How to Run a Flash Column

Flash chromatography is performed according to the method of Still ("Rapid Chromatographic Techniques for Preparative Separation with Moderate Resolution." Still, W. C.; Kahn, M.; Mitra, A. J. Org. Chem. 1978, 43 (14), 2923-5). All flash chromatography should be done with Silica 60.

1. Choosing a Chromatography Solvent System
   1. Identify a suitable solvent mixture for your compound or reaction mixture. As a general rule the desired compound should be at about rf=0.3 on the TLC plate. Two spots which are close or which co-spot in the regions of rf=0.7-1 or fr=0-0.2 may in fact be very easy to separate.
   2. For most application, mixtures of hexanes and ethyl acetate (100:0 - 0:100 hexanes/ethyl acetate) are best. Other useful solvent systems include methylene chloride/methanol (100:1 - 100:10); ethyl acetate/acetone (100:0 - 50:50); and toluene with acetone, ethyl acetate, or methylene chloride.
   3. For basic (i.e. nitrogen containing) compounds, it is sometimes useful or necessary to add a small amount of triethylamine or pyridine to the solvent mixture (about 0.1%).
   4. For acidic compounds, a small amount of acetic acid is sometimes useful. In this case, be very careful in concentrating the solvent as trace amounts of acids can be very dangerous when they are concentrated with a product. In these cases, the acetic acid can often be safely rotavaped away by adding portions of toluene and concentrating to a few mL volume and repeating this several times. As acetic acid boils at a lower bp than toluene, this will remove the acid without exposing the neat compound to it.


2. Packing the Column
   1. A chromatography column is plugged with a small piece of cotton wool, just enough to fill to stopcock hole.
   2. Sand, about 2 cm ,is added so that the diameter of the sand is approximately the same as the column.
   3. Silica gel is added dry. Usually, it is best if the silica is not too long, about 6 to 10 inches is best in most cases.
   4. Attach the house vacuum to the bottom of the column via the stopcock. Open the vacuum and the stopcock; this will compresses the silica gel and hold it tight for the next steps.
   5. Add sand to the top of the column, about 1-2 cm is enough. With the vacuum still applied, pour the solvent (premixed, i.e. 4:1 hexanes/ethyl acetate). Allow the solvent to flow though the column until it is almost eluting. At this point, close the stopcock and remove the vacuum line.
   6. Make sure enough solvent is in the column for 5-6 column volumes worth to flow though, to ensure complete packing. Now elute all of the solvent with air pressure, taking care not the let the column run dry. Stop with the solvent level parallel with the sand. A well-packed column should not have any cracks or patches. The solvent eluding from the stopcock should not be warm or hot.


3. Loading the Column
   1. Prepare a solution of your reaction or compound mixture in the minimal amount of methylene chloride possible. Using a pipette, add this carefully to the top of the silica, washing the flask 3-4 times with methylene chloride or the chromatography solvent. After each addition, allow the solvent level to descend into the very top of the silica gel (below the sand).
   2. Carefully added 2-3 pipettes of chromatography solvent and push this into the column (repeat 3-4x).
   3. Now, carefully fill the remaining column space with the chromatography solvent and elute using compressed air. A flow rate of about 2 inches/minute is ideal. This is measured by how fast the solvent column descends in the straight part of column, above the silica gel. It is most convenient to measure and adjust the flow rate before adding the compound!
   4. In cases where a reaction mixture or compound is not soluble in a suitable solvent for loading, it can be absorbed onto silica gel. This is done by dissolving the compound in acetone, adding silica gel and carefully concentrating the silica gel to dryness (careful: it bumps!). The dry silica is then added to the top of the packed silica column. In this case, sand should not be added to the column until after the silica-compound mixture is added. This method is recommend only as a last resort as separations are often inferior to solution loading.


4. Running the Column
   1. Column fractions are collected in test tubes, of a size appropriate for the type of column and polarity. Use the 13 mm test tubes for small scale (ie 5-50 mg) and larger test tubes for bigger columns. Refer to the guidelines in Still's paper for choosing fraction sizes.
   2. Start collecting the fraction immediately after adding your compound; it does not take long for very non-polar compounds to elute from the column.
   3. Once you have loaded a column, it is best not to stop it for any length of time. This is due to slow diffusion of the compounds on the silica gel, resulting in poor separation and diminished yields.
   4. To find your product, spot each fraction or so on a TLC plate and check which fractions contain compounds. Fractions containing the same compounds are combined, the test tubes washed with methylene chloride or (probably better for the environment), distilled ethyl acetate, and the solvent concentrated under reduced pressure.
   5. Do not let a column run dry or elute the solvent until after you are sure all of the compounds have eluted! This is an easy mistake to make!


5. After the column-cleaning up
   1. After you have finished, elute all of the solvent from the column using compressed air. Flowing air through the column for ~2 hours will give dry, free flowing silica gel.
   2. Pour out the contents of the column into the silica waste container.
   3. In most cases, washing the column with water and acetone is sufficient. If necessary, a small amount of liquid soap can be used. Try to avoid scratching the columns with abrasive brushes or soaps.