Troubleshooting the Experiment

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Problem: Reaction proceeds for a while, and then seems to stop.

Problem: The reaction looked good, but the yield was low.

Solution: perhaps the reaction was high-yielding, but you lost some product during workup or isolation.   See How to Improve Your Yield.

Problem: Your reaction was clean, but the product is clearly not the one you wanted.

Solution: These can be the most interesting reactions, so always isolate and identify your product, if the reaction seemed efficient.

Problem: You can't reproduce an experimental procedure from 1) the literature;   2) someone's notebook.

Solution: See Notes or Tips on Reproducing Experimental Procedures (coming soon)

Problem: TLC of your product mixture changed after work-up.

Explanations and Solutions:

A. Your product may not tolerate exposure to acid or base. If you used these during quench or workup, you can test the stability of your compound this way:

1. Remove a sample of your reaction mixture before quench, place it in a vial and treat it with the reagent in question.

2. Compare the TLC of the material in the vial with the material in the reaction vessel. If you   observe a reaction in the vial, you've identified your problem.

B. Your product may not tolerate exposure to water or air. Test as above.

C. An unknown contaminant may have entered your material at some point. Purify and see if things improve.

Problem: After workup, you can't find your product.

Explanations and Solutions:

A. Your product may be soluble in the aqueous layer- check it (you still have it, right?)

B. Your product may be volatile: check the solvent in the rotovap trap.

C. Your product may have gotten stuck in filtration media- if you had a filtration step, suspend the solid in an appropriate solvent and TLC the suspension.

Problem: Crude NMR looks awful, and you can't see the peaks you expect for your product.

Explanations and Solutions: Crude NMR is not always the best way to determine whether your reaction worked.   Situations when crude NMR is misleading:

A. Reagent peaks dwarf product peaks. Sometimes a reaction has worked perfectly, only you can't tell until you remove leftover reagent.

B. Solvent peaks dwarf product peaks. This is particularly true of reactions run in high boiling solvents, which are not always completely removed during workup.

C. The reaction gave a mixture of isomeric products. In these cases, NMR of the crude mixture is extremely complex, but simplifies upon purification.

D. Your reaction gave an unexpected product. These can be the most interesting reactions, so always isolate and identify your product, if the reaction seemed efficient.

Problem: The reaction looks bad, and you can't decide whether to continue with isolation.

Solution: See Examples (coming soon).

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