Dec 2, 2009

RBF Teaches: How to perform an extraction

Ok kiddies,

While it might seem simple and easy, I can tell you now, a lot of you are doing it WRONG! The seperatory funnel is an integral part of the organic and though I hate to say *GUH*. The principle is pretty straight forward - desired product + byproducts go in, desired product comes out pretty clean and dry and ready for analysis.

The general method is to use some sort of aqueous phase, usually used at the end of your reaction to "quench" (neutralise the reagents) and a polar solvent of some sort to draw out your desired compound. The aqueous "phase" or layer can often have some sort of salt dissolved in it (NaCl is common, as is NH4Cl) this is to saturate the water layer with salt so that the organic compounds dissolved in it are more readily taken up by the organic solvent phase as they are less soluble in the aqueous phase due to the salts.

The organic solvent that you add is really quite dependendant on the product you are making, for example some polar compounds can only be drawn out with a very polar solvent like Ethyl Acetate (EtOAc) or Chloroform (CHCl3). The one thing about the organic solvent is that it MUST NOT BE MISCIBLE with water i.e. does not dissolve in water. This can be gauged by the density of the solvent if the solvent is  significantly more dense (density >1) then the solvent will sit below the water layer. Conversely, if the solvent is less dense (density<1) then the solvent will sit above the water layer. Usually, lighter solvents are chosen as they tend to be cheaper than the more dense.

Ok, so here is the IMPORTANT part.
  1. Make sure the tap is closed and clamp the sep. funnel by the NECK (i.e. the small region where the stopper inserts) don't clamp it anywhere else, it will break. 
  2. Wash your sample into the sep. funnel (usually use both a small amount of the aqueous and the organic solvents AND FOR THE SAKE OF ALL THINGS GOOD AND HOLY USE A FUNNEL). 
  3. Put a stopper on the top of the sep. funnel and place your index finger over the stopper and hold the flask with your dominant hand. Unclamp the sep. funnel and with your index finger still in place invert the funnel. 
  4. Shake the funnel to mix the solvents, don't be a baby about it but don't go overboard - shake too vigourously and you will most likely end up with an emulsion of layers that will take quite a while to seperate. Every 5 shakes or so it is a good idea to point the inverted sep. funnel into the fume hood and open the tap to release the vapour pressure that has undoubtedly formed. 
  5. Once, you feel you have shaken enough, usually after about 20sec you can clamp the flask by the neck again BUT MAKE SURE THE TAP IS CLOSED. 
  6. Then REMOVE THE STOPPER - if you don't the sep. funnel will not pour. 
  7. Allow the layers to seperate nicely and then begin draining the lower layer. As a general rule I usually say "if you want the top layer leave a bit of the bottom layer in the funnel, if you want the bottom layer take a bit of the top through as well". While I know it isn't exactly necessary you often find that that way you don't really start worrying about getting the seperation exact. 
  8. If you were after the top layer then collect this in a different collection flask. Make sure the collection flask is quite a bit larger than the amount of solvent you intend to collect.
  9. Pour the AQUEOUS layer back into the seperatory funnel (needless to say, if your aqueous layer was the top layer you don't have to drain this first then pour it back in).
  10. Add again the same amount of organic solvent as in step 2 and repeat the steps 3-9. Do this twice so you have 3 extractions overall. 
  11. It is a good idea to TLC your extracts to make sure you are taking the desired spots through and when they have stopped coming through. A good way to do this is to take a TLC spot from a drop of organic solvent on the tip of the sep. funnel.
  12. OPTIONAL - sometimes unwanted material may also come through with the organic solvent, in this case a wash of the organic solvent with clean brine or water may remove these impurities. This simply requires you pouring the organic solvent into the emptied sep. funnel and adding the aqueous wash. (PLEASE USE A FUNNEL)
  13. Once you have collected all of your organic solvent you can add a drying agent to remove any water that may have inadvertantly come through. Usually, sodium or magnesium sulfate works a treat. Simply take your collection flask, which should only be 1/3 full or thereabouts and gently swirl the solution while sprinkling in the drying agent. Swirl the flask for about 1-2min to ensure the water is absorbed by the drying agent. You should see clumping of the drying agent that indicates water is being taken up but once the drying agent stops clumping you should have a dry solution.
  14. Filter off the drying agent and make sure to wash the filter with more of your organic solvent to ensure all of the extracted compound is taken through. Usually you would filter into a PREWEIGHED round bottom flask of sufficient volume (twice as large RBF as the volume you have) and then place the RBF onto the rotavap to remove the solvent.
  15. Pump the resultant product down and Bob's your uncle. You may have to run a column on your product after this but any tricky ionic/salt compounds will be removed and you will have at least a crude weight and something to analyse by NMR or GCMS.
Important points to remember
  • Make sure the tap is closed before you add your solution or turn the sep. funnel upright.
  • Use a damn funnel for pouring solvents.
  • Hold the sep. funnel stopper with your index finger before you unclamp invert it.
  • The sep. funnel should be inverted the entire time it is in your hands.
  • Don't shake too hard or you will get an emulsion. 
  • Remember to release the vapour pressure. 
  • Make sure the tap is closed before you turn the sep. funnel upright.
  • Remove the stopper once you have your sep. funnel clamped.
  • Don't add too much drying agent. It is a waste.
  • Pre-weigh your RBF!


  1. I never clamp mine! I find a ring stand is much less of a pain to deal with--with the right size of ring, of course.

  2. This is true but as it is your lab and fume hood you can afford to go searching for a ring stand. Try finding 20-50 odd ring stands for students and you waste a hell of a lot of time. I knew I would get that comment sooner or later tho :P

  3. It's probably a case of the undergrad labs not having enough ring stands. I think there's about 3 stands in the whole lab...

  4. If you are quenching acid with bicarb or vice versa, make sure the mixture has finished reacting and "schweppervescence" has ceased before putting the stopper in the sep funnel and shaking the hell out of it.