Separating Isomers: Efficient Method for Chemists?

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Separating isomers can be a tedious process, especially when using silica gel columns and requiring multiple steps like evaporation and LC/MS analysis for each fraction. The original poster expresses frustration over the inefficiency of their current method, which involves handling over 80 fractions to identify unwanted isomers. Suggestions from other chemists include exploring different solvent systems, solid phases like alumina and Florisil, and considering gas chromatography (GC) for quicker analysis. The use of preparative HPLC with an automatic fraction collector is also recommended for better separation and efficiency. Overall, there are alternative methods available that could significantly reduce the time and effort involved in isomer separation.
gravenewworld
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is any other chemist on here familiar with trying to separate isomers? I hate how tedious it is, after I run a silica gel column, I have to take each fraction evaporate the eluent, dissolve what is left behind in methanol, prepare LC/MS sample, and wait 3.2 min for each sample to run in order to find out which fractions have the isomer i don't want. This is extremely tedious and time consuming when you have about 80+ fractions all for the same compound. you can't see the isomer separate on TLC (the spots will just loot like one spot) so LC/MS is the only way I know of so far that will work. Does anyone on here have a trick up their sleeve and know a more efficient and time saving method to figure out which fractions contain the unwanted isomer?
 
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Well, it could be worse. At least your LCMS run is fast.

Have you tried a lot of solvent systems? What about different solid phases (alumina, Florisil)? That might get you enough separation.

Do you really have to strip down all of the fractions? What about using GC instead? That might save a lot of time.

What about prep HPLC? Our lab has a prep HPLC that has an automatic fraction collector and measures the UV absorbance of everything that comes off of the column. You can usually get better separation with that too.
 
I will have to bug our analytical chemist so I can use the GCMS machine. He doesn't let anyone use it. Other than that, yeah I really do have to strip down all the samples I take from the fractions. I mostly use a ethyl acetate/hexane eluent for the columns that I do because it seems to work the best. The columns I used are also prepacked (i just load the column and put it on the ISCO machine that basically does everything else for me), so the company only has loads of silica gel ones. I will see if i can order alumina and florisil columns too. Thanks again.
 
That much automation and you're still complaining?! :)

If you could use GC then you might be able to just take an aliquot from each fraction and shoot it on the GC without having to strip it down.

Do you need the MS part? You might be able to do it with just regular GC.
 

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