Dr. Garner’s lab favorites (as of June 2019)
¼” polyethylene tubing is great for running gas lines, and it accepts ¼” Swagelok fittings flawlessly. I order it from VWR, but it is also available at Home Depot or Lowes, but check to make sure OD fits Swagelok snugly (once I have found it a little too large). We use Swagelok needle valves mounted in holes in the hood wall to control gas flow. This size tubing interfaces well with butyl rubber tubing (see below).
The best anti-suck-back bubbler is made by Chemglass (item # CG-4522-01), currently ~ $112 each after discount. Very reliable at preventing oil return under all conditions, avoids the hazards of mercury. (larger version is unnecessary)
Butyl rubber tubing is the best type, especially for manifold hoses. This is a black tubing, very flexible yet won’t collapse under vacuum, and has highest resistance to oxygen permeability. Expensive but lasts almost forever; ends will eventually crack, but you can cut off ¼” and it’s good for 1-2 years each time (and a layer of Parafilm will prevent even that). Only available from Fisher and only in ¼” ID, all look-alikes are fakes. Currently ~ $10 per foot, Fisher #14-168B. Update August 2019: This appears to no longer be available from Fisher, but is available from LabSupplyOutlaws.com for about $13 per foot. Update October 2021: Its available on Fisher again, catalog # NC1981076., 10 ft/$102
Chemglass sells weighing boats that are also funnels, make handing solids easier. Also come in anti-static versions. Polypropylene, completely reusable.
The Chemglass double manifold #CG-4440 or 4441 are very good, ~ $100 per valve if you ask for a quote (important!). These have the high vacuum stopcocks, which can be further secured with 19/22 Keck clips (VWR # 80061-128). A convenient vacuum trap is Lab Glass # LG-11013-110; convenient because it accepts ¼” hoses.
Aldrich makes something called a Kramer filter which is really handy for doing filtrations or passing solvents through alumina under inert atmosphere using a cannula. Basically, it’s a fritted tube with 14/20 F joint at top and a stainless needle adapter at bottom. With skill, even hot filtrations can be done. Item # Z101397.
If you have the time, you can often find good deals on used equipment at Labx.com. It is buyer beware, but I have gotten many things there and only once been cheated.
Recirculating chillers are superior to tap water for running condensers because you can run sub-ambient and the risk of spills is limited. We use quick disconnects by Colder Products (VWR #16001-750 and #16001-768, for female and male ends, resp.) which are much less expensive (only about $4 per piece) than competing products. These stop the flow when disconnected (convenient) but it also means that you must reconnect to resume flow. I recommend running at 15 °C (or as cold as you can go without condensing water on the outside).
The rare earth magnet stir bars are really good and not very expensive, see VWR # 89030 (various sizes listed there). These have a black dot on them to distinguish from others.
When applying vacuum to powdery solids that could get carried into your manifold, always use a fritted adapter (Chemglass #1011, avail in 14/20 and 24/40).
The only way I know to quickly get a solvent-free NMR tube after cleaning is to apply vacuum. This is easily done by inserting a short 20-22 gauge needle (e.g., VWR# BD305176) through an NMR tube septum (Aldrich # Z553891) and applying vacuum through a “hose to needle adapter” (the barrel of a 1 mL syringe with the handle cut off). Something like 10-20 seconds of vacuum (aspirator or pump) removes solvent vapors efficiently. I like to rinse my tubes with distilled hexanes after acetone because hexanes leave no residue whereas acetone could have some aldol present.
Products that are oils tend to hold onto solvent (esp. ethyl acetate) even after prolonged pump vacuum. One way to reduce this is to add CDCl3 (or other deuterated volatile solvent) then pump it off. The evaporation process tends to carry off the residual protic solvents. The best way to know how long your product needs to remain under vacuum to remove residual solvent is to bring it to constant weight (weigh at intervals until constant).
Besides the all-plastic syringes, Air-Tite makes a nice disposable 4” 22-gauge needle, VWR #89219-270. These are long enough for many uses and only $ 0.40 each. My habit is to wash and re-use “disposable” syringes and needles. They also make a cap for syringes that is sometimes handy (VWR #97001-202).
Inexpensive vacuum gauges are handy indicators of vacuum level, especially in situations where there is some uncertainty of the pressure. For example, with rotovaps there can be leaks in the shaft seal or poor performance of a water aspirator. The inexpensive gauges read in inches of water (!) not Torr, but are only ~ $15-20 (e.g., VWR# 300007-467) plus a fitting to connect to hoses. Electronic gauges are also available, though more expensive. Grainger has one (#3KNP6) with a range of 0.015 to 12 Torr ($141). Or Grainger # 9XHF8, 0.01 to 25 Torr, $304. I do not have experience with these.
Polyethylene stoppers for reaction flasks are really handy and very inexpensive, for example, Chemglass #CG-3021.
The best (and surprisingly, the cheapest) butyllithium is from Alfa Aesar through VWR. Item # AA41248 is for 4 x 0.5 mol bottles (~ $100 total), somewhere in the 2.2-2.8 M range (but specified on the bottles), already equipped with a septum cap. We place an upside-down 24/40 septum over (not in place of) the cap, and seal that with a never-punctured 14/20 septum. We have used this stuff for 4-5 years without titrating and have never had any problems. Stored in our freezer (~ -20 C), any one bottle has at least a 1-year lifetime after opening, probably 2 years if handled carefully.
A quick way to dry triethylamine is to treat it with a little powdered sodium hydroxide (do the grinding quickly to minimize water adsorption) in a septum-capped 15 mL polypropylene centrifuge tube (VWR# 89039-670). Shaking followed by spinning down gives a clear liquid and also seems to remove the yellow color of N-oxide present.
If you are having trouble condensing a solvent (say during reflux or distillation), a Graham condenser (Chemglass #1214) is far more efficient than the alternatives. Has to be used in a vertical orientation.
When doing hydrogenations, or as a “cannula bypass valve” (see description below), a syringe-type stopcock is handy. There are plastic versions available (e.g., Kontes) but these break quickly. A nearly indestructible metal one is VWR #20068-461, a Cadence Science product (or at twice the cost, Aldrich # Z506559). For hydrogenations, you attach a “hose-to-needle adapter” (1 mL syringe barrel) that has a doubled-over balloon (one inside the other for more strength) that has been secured air-tight (I find that tightly stretched Parafilm is good for this). You fill the balloon from a hydrogen tap (rinse a couple of times to get air out). After evacuating the flask with alkene/catalyst, you apply the hydrogen through the stopcock with a needle attached. This gives you 100% hydrogen atmosphere and no oxygen.
How to setup a manifold for cannula transfers. For cannula transfers, you want to be able to pressurize the source flask while maintaining the destination flask at bubbler pressure. To do this, place a stopcock at the inert gas exit of your manifold, followed by a “T” (see diagram below). One arm of the “T” goes to your bubbler while the other is attached to a hose that terminates in a luer stopcock valve (“cannula bypass valve”). This valve is normally kept closed to keep air out of your system. But to do a cannula transfer, put a needle on the bypass valve and insert it into the destination flask septum (already under inert atmosphere by doing ~ two vacuum/inert atmosphere purges). Then close the manifold exit stopcock, apply some inert gas flow (pressure should be set to no more than ~ 5 psi), and insert the cannula through the source flask septum then into the destination flask. When you push the cannula below the level of the liquid in the source flask, transfer should start. There is no need for continual gas flow; a non-leaking system will hold the pressure for awhile.
How to transfer relatively large amounts of anhydrous solvent without using syringes. Syringes are OK for small amounts of solvents or reactants, but only to about 20 mL. And they allow more air exposure than a cannula will. You can use vacuum to pull over solvents or reactants using a cannula. If you need to measure the amounts, pull the liquid into a septum-capped graduated cylinder (Chemglass #CG-1223) then use regular cannula technique to transfer it to your reaction flask.
Filtration through a small plug of cotton in a pipette is more efficient for small samples than a fritted filter is. You can add a little Celite for cloudy samples. For samples containing water, you can filter through anhydrous magnesium sulfate or (less efficient) sodium sulfate. If you use a bulb to push through (a good idea) be careful to remove the bulb before releasing it, otherwise a suck-back can happen.
The best TLC plates (you can actually write on these unlike the cheaper ones) are made by EM Science, VWR # 16485-1 (EMD-16485-1). These are glass-backed and have the fluorescent indicator. The best TLC cutting device is Sorbent Technologies TLC-cutter (and that is their part number), $650 but saves a lot of broken or defectively-cut plates.
Capillary GC tubing (~ 0.32-0.25 mm ID) is great for spotting TLC plates, so never discard an old column. But getting clean cuts is critical; use a ceramic cutter to get square edges (also great for any needed scratching of glass tubing): VWR # HP-5181-8836. These are inexpensive ( ~ $4 each) and last forever.
You can also use capillary GC tubing as a micro cannula to remove microliter samples from reactions under inert atmosphere. See Aldrichimica Acta 1988, 21, pg 2.
The best single way to visualize non-UV-active compounds is to stain the plate with PMA (phosphomolybdic acid) followed by heating to 120-150 ° on a hot plate for 20-60 seconds. The PMA should be a 2-5 wt. % solution in ethanol, and you can stain by quickly dipping the plate in and out of the solution, followed by drying (paper towel) before heating. Compounds appear as dark blue spots on a green background. Very sensitive for alcohols.
A way to make sure you don’t get syringe-caused cross-contamination between GC samples is to start with a clean syringe, take up 1 µL of clean (distilled) DCM, 1 µL of air then 1 µL of sample, then pull back the plunger until you can see the sample in the barrel of the syringe. When you inject, the clean DCM pushes out the sample, and a few rinses with DCM leaves you with an absolutely clean syringe. If you let the sample get around the plunger, it is much more difficult to clean the syringe.
To separate a volatile compound from non-volatile (or much less volatile) on small scale, Kugelrohr distillation is best.
Quick guidelines for doing column chromatography: for X amount of compound to purify, use 50X grams of silica gel (= 100 X mL silica, since d = 0.5), prepare about 350-500X mL of solvent, collect at least 50 X mL of forerun* and collect fractions that are 8-16 X mL in volume. Be prepared to collect at least 24 fractions, maybe as much as 48. * assumes your TLC Rf is ~ 0.3, the proper value for a column solvent.
For storing chromatography columns that have integral reservoirs: if you have a corner in the lab somewhere, mount a piece of plywood with 2” diameter holes drilled in it (use a hole bit) maybe 6-8” apart; the columns will hang down nicely.
If you have a non-polar dye around that is quite a bit less polar than compounds you care about, you can add a little to your crude product before column chromatography to mark the solvent front. You don’t have to collect any fractions until the color reaches the bottom of the column. We use trimethylazulene (permanganate purple) pretty routinely for this. I can send some on request. Guaiazulene (blue) is commercially available at low cost, but it needs to be protected from air to avoid slow buildup of brown air-oxidation products. Ferrocene might work. But make sure that any dye you use moves quite a bit faster on TLC (in a solvent that moves your desired compound to an Rf of ~ 0.3) than the compounds you are after.
If you find yourself in a laboratory with the equipment to do radial chromatography, I recommend that you go to the trouble to learn this technique. It gives a better separation than a column will (more like TLC in that regard), is quick to set up and run. The plates are easy enough to make, or you can buy pre-made ones from Analtech, which is the only place that sells the instrument nowadays. A 4 mm plate can take a gram of compound, and from loading to elution is around 20-30 minutes. With some care to clean up messy mixtures ahead of time, the plates are reusable for several separations. I have sometimes observed separations that would have been impossible on a column.
The best fractionating column (short of the expensive spinning-band types) is the Snyder column (Chemglass #1304). This has glass “bubble valves” that rattle as distillation progresses. Gives easily the best separation I have encountered and is somewhat entertaining to watch too. Only available in 24/40 joint size from Chemglass, but Aldrich makes a 14/20 version (#Z516961 or Z517011). These are fantastic for cracking dicyclopentadiene, zero dimer distills.
If you use only deionized water in rotovap baths there will not be the unsightly buildup of minerals, etc., that is so common.