Compound Isolation/Purification

    It is a rare event in synthetic chemistry that a reaction product is isolated in pure form,  More often, whether it is a solid or liquid, it's off-color (not white or clear) and TLC analysis shows the presence of one or more impurities.  Since you're usually making a compound that's never been made before (at least by you), you need to decide how to purify it before going no to the next step.  First, let's look at the most efficient way to check compound purity while it's being isolated.

    Unless the reaction you are running has been run many times in the past - by you - do not skip any of the following steps.  I know of no researcher, including myself, who has not had to go back and repeat reactions because assumptions were made about the purity of the product, which was then carried on to the next step, only to have the next reaction fail spectacularly because of starting with impure starting material.  As they say in computer programming - garbage in, garbage out.


Isolation - Initial TLC/GC Analysis

    Usually, a workup procedure involves pouring the reaction mixture into an aqueous solution (or just water) and isolating the organic material via extraction with ether, dichloromethane, or other solvent.  After the extractions, which are combined and dried (usually over anhydrous magnesium sulfate or other drying agent), the extraction solvent is stripped on the rotary evaporator (aka the "rotovap").

    The best time to get a TLC is when you've stripped most, but not all, of the solvent (maybe 50-100 mL remaining).  Stop the rotovap, remove the flask, and remove several drops with a pipette into a small test tube; then, continue stripping the remaining solvent.  Meanwhile, analyze the material you removed via TLC; you should spot the reaction product next to the starting material (unless prior TLC's, run during the reaction, have established that the starting material is gone). 

    The best eluant to start with is dichloromethane.  If the spot(s) are too low, go to a more polar eluant, like 10% ethyl acetate-hexane (you can, of course, increase the amount of ethyl acetate used, if the Rf values are still not large enough).  If the spots run to the top of the TLC plate, move to a less polar eluant, like hexane.

    This first TLC will tell you much about the reaction - whether it consumed all of the starting compound, how many products were formed, and what their polarity is relative to the starting material.  Obviously, if you see many spots of equal intensity, the reaction is likely not useful.  But, if you get a single spot (or accompanied by just a couple of faint impurity spots), that is clearly not the S.M., it's promising.

    If the TLC looks good, and you know that your product is fairly volatile (between 6 and20 carbon atoms), you should then obtain a gas chromatograph for the mixture.  GC has many advantages over TLC - it's faster (usually), and gives a quantitative measurement of the number of components and the percent each component contributes to the mixture.  Also, you can print the GC trace and tape it into your lab book as a permanent record of what it looked like, both before and after purification.

    When you're done getting TLC/GC data, finish stripping the solvent, then place the flask on the high vacuum line for 30-60min to remove the last traces of solvent.  The time NOT to do this is if your product has fewer than about 12 carbon atoms, because its volatility will cause it to evaporate under full vacuum and it will be lost.


IR Analysis/Melting Point Determination

    As soon as the crude material has been isolated, obtain an IR spectrum.  ALWAYS do this!  Also, if it is a solid, obtain a melting point for the compound, regardless of how pure you think it may be.  Both the IR and mp will tell you about the purity and identity of the product.  If necessary. compare the IR with that of the starting compound; this way, it is clear what functional groups may have been lost or generated.  Also, the IR of a pure compound is characterized by many sharp, deep absorbances, especially in the fingerprint region (< 1000cm-1), while a mixture of compounds gives IR spectra with fewer, rounded peaks.  With a little experience, you'll be able to gauge the purity of a compound just by its IR spectrum.

    From the IR/mp data, you can determine whether purification is necessary.  If the compound - liquid or solid - is highly colored, chances are that it's impure, although this is not an infallible rule!  Just a tiny amount of highly colored impurity can cause the entire batch to look impure, when, in fact, it could be 98+% pure.  The true measures of purity are the IR/GC/mp data.

    If you have an impure solid, you'll need to recrystallize it; impure liquids are usually distilled.  For the background on these techniques, see the appropriate section of the Techniques page.