Use of a separatory funnel (“sep funnel”)

1. Setting up. Choose a separatory funnel with a capacity of at least double the volume of solvent that you will be extracting from (e.g. the reaction mixture). Before use, the separatory funnel should be clamped or supported or over a conical flask. The sep funnel can be carefully clamped on its ground glass joint, or supported in a circular metal ring stand.

You should also ensure that the stopcock is securely fitted. Some stopcocks are ground glass, which should be lightly greased (so as to not contaminate the solutions).  Teflon stopcocks do not need to be greased.

You should ensure that you have the right size stopper for it. The sep funnel will need to be stoppered and unstoppered during the procedure, so it is crucial that the ground glass surfaces are not contaminated with product – hence the solutions should be transferred in using a funnel. In general, it is better to avoid greasing the stopper, as this risks introducing contamination – particularly if the organic layer is to be poured out through the neck of the funnel (see 4. Separating the layers). However, lightly greasing the top part of the ground glass surface of the stopper may be appropriate.

2. Transferring liquids in. Check the stopcock is closed, and pour in the mixture to be extracted, and the extraction solvent, using a funnel. The solvents should not be hot. Remove the funnel, but do not stopper the separatory funnel. At this point, two layers should form. Typically, one layer is aqueous, and the other is organic. The separatory funnel should never be more that 2/3 full – there needs to be room to mix the layers, with spare room for solvent vapour. If the volume of the mixture to be extracted is too large, then it should be done in batches, or in a larger separatory funnel.

3. Swirling and shaking. To carry out an efficient extraction, the aqueous and organic layers need to be thoroughly mixed. However, mixing the layers can generate surprisingly high pressures under some circumstances, so care is needed. If the separatory funnel is mishandled, these pressures can very easily expel the stopper/stopcock/chemicals with great force.

(a) After adding the liquids to the separatory funnel, and without inserting the stopper, it is good practice to gently swirl the separatory funnel. This causes some preliminary mixing of the layers, which reduces potential pressure build-up later. This is especially important in the special cases outlined in (d). After some gentle swirling, put the stopper into the separatory funnel and return it to its support.

(b) Before mixing, the separatory funnel needs to be lifted from its support, and held securely. To hold the separatory funnel securely, the following steps are required:

• hold the separatory funnel with both hands

• use one hand to hold the curve of the separatory funnel, using a finger to hold the stopper securely in place

• use the other hand to hold around the stopcock of the separatory funnel, so that you can hold the stopcock in place, and also so that you can open and shut the stopcock quickly and easily.

(c) In order to mix the layers thoroughly, you should:

• hold the separatory funnel as described in (b).

• invert the separatory funnel, so that the stem is pointing upwards. Immediately “vent” the separatory funnel, by pointing the stem somewhere safe (i.e. away from people - the top corner of the fumehood is advised), opening the stopcock to release any pressure build-up (you may hear a slight hissing sound – if so, wait until it subsides), then closing the stopcock again.

• keeping the separatory funnel inverted, gently swirl the contents, then vent it again. If there is an evident pressure build-up (such as an audible hiss), repeat the gentle swirling/venting multiple times, until it diminishes.

• keeping the separatory funnel inverted, and a strong grip on the stopper and stopcock, shake it vigorously for a few seconds, then carefully vent again. Repeat for a total of ~10 seconds of vigorous shaking. Vent the separatory funnel, then return it to its support.

(d) There are two common scenarios in which high pressures are generated in the separatory funnel:

• in “chemically-active extraction” (see below for more detail), exothermic neutralisation reactions take place; this is particularly hazardous when acidic organic molecules are reacted with aqueous sodium bicarbonate, since this neutralisation generates CO2 gas, which causes a large increase in pressure inside the separatory funnel.

• when the organic solvent is especially volatile, such as diethyl ether (b.p. 35 °C), the amount of vapour pressure generated by the solvent will be high; this effect is magnified by the heat transferred into system by holding the separatory funnel securely.

4. Separating the layers. Let the separatory funnel stand for a minute. The organic and aqueous components should now separate into clear layers (if they do not, see Problems with extractions, below). Which of these is the upper and lower layers is difficult to predict with certainty, as it depends on the relative densities of the solvents, and also the species which are dissolved in them. In general, chlorinated solvents (such as dichloromethane) are more dense than water, and will form the lower layer, while other organic solvents (e.g. diethyl ether, petroleum ether, ethyl acetate) are less dense than water, and will form the top layer. A convenient way to tell which layer is which, is to examine the separatory funnel to see the relative sizes of the layers, and then add a small volume of water – the aqueous layer will increase in size.

Place a clean conical flask under the separatory funnel, and remove the stopper. While watching the interface between the layers, hold the funnel, and open the stopcock carefully – the lower layer will begin to drain out into the conical flask. The flow rate should be slow, so that there is no disturbance in the flat interface between the layers. Fast flow will cause a vortex to form, which might drag some of the upper layer through the stopcock, and also makes it very difficult to close the stopcock at the right moment.

Close the stopcock at the point where the interface is passing through. Label the conical flask immediately – it is very easy to forget the identify of several similar-looking flasks. The top layer should be collected by pouring it out of the neck of the separatory funnel, as this avoids any contamination of the top layer by the residual material in the stopcock and stem. Label this flask as well.