Troubleshooting: Thin Layer Chromatography (TLC)

Not Voodoo Home / TLC Notes / Chromatography Notes / Comments?

TLC Tips: for when conventional thin layer chromatography
on the crude reaction mixture is problematic:

#1: Do a mini aqueous workup on a small amount of the reaction mixture, in a vial. Then TLC the organic layer.

#2: For very polar compounds, use

  • 10% NH4OH in MeOH solution as your polar solvent: try 1-10% of this mixture in dichloromethane.
  • EBAW: EtOAc/butanol/HOAc/H2O in a 80/10/5/5 ratio (note: this solvent system CANNOT be used for flash chromatography).

#3: Use Gas Chromatography (GC).

#4: If all else fails, remove a sample of your reaction mixture and take an NMR.

Problem: My reaction is in a high boiling solvent (DMF, Pyridine, DMSO, Amine solvents) and TLC just looks like a huge smear.

Solutions: Spot the plate as usual and then put it in a flask under high vacuum for a few minutes, and then run it, OR use TLC tip #1.

Problem: My reactant and my product have very similar Rfs. I can't really tell what is happening. How do I know when the reaction is complete?


#1: The cospot could help. If it looks like a snowman, your reaction is complete.

#2: Try changing solvent systems.  

Tip: There are three classes of solvent systems for chromatography that give distinctly different results. They are:

•  Polar/ hydrocarbon systems (ethyl acetate/hexane; ether/petroleum ether)

•  Polar/ dichloromethane systems (ether/dichloromethane;ethyl acetate/dichloromethane; methanol/ dichloromethane

•  Polar/benzene systems (ether/benzene; ethyl acetate/benzene)

#3: Try staining with anisaldehyde. Compounds are different (bright) colors. Sometimes color differences are also visible with molybdenum stains.

Problem: My compound might not be stable to silica gel (acid sensitive compounds can be a problem.)   How can I find out if it is stable to silica or not?

Solution: Run a 2D TLC:

•  Using a square silica plate, spot the sample in one corner.  

•  Run the plate in one direction (all components of the sample will appear in a vertical line of spots).

•  Turn the plate 90 degrees (your "line of spots" should be at the bottom) and run the plate again.

•  If the sample is stable to silica, all spots will appear on the diagonal. If a compound is decomposing, it will appear below the diagonal.

Problem: My compound is unstable on silica. How can I monitor the reaction accurately?

Solution: Try TLC tip #2, 3 or 4.

Problem: I don't want to expose my reaction to air- how do I get a TLC sample without opening the reaction vessel?

Solution: Set up your reaction flask such that it has a septum and is not under strong positive pressure of an inert gas. Thread a capillary spotter into a 20 gauge disposable needle, and put the needle into the septum. Use the spotter to get your sample, reinstall your inert gas, and remove the needle. This procedure involves minimal exposure to air.

Problem: When I dip my capillary into my reaction to take a TLC, the reaction mixture clogs the pipette and I can't spot it onto a plate. How do I TLC a heterogeneous or viscous reaction mixture?

Solution: TLC tip #1.

Problem: My reaction looks streaky on TLC.

Explanations and Solutions: This could mean a number of things.  

•  Massive decomposition. However, don't assume this just because your TLC is streaky.

•  One of the reagents streaks: try TLC Tip #1.

•  Your product is intact, but unstable to silica. Try a 2D TLC (above).

•  Your solvent is interfering with the TLC. See the first problem on this page.

Problem: My compounds are very polar and stay on the baseline. I can't see what is happening during the reaction.

Solutions: Try the solvent system described in TLC Tip #2, or use reverse phase silica gel plates.

Problem: The TLC of my product mixture changed after work-up!

Explanation/Solution #1: Your product may not tolerate exposure to acid, base, air, water, etc, and a reaction is occurring during workup. You can test small samples of your reaction mixture before you quench it to figure out what causes the problem, which may allow you to prevent the reaction.  

Explanation/Solution #2: An unknown contaminant may have entered your material at some point. Purify and see if things improve.

For more on thin layer chromatography, including troubleshooting, see:

*If your problem is not on this list, post it on Q & A!*