December 05, 2019, 04:47:47 PM
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Topic: Silica gel chromatography for less soluble compounds  (Read 1034 times)

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Online Babcock_Hall

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Silica gel chromatography for less soluble compounds
« on: October 15, 2019, 10:49:12 AM »
Good Morning Everyone,

Recently I have had a couple of instances in which the solid was not very soluble in the solvent used for silica gel chromatography.  In the second instance I was using 50:50 ethyl acetate/hexanes and I used a very large volume of solvent yet I did not dissolve all of my product.  In the second instance there is one major and two minor products by TLC, and I obtained a number of mixed fractions.  If the volume could have magically been lowered, presumably there would have been fewer mixed fractions.

A second method is to dissolve in a solvent, add silica gel and remove the solvent by rotary evaporation (I read this in a book on advanced organic techniques, but I do not have the page number in front of me).  Then one applies the impregnated silica to a column.  I have heard that one must put a plug of cotton into the top of the flask to keep the silica from entering into the rotary evaporator.  Are there any other problems that one might encounter along these lines?  Thank you.

Offline OrganicDan96

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Re: Silica gel chromatography for less soluble compounds
« Reply #1 on: October 15, 2019, 03:07:50 PM »
yes there are a few, you can get separation on the silica you load with, this is why some people use celite instead. another problem is that if the compound doesn't disolve immediately in column solvent then the compound will gradually be dissolved off the silica resulting in horrible streaking. another way you could load is by using a more polar solvent for the load (must be a small volumn as not to mess up the column polarity too much) DCM works particularly well

Offline hypervalent_iodine

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Re: Silica gel chromatography for less soluble compounds
« Reply #2 on: October 15, 2019, 06:35:50 PM »
Good Morning Everyone,

Recently I have had a couple of instances in which the solid was not very soluble in the solvent used for silica gel chromatography.  In the second instance I was using 50:50 ethyl acetate/hexanes and I used a very large volume of solvent yet I did not dissolve all of my product.  In the second instance there is one major and two minor products by TLC, and I obtained a number of mixed fractions.  If the volume could have magically been lowered, presumably there would have been fewer mixed fractions.

A second method is to dissolve in a solvent, add silica gel and remove the solvent by rotary evaporation (I read this in a book on advanced organic techniques, but I do not have the page number in front of me).  Then one applies the impregnated silica to a column.  I have heard that one must put a plug of cotton into the top of the flask to keep the silica from entering into the rotary evaporator.  Are there any other problems that one might encounter along these lines?  Thank you.

You can also use an adapter for the rot evap with a frit (if you have them), or I have attached the flask to a splash guard with a cotton wool plug. As mentioned above however, if your compound is minimally soluble you will likely still get streaking. I would also advocate DCM for the loading, or switching solvent systems entirely to something like DCM / MeOH if feasible. 

Offline rolnor

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Re: Silica gel chromatography for less soluble compounds
« Reply #3 on: October 16, 2019, 01:33:13 AM »
You can use EtOAc/Toluene instead, this mixture is a much better solvent. Its a little more polar so you need to adjust the mixture.

Offline wildfyr

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Re: Silica gel chromatography for less soluble compounds
« Reply #4 on: October 16, 2019, 08:45:06 AM »
Usually with more polar eluent systems I've seen people using DCM/MeOH in place of Hexane/EtOAc.

Dry loading is virtually always a good idea, independent of the specifics of the molecules.

Offline rolnor

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Re: Silica gel chromatography for less soluble compounds
« Reply #5 on: October 16, 2019, 11:34:04 AM »
Yea, DCM/MeOH is even better solvent but more work is needed to get the right RF.

Offline BobfromNC

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Re: Silica gel chromatography for less soluble compounds
« Reply #6 on: October 16, 2019, 04:21:57 PM »
We will sometimes do DCM to EtOAc gradient for hard to dissolve compounds.   But more mixed waste, so not ideal. 

If very polar, supercritial fluid chrom. works wonders, I just used it for some compounds that are quite polar and hard to do on silica, but on SFC, the compounds gave sharp peaks, good separations of similar materials, and high loading using 0 to 20% EtOH in CO2.   Very hard to get any purification on silica, but got 100 mg at a time done in 10 minutes on SFC with a semi-prep column.  Just have to find someone with a system, but becoming very popular now.

Plus you can drink the organic waste. :-)

Offline OrganicDan96

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Re: Silica gel chromatography for less soluble compounds
« Reply #7 on: October 17, 2019, 06:54:39 AM »
if very polar then reverse phase may work

Offline rolnor

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Re: Silica gel chromatography for less soluble compounds
« Reply #8 on: October 17, 2019, 09:32:45 AM »
What is the stationary phase when using SCF?

Offline rolnor

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Re: Silica gel chromatography for less soluble compounds
« Reply #9 on: October 17, 2019, 09:35:47 AM »
if very polar then reverse phase may work

Yes, RP-silica is very good for polar compounds but in my experience the separation, at least for low-pressure systems, is not as good as for straight-phase.

Online Babcock_Hall

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Re: Silica gel chromatography for less soluble compounds
« Reply #10 on: October 17, 2019, 10:16:23 AM »
Although I have often worked with very polar molecules in the past, my present molecules are aromatics with either an aldehyde or ester functional group, as well as a sulfone derivative.  On TLC they move when I use 40-50% ethyl acetate.  With respect to the question of whether dissolving in DCM and eluting or pre-adsorbing the compound on silica is the better option, is there any way to know in advance, or is it a matter of trial and error?

Offline hollytara

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Re: Silica gel chromatography for less soluble compounds
« Reply #11 on: October 17, 2019, 11:26:05 PM »
Working out these chromatographic systems is always tedious trial and error.  I have never liked pre-absorbing - as others have noted, it often leads to streaking or tailing of the bands.  I have used DCM/acetonitrile in the past, but of course acetonitrile was much less expensive back then (it was a side product in a now abandoned industrial process I believe). A lot of compounds have a very low Rf (approaching zero!) with straight DCM.  So adding the crude mixture as a concentrated DCM solution and then ramping up to the desired eluent is often pretty effective. 

Online Babcock_Hall

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Re: Silica gel chromatography for less soluble compounds
« Reply #12 on: October 21, 2019, 05:51:39 PM »
I was able to dissolve the remaining crude product in DCM.  The compounds eluted quickly, suggesting perhaps that they were pushed along by DCM (I did not try a TLC in DCM)  The column worked reasonably well running in 50% ethyl acetate.  I noticed that some of the stronger fractions showed some tailing in the TLC plates, which I had not seen in the previous column.  In some of the fractions containing the highest concentration of product, I saw crystals forming in the bottom of the test tubes I used for collection.

Offline kamiyu2550

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Re: Silica gel chromatography for less soluble compounds
« Reply #13 on: October 21, 2019, 08:58:28 PM »
I was able to dissolve the remaining crude product in DCM.  The compounds eluted quickly, suggesting perhaps that they were pushed along by DCM (I did not try a TLC in DCM)  The column worked reasonably well running in 50% ethyl acetate.  I noticed that some of the stronger fractions showed some tailing in the TLC plates, which I had not seen in the previous column.  In some of the fractions containing the highest concentration of product, I saw crystals forming in the bottom of the test tubes I used for collection.

A couple of things:

1. If you see tailing in TLC, it might be something amine or pyridine (or your TLC concentration being too high). If so, you need to add ~1-3 volume % TEA (triethylamine) in the eluent. The tailing should be gone.

2. Wet loading and dry loading have both their pros and cons. Yet, wet loading is more welcomed due to 1) simpler and faster procedure and 2) higher recovery

3. You mentioned some crystals formed at the bottom of test tubes. Two possible reasons: 1) The elution concentration is very high (i.e. the polarity of eluting solvent is too strong). The eluting fraction at the beginning is clear but this is just a metastable state which slowly crystallised. If this fraction is what you want and you need a high purity, then very likely a good news for you. What you have here is column chromatography tandem with recrystallization. Very likely the product is very pure. 2) The product indeed has a low solubility in the eluting solvent. The initial clear state is metastable only.

4. If you use dry loading, make sure your compound is stable when being adsorbed on silica gel. Not everything is happy with silica gel, especially you need to heat it up a little bit during rotavap.

Offline wildfyr

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Re: Silica gel chromatography for less soluble compounds
« Reply #14 on: October 22, 2019, 10:54:23 AM »
I've never had product crystallizing in the fraction vials turn out to be bad.

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