower is often asked to make manifolds for the entire group – that way they could save hundred bucks or so on each manifold. One can improvise and do without – have spagetti lines branching off from a hose (I have done some sensitive catalyst study like this ) but I think it is important to have at least one good shared highvac line in the lab so that people can actualy dry their products. It then makes a good sense to buy a decent pump for the group – the price difference between a powerfull and a whimpy pump is not that big – and also equip the shared vacuum line with a refrigerated cold trap so that things don’t get ruined when people leave for Christmas.

    Also an oil pump hooked up to rotavap does wonderful job for evaporating solvents like DMAc or DMSO – but one has to use the dry-ice cooled Buchi and have an additional cold trap before the pump. Again having one higvac-hooked rotavap with refrigerated cold trap for this kind of solvents is a good idea.

    I don’t think that spending $4000 on the entire highvac setup including the pump is that unreasonable in US – because the same amount of money will buy you just one basic rotavap and bath (but without the teflon pump and vacuum controler) or couple of IKA stirplates

    Comment by milkshake — January 16, 2007 @ 11:20 pm

  5. Thanks for the detailed post, milkshake. I would a comment that an additional bulb between the inert gas line and the bubbler can also be useful for providing more dead volume of inert gas during evacuation/backfill steps. This can modulate the pressure drop on the inert gas line during this common step and prevent pulling too strong a vacuum on your inert gas source. cheers, cjdquest

    Comment by cjdquest — January 17, 2007 @ 10:20 pm

  6. Why not a liuid nitrogen cold trap? Seems much less messy than dry ice/acetone.

    Comment by andrew — January 17, 2007 @ 10:23 pm

  7. N2 trap is absolutely awesome. (Although the re-filling has to be a bit more frequent and one has to watch out for liquid O2 condensing into the cold trap when opening the system.)

    Comment by milkshake — January 18, 2007 @ 1:33 am

  8. we use silicon tubing for connecting manifold with flasks. it is flexible, transparent, and resistant enough for the purpose. btw, absolutely great post. simmilar ones covering lab practice would be highly appreciated!!!

    Comment by petr — January 22, 2007 @ 10:24 am

  9. Was often warned about the dangers of O2 condensing in the liquid N2 trap but in 5years of running a Schlenk line I never saw the blue peril in my trap. I used to make it (liquid O2) for display days (when hordes of high school kids toured the dept) by running a stream of oxygen through a copper tube immersed in a liquid N2 dewar. Liquid O2 has the most beautiful ethereal blue color and is great fun to play with. Though I told them it was not so, I always got the feeling people left my display area thinking ‘Oh, THATS why the sky is blue’.

    Comment by agogmagog — January 22, 2007 @ 11:30 am

  10. If you’re really on a tight budget a 200$ vacuum pump from home depot, pirated glassware (ie local glassblower), some good tubing and a dewar flask with liquid nitrogen will work perfect 9 out of 10 times and will probably set you back no more than 1000 bucks. We also use tubing instead of a “real” manifold. Much more flexible and versatile, easy to clean and definately much cheaper (especially since glassware tend to break every other day).

    Comment by kosmisch — February 6, 2007 @ 3:59 pm

  11. Noticed that I might not have been completely clear on my last comment 🙂 What I mean was that we are using 3-way double oblique stopcocks for each station you want on the “manifold” and simply connecting all of them together with tubing and t-connectors. Much better than glass manifolds IMHO.

    Comment by kosmisch — February 6, 2007 @ 4:19 pm

  12. I am trying to set a schlenk line in my lab, but confused regarding the tubings. Simple silicon tubings can not tolerate the high vacuum. The tygon vacuum tubings are quite expensive. What is the alternate? Can anybody help me?

    Comment by Pradeep — July 30, 2008 @ 5:11 am

  13. why it does not tolerate high vacuum? The walls collapsing? For vacuum applications you need a wall thickness thats at least one half of the internal diameter (the hole). And silicone is too soft anyway, and gets damaged by common solvents such as THF or DCM.

    You can use cheap vinyl tubing inplace of Tygon, the main disadvantage is that the plasticisers+vinyl will leach out from the tubing by organic vapors and accumulate there over time as thick dropplets that can make its way into the glass manifold.

    Also you can use polyisobutylene, the butyl rubber – it has a good chemical resistance and low gas permeability (compared to polybutadiene or natural rubber) and does not weather / crack as fast.

    Comment by milkshake — July 30, 2008 @ 11:13 am

  14. How about using PVC tubing, I would think it’s not realy permeable to gasses, and pretty chemically resistant.

    Comment by Bob — November 3, 2008 @ 12:42 pm

  15. I don’t like PVC tubing on manifold (since I can afford to buy Tygon) – PVC plastic is full of phtalate plasticisers (like 50% by weight) and after while you see viscous dropplets forming inside the PVC tubing on manifold, from these plasicisers leached out by action of organic solvent vapors.

    Comment by milkshake — November 3, 2008 @ 4:05 pm

  16. Hey Milkshake, I just set up a Chemglass double bank manifold with apiezon H grease on the stopcocks, a medium-sized Welch belt drive 1402 N (chemstar) pump, and 1/2″ thick walled Tygon tubing (about $10/ft!) between the pump and LN2 trap and the LN2 trap and the manifold. There are a total of four tube/glassware/pump connections, each clamped and sealed with teflon tape wrapped around the connection. The total tubing used (since the pump is kept outside of the hood) is about 6′. I attached a Welch thermocouple vacuum gauge to a Tygon line from the manifold (since that is where a vacuum distillation or solvent removal/drying would take place), and the gauge only reads 1 Torr! I checked for leaks with soapy water at every joint and no bubbles are observed. Any ideas on what I’m doing wrong? Any hints on how to get that pressure down under 10 mTorr? Thank you.

    Comment by Steve — January 13, 2009 @ 12:48 pm

  17. Newly assembled and greased manifold almost always leaks somewhere. I checked the catalog and your pump has pumping rate (“free air displacement”) 160L/min, so it should be adequate for a manifold. But you need to start with checking the vacuum right at the pump, to see that the pump itself produces a good vacuum without any load. Then you measure vacuum after the cold trap, to make sure the leak is not there either. Gradually you work your way up to the end of your system, with a manometer. Bubble water test will not help you to test for vacuum leaks, you need a manometer. This may seem frustratingly slow but you need to identify, by elimination, which parts of your system are good and which ones leak.

    Make sure that all your connections fit snuggly. The screw-clamps and teflon tape-over are worthless as a seal (The clamp is good only for preventing the tubing from slipping), the tubing has to seal by itself on contact with glass (or the inlet port of the pump).

    I suggest that you also rotate your freshly greased stopcocks with manometer attached, to see if there is a sudden improvement. Freshly greased joints tend to develop leak channels in the grease for the first few days. You need to wiggle them around, one by one, and once you find the leaky one the vacuum should promptly get better.

    Also even if nothing leaks you may expect a mediocre vacuum (0.3-0.4 Torr) initially, it should gradually improve on running overnight, as all volatiles get gradually pumped out from the system and the pump oil.

    Best luck – and please let me know how it goes.

    Comment by milkshake — January 13, 2009 @ 6:22 pm

  18. Hi Milkshake,

    I was surprised to have missed it on your blog, and to find it while I was searching (googling)for the vacuum manifolds. So, having stumbled on this informative post, I thought of checking if you or (your readers) know of any suppliers for manifolds made up of steel or copper. I am sick of breaking the joints on the glass ones, and the dirty look it picks up in the hood after a while. Also, if you know if there is a way to custom make them (say 10 outlets, one side double open dual columns (2 inlets one for gas, and the other for vacuum), and the other end only the inert gas line open in to bubbler while vacuum line being closed … Also, is it good to have a nitrogen generator than the tank?

    Thanks in advance as usual.

    Comment by xyz — June 3, 2009 @ 8:06 pm

  19. I have no experience with metal vacuum manifolds (except for the one that I bought as a part of a Labconco lyo – the manifold was very expensive). Ruining a $600 glass manifold definitely teaches one to be more careful the next time.

    I think nitrogen generator is a bad idea: big, noisy and it leaves non-zero levels of oxygen in the produced gas. One tank of argon (about $50-60 for a re-fill of ultra-high purity Ar grade) can last for at least three months if you set the pressure in the system and the bubbler at low flow. You also need to put the Drierite drying column in between the tank and the manifold. The important thing is to check every night before leaving the lab to make sure that you didn’t forget to shut off all manifold stopcocks that are not in use. Forgetful chemists run out of Ar or N2 all the time. For that reason it is generally bad idea to share the tank. Each to his own.

    Comment by milkshake — June 3, 2009 @ 8:31 pm

    • I built an all-metal inert gas manifold for less than $30 using parts from….see link below for pics

      I can provide more detailed description/specs if anyone’s interested. Just let me know.

      Comment by Ian D. — December 5, 2015 @ 9:54 pm

  20. Chemglass double bank manifold – is it a new addition to their catlog? Do you have their catalog number/? is it available on-line? Do not ahve a latest catalog though.


    Comment by xyz — June 4, 2009 @ 2:42 pm


    is this the one you recommended? Looks like quite expensive….$1200.

    Comment by xyz — June 4, 2009 @ 2:44 pm

  22. No, I would recommend this one: CG 4441, five-port

    Looks like their prices went up since the last time I checked. But these are just their list prices; our institute used to have a significant discount with Chemglass.

    Comment by milkshake — June 4, 2009 @ 4:21 pm

  23. Thanks. My boss says that it is about 20% discount that they give to our institute. Planning to buy bulk of glass ware. Do you know any vendor who is good at their stuff, and yet dicount to comepte with CG.

    Comment by xyz — June 5, 2009 @ 9:03 am

  24. Aldrich manifolds are decent (and one can probably negotiate bulk discount with them) but I like Chemglass as the glassware company better.

    Comment by milkshake — June 5, 2009 @ 9:20 am

  25. Can you recommend any specific Leybold pump that is on par with the Fischer M12C?

    Comment by Art — July 20, 2009 @ 4:18 pm

  26. My experience with Leybolds is somewhat limited – I mostly got to use them as a set part a part of lyophilizer, and the impression was very good (my European colleagues are saying the same thing). On the other hand I bought at least dozen – if not more – pumps from Welsh-Rieshle and my impression is mixed, I think M12C would be a decent and reasonably priced pump model if they could get under control their recurring shaft seal oil seepage problem bug, and if their customer service was less flaky. But right now I think they don’t care to do anything about the problem.

    When you are shopping for a manifold pump, the most important parameter is the pumping speed (aka air displacement), you want a pump that does 200 liters per minute. 300L/min is better still – at certain size you get limited by what fits under the hood. The ultimate vacuum is less important because you are unlikely to achieve it in your system unless you have Schlenk line manifold and liquid nitrogen cold trap. 50-150 mTorr is a decent vacuum in a common manifold so it does not matter really if the pump makes 0.1mTorr or 0.3 mTorr ultimate vacuum

    Comment by milkshake — July 21, 2009 @ 3:10 pm

  27. Great post! Definitely helped me a lot in the past, and think it will in the future. After using all our PVC tubes ordered by my predecessor, I’m finely up to ordering some tubing myself. Helped by the fact that the previous tubing is not available anymore, I went somewhat deeper into other tubing. In the inorganic laboratory, they switched to Tygon tubing, but of a type I have some doubts about. They use the B-44-4X type (see Is this the type you recommend, or does it have some downsides. I would think the R-3603 type is more the way to go (see but this one is also more expensive. (I think there’s also some marketing involved with all the different tubings they have)
    The inorganic laboratory is using the B-44-4X type for a month now, without any complaints. How do you comment on that?

    Thanks in advance.

    Comment by Bob — November 24, 2009 @ 12:22 pm

  28. It is difficult for me to recommend a particular catalog # because it has been 5 years since I have been setting up mine and I don’t have the original catalog numbers anymore. What you need is a tubing that is as wide as possible while fitting the manifold (and cold trap) and sufficiently thick-walled as to not to collapse under vacuum. An approximate rule for the wall thickness of vacuum tubing is that the wall should be about one half of the INNER diameter of the tubing (=the hole)

    Comment by milkshake — November 24, 2009 @ 1:49 pm

  29. and to think I was considering a Welch oil-less vacuum pump that pulls no more than 2 TORR!!!

    Comment by Richard — January 23, 2010 @ 1:35 am

    • It depends what you need it for. The pump you mention has a lousy pumping rate and not-so-great ultimate vacuum. I think it would give you something like 5-10 Torrs when measured at the manifold. The setup would probably work for degassing reactions by the vacuum/argon purges but it would be insufficient for drying samples from things like EtOAc residue.

      Typically these pumps are used with a rotovap. Also, I think KNF makes better teflon pumps than Welsh. My experience with the Welsh built-in manometers and pressure controllers is that they are not very reliable, and they tent to be pre-set by the manufacturer to read a better vacuum than what is actually in the system.

      Comment by milkshake — January 23, 2010 @ 3:29 am

  30. Well funny you say that because this is the precise use I am looking for…ie, purge/fill for colloidal synthesis of nanoparticles…however, I had always used an Alcatel oil pump during University work and that system was capable of at least 100mTORR…….I was just considering a way to worry less about pulling solvent vapor into the pump by using a oil-free teflon lined model…looks like I should just go ahead and use the oil-pump again with suitable solvent traps

    Comment by Richard — January 24, 2010 @ 12:18 am

  31. I use Krytox. Works like a charm. It’s other vacuum greases I’ve had solidify and seize taps.

    Oxygen condenses around -180C. Hydrogen chloride does the same at -85. Use LN2 and add boiling point raisers to bring it over the oxygen problem but below the HCl one.

    There is zero point connecting a rotary or high vacuum line to a rotovap for most work. The BP of the solvent will rocket below zero, bumping may ensue and the solvent will go straight for the pump.

    Buchi sells the V series of pumps for rotovaps, they reach something around 20mBar.

    Diaphragm pumps do about 100mBar.

    The V series costs $1.5 – 2k?

    I can let you in on a secret. The compressors from fridges run between 80 and 20mBar. They’re free from the tip. They’re designed to handle things like iso-butane around the windings. They’re silent under vacuum and very easy to move around. They have flow rates of around 0.2CFM, so they intrinsically apply the vacuum gently without a controller or special tap, yet can overcome taper leaks.

    I have three alcatel / edwards pumps, and still use fridge pumps for solvent ripping.

    I have also opened numerous laboratory pump and taken them to bits at the nuts, washers and bolts level. I can assure you, and you have to trust me, they are not as pretty inside as they look outside. They’re rough castings with sparsely machined/ ground contact surfaces, identical to the way a fridge pump is made. Older pumps will also be CAKED in rust. Whereas a fridge pump pulled from even an old fridge will be spotlessly clean.

    If you stick a $1-2k rotary on the rotovap and then rip off a low boiler, it’s going through in the wrong sense. Add to that, the cost of the rotovap, the vacuum controller (or playing around with the stopcock), the cold finger, the cryogenics, storage, handling. For what? Solvent in the pump? Stress? Time supposedly saved but then wasted playing with the cocks? And resetting bumps?

    1CFM will apply the vacuum far too quickly; stick it straight on there and the liquid will be out the flask instantly, in the wrong sense. Never mind the 5’s and 10’s the bigger desktops well manage. The system should be at 0CFM when it’s under vacuum (plus any taper leaks). If it’s drawing significant CFMs, you’re running the pressure too low and the solvent is going through to the pump.

    Also note, there are TONS of dual stage rotary pumps now available that do laboratory rotary pressures for as little as $90, new. They’re sold as HVAC pumps on eBay. Just because it doesn’t have Edwards / Welch / Varian / Pfifififififer / Alcatel / Leybold ‘laboratory super duper special, twin turbo, 2391X edition’ written on the side, don’t let that put you off. They’re ALL the SAME THING inside, no matter how much the big names want you to think this newer, more space aged looking gizmo is super different. It’s not. Same thing, different box, another cheque from another sucker.The guys from China on eBay will usually reply as soon as they get your payment, and get it in the post quickly and cheaply. If they have 10,000 feedbacks and 99%+, it’s going to turn up and work or you’ll get your money back.

    Rotaries and diffusions for the hi-vac line and getting those last traces out, certainly! For solvent boil offs, use a fridge pump, genuinely recycle, save yourself a few $k’s, simplify and spend the money more wisely elsewhere.

    1.) High vacuum rotary work = Go to eBay, search for “HVAC pump”, pick the smallest one there (a 1.3CFM usually) from China. Spend the other $2k on beers and champagne and have a lab party.

    2.) Solvent boil offs = Go to tip, locate stack of tens of fridges / freezers, find one that’s already burst, remove pump (takes about two minutes with a spanner and pair of pliers). Spend other $2k on strippers and a lab party.

    Comment by John — September 28, 2010 @ 5:03 pm

  32. Oh, with regards to Tygon. Use heavy walled ‘whatever’ tubing to port the vacuum around. For glass to glass work where it will be in contact with chemicals, switch to Tygon.

    You shouldn’t have Hydrogen Chloride and solvents on their way out of the glass in the first place; you’re doing something wrong if they are. Using ultra-expensive tubing there is like thinking it’s okay to cut your hands off, because you’ve got some plasters.

    You need SPECIFICALLY Tygon ultra-chemically resistant tubing. Not standard Tygon. I think the newest UltraChem version is 2375. I’ve was sent some to try and exposed to Hydrogen Chloride with DCM. Turned slightly opaque, but still as flexible and fine as when I started.

    Fluoropolymers tend to swell around halogenated solvents. Things like DCM help the reactive gases penetrate the polymer, hence the opaque colour of mine after exposure.

    A bigger problem is that the swelling will bind the tubing to the glass, so tightly that it needs cutting back off. I’d recommend some grease on the hose barbs and possibly a clip on the hose after the barb.

    Comment by John — September 28, 2010 @ 5:13 pm

  33. New rotary vane, $1-2.5k.

    HVAC pump from eBay, 0.01 mBar, 0.0075 torr (too low for volatile work), 1.3CFM up (too fast to avoid bumping when directly connected). $90 – $150

    Fridge / Freezer compressor, ~80-20 mBar, 60-15 torr (ideal for solvent boil off), 0.2CFM (applies vacuum gently), designed to handle iso-butane internally. $0

    Comment by John — September 28, 2010 @ 5:19 pm

  34. Dear Milkshake

    I am trying to set up a high vacuum system in our laboratory. Your post seems really helpful.

    Can you provide specific companies/product numbers for a vacuum pump and cold trap you recommend? It seems you no longer recommend the Maxima M12C pumps…any suitable replacement? You suggested M12C pump would cost $1600 but the Fisher site has it for $3400. Would you buy used?

    Also, you cite a price of ~$1500 bucks for a cold trap – can you suggest a model?



    Comment by Doug W — August 15, 2011 @ 11:53 am

    • If you need to buy an oil pump in US and go by a catalogue I would recommend Welsh belt-driven oil pumps like the 1402 Duoseal – they are quite rugged but take lots of space under the hood.

      The prices you pay with companies like Fisher and VWR vary great deal depending on the discount you can get. (Like expensive department stores, these companies have a ridiculous markup on their list prices so that they can give 70% off to some of their selected customers – some get only 30% off and some get the full list price). Call up your local Fisher and VWR sales rep and ask him for a quote, and ask him if he can help you to bring their price down a bit since you are making a large equipment purchase.

      Refrigerated cold trap – I can’t recommend any, I grew progressively more disappointed with them, and they are getting more and more expensive. I would buy some dry-ice cooled type that is wide and has a wide inlet inner tube, ideally with O-ring seal and large clamp. (The cold traps with a ground joint have tendency to get stuck.)

      Comment by milkshake — August 16, 2011 @ 1:32 pm

  35. This might sound like a stupid question – How can I ensure a good seal between the tubing and the manifold? You mentioned that the tube should seal itself on contact with the glass. Do I need to melt the tubing or use some solvent to dissolve the tubing a bit to seal it well? If not, what kinds of tubing can seal itself automatically? I am a new postgraduate student setting up my manifold, and there seems to be some leaks in the systems…

    Comment by Elvis — September 13, 2013 @ 8:28 am

    • this is a completely reasonable question. Transparent vinyl tubing like Tygon lets you see if there are any air-channels in the connections. With rubber tubing, especially the wide one used between pump and cold trap, it is recommended to use the tightening ring clamp – the one that looks like ring, has groves and a screw. If you need to temporarily lubricate the tubing, you can dip it in toluene. For flask connection to manifold I quite like to use amber latex natural rubber heavy wall tubing – it is much lighter than the black rubber tubing and clings better. It is more also bendable and does not sweat out plasticizer like vinyl tubing. Amber natural rubber tubing It is somewhat difficult to get, VWR charges something like $230 for 50ft but we get it from Fisher at about $140/ box (50ft), the catalog # is NC0484922 (Primeline industries, tubing latex No. 126XAF50., 1/4 inch inside diameter, 3/16 inch wall)

      Comment by milkshake — September 16, 2013 @ 1:51 pm

  36. Thanks for your reply! Just one more question… Have you ever used thick-wall silicone tubing? Is it good as a vacuum tubing? Really thanks for your reply.

    Comment by Elvis — September 17, 2013 @ 10:30 am

    • I have not used silicone rubber tubing. If I remember correctly, the drawback was that it was too flexible – which is good for applications like peristaltic pump but not for vacuum work because the tubing can easily collapse when evacuated

      Comment by milkshake — September 17, 2013 @ 3:36 pm

  37. I’m fairly new to Schlenk lines, so this might be a silly question: If my oil pump is rated for 0.001 mbar and the manometer shows a max vacuum of around 0.05 mbar – is that ok? I’d hate to condense liquid oxygen.

    Comment by Steffen — August 17, 2014 @ 11:34 am

    • If your manifold lacks a diffusion pump (typically dif. pump comes as a part of the manifold setup), the best you can hope for with a liq. N2 cold trap and a good oil pump s 15-20mTorr. That is, if you have a pump with a decennt pumping rate (at least 160L/min). I would recommend that you get hold of mercury-filled McLeod vacuum gauge and a pump outlet nipple with a narrow hose barb and measure right at your pump. Even though the nominal rating is 1mTorr (some pumps are 3mTorr) if you get 5-10mTorr at the pump it means the pump is fine. If not, change oil, have the pump run overnight and measure again, while the oil fill is warm.

      The electronic vacuum meters cannot be trusted without calibration by comparison with a mercury-filled gauge.

      By the way, what type oil pump you are using? I like belt-driven Welsh 1402B, we run them all the time without shutting them overnight/over weekend. They seem quite rugged and tolerant of small quantities of volatile organics getting through. Obviously, if someone pumps in HCl gas, and leaves it like that without immediate flushing and oil changes, the pump is never good afterwards and is likely to seize in few days.

      Comment by milkshake — August 18, 2014 @ 3:09 am

      • Milkshake, if I attach a high vacuum pump to my manifold, what is the best way to regulate the vacuum pressure if I need to use the pump at only 70% of its maximum vacuum? Would you suggest I use a vacuum regulator, or an external needle valve? Would you suggest I bleed in air or gas (Ar or N2) to reduce the effect vacuum on the system? Can you make a recommendation for a purchase?

        Comment by DIBAL — March 14, 2017 @ 1:36 am

        • Unfortunately I never had to solve this problem on a manifold, when I needed worse vacuum I simply used worse pump, but I suppose the needle bleed valve is the way to go – thats what we used for our rotovaps when the fancy vacuum regulators from Buchi eventually died. We used old regulator valve from Aldrich lecture bottles, and another one that came as a part of Swagelok kit, but this was just for teflon piston pump vacuum, I don’t know about regulating highvac on manifold.

          Comment by milkshake — March 14, 2017 @ 7:58 pm

          • I would be somewhat wary of bleeding air into your manifold if you’ve got a diffusion pump setup and LN2 cold traps…There is the remote possibility of condensing LOX, but more importantly you’re probably gonna condense the humidity in the air and fill up your vacuum/cold traps a lot quicker. I would definitely use UHP argon/N2 to bleed your vacuum manifold instead.

            Comment by Ian D. — March 16, 2017 @ 2:35 pm

          • good point

            Comment by milkshake — March 16, 2017 @ 10:57 pm

  38. how do you purify the gas here? do you pass through copper catalyst?

    Comment by kudumi — July 17, 2016 @ 11:47 am

    • I didn’t. I my last job, we had a large source of house nitrogen from Dewars of liquid N2 – it comes cryogenic so it is bone dry (but one has to worry about residual oxygen content) – this is what I would use if I needed lots of working gas, i.e. for filtration under nitrogen blanket flow overnight, to prevent moisture getting into filter cake after precipitating polymers such as PEG with ether or MTBE.

      For actual oxygen sensitive chemistry we were using tanks of Argon, for which we had separate pipes. We were using high grade (“five nines”) argon that was guaranteed oxygen free – it cost here about 50 dollars a tank – with the delivery charge only few dollars more than low grade argon, so we were buying the best grade. With Ar tanks I would worry about moisture (it is very humid here in Florida) so for my needs I would buy a drying tower filled with Drierite (blue indicator) and activated molecular sieves, and I passed my argon though it before it went into the manifold.

      Obviously, with a common size compressed argon tanks one has to make sure there is no leak in the connections, and that all manifold ports not in use are shut before leaving in the evening, otherwise the Ar tank can run empty the next morning.

      Comment by milkshake — July 17, 2016 @ 1:06 pm

  39. I am new with the Schlenk lines. I was reading that it is possible to use PTFE diaphragm vacuum pumps in order to avoid cold trap (and condensing the oxygen).
    If this is correct, would it be possible to use this pump (, is the ultimate vacuum enough for the air-free synthesis?

    I must say that blog is really helpful and great.

    Many thanks in advance.

    Comment by redza — September 4, 2016 @ 2:31 pm

    • KNF teflon pumps (and their Fisherbrand clones) are good for drying ovens, or rotovaps – but they produce at best 10-15 Torr vacuum, which is not nearly enough for your purposes. Also, their pumping rate (in liters per minute) is low. For comparison, with liq. N2 cold trap oil pump can deliver 0.05Torr in the manifold and for dry ice trap with oil pump it is about 0.25 Torr.

      You need a cold trap and a good oil pump for your manifld

      Comment by milkshake — September 4, 2016 @ 11:48 pm

  40. Hi thank you very much for the blog. It is really helpful for the Schlenk line users.

    How can we avoid condensation of liquid oxygen in the trap. Can we use dry ice instead of liquid nitrogen or any other way.
    If there is condensation of liquid oxygen the what the steps should be taken to avoid any risk?
    Thank you very much in advance.

    Comment by Ravi — January 23, 2020 @ 1:50 am

    • Hi Ravi, 1) with dry ice cooling there is no risk of liquid oxygen condensation. Dry ice/acetone also has longer-lasting cooling capacity so it will be good overnight without risk of cold trap warming up, and contaminating your pump oil. I would use dry ice when dying material from a large quantity of solvent.
      2) Liquid nitrogen allows you to achieve much better vacuum in the mTorr range, but this makes mostly difference when you are distilling poorly volatile compounds (and need as good vacuum as possible). Liquid oxygen can condense in the trap if there is faulty connector and when large volumes of air are passed through the liq. nitrogen trap (= there is no measurable vacuum in the system in the sub-Torr range, while the pump is running and the cold trap is filled with liq. N2, and all that air is being passed through the trap). So you have to make sure to have good joints, seals, see if you can get down to 0.2 Torr with dry ice, and if yes, then you can maybe try with liq. N2 cooling. Make sure the cold traps are clean, without organics. If you by accident condense liquid oxygen (bluish liquid), remove the dewar with liquid N2 and put a blast shield in front of the cold trap, keep the pump running, disconnect everything else from the manifold, and inform people in the lab about the hazard, so that they don’t work in the vicinity until liq. O2 evaporates – this goes away within 20 min if you remove the cooling source.

      Comment by milkshake — January 23, 2020 @ 4:11 am

      • Dear milkshake, thank you very much for the detailed informative answer. It is really helpful.

        Comment by Ravi — January 24, 2020 @ 2:44 am

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