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Author Topic: Purification of a sugar on chromatography column  (Read 6126 times)

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katlly

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Purification of a sugar on chromatography column
« on: January 15, 2009, 11:05:00 PM »

Dear all,

I am trying to synthesise a sugar (peracetylated 6-azidofucose) and
have at long last reached the final step of peracetylation. The protocol I am following suggests using Hexane:Ethyl acetate 2:1 but my product gets stuck on top of the silica if I use it (even though it runs at an Rf of about 0,4 on a TLC). I therefore thought of using a more polar eluent like Dichloromethane:Methanol 98:2 (which makes the product run at about 0,5 on TLC) but surprisingly, it stayed stuk on top of the silica again. For curiosity's sake, I eluted the product with pure methanol (at least to see if it was indeed my product) and it seems to be. But of course, no seperation occurred so my product
is not purer than before I started the column!

I nevertheless evaporated the methanol and obtained an oil. For some reason, added pure dichloromethane to the flask. To my surprise, the oil dissolved in the DCM but a white precipitate formed. I checked it on a TLC and it seems to be my sugar (it is now at the NMR for confirmation).

I would like to understand better what has been going on in order to start my synthesis again and purify it in a more controlled manner Would any of you have an explanation to this phenomenon? And would somebody have a suggestion to help me "unstuck" my product AND get a sepration?

Thank you very much in advance!

Thank you for your help"
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Arkcon

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Re: Purification of a sugar on chromatography column
« Reply #1 on: January 16, 2009, 02:10:21 AM »

Quote
The protocol I am following suggests using Hexane:Ethyl acetate 2:1 but my product gets stuck on top of the silica if I use it (even though it runs at an Rf of about 0,4 on a TLC).

Working with this part, right here, only -- I'd first make sure you're using the same grade of silica that the protocol suggests, or the same grade as your TLC plate.
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katlly

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Re: Purification of a sugar on chromatography column
« Reply #2 on: January 16, 2009, 02:25:37 AM »

Thank you for your answer.

I am using the same silica as specified in the publication for the column. I do not know about the TLCs but this purification is the last one of three steps and I had no trouble in comparing the TLCs to the column with the other purifications ever.
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azmanam

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Re: Purification of a sugar on chromatography column
« Reply #3 on: January 16, 2009, 03:08:06 AM »

careful... methanol can dissolve silica gel.  the white precipiate you may be getting may be silica gel with the sugar absorbed on it.
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katlly

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Re: Purification of a sugar on chromatography column
« Reply #4 on: January 16, 2009, 04:44:23 AM »

I thought about that but the way I reveal my product is specific (a react the azide with PPh3 to create an amine and then reveal the amine with nynhidrin) so it wouldn't show on the TLC if it were silica. And I don't think it is silica with traces of solvent because it dissolves in water. (does water dissolve silica as methanol does?)
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Dan

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Re: Purification of a sugar on chromatography column
« Reply #5 on: February 03, 2009, 07:28:02 AM »

Is the material you recover from the column after methanol washings still peracetylated?

The only other explanation I can think of is that somewhere between running the TLC and loading your compound on the column (perhaps in the workup) you are getting some deprotection (the anomeric acetate is the most likely culprit - I am assuming we're talking fucofuranose/pyranose here). Maybe the anomeric acetate is acid labile enough to deprotect on silica, I've heard tales of stranger things.

Does the material from the methanol washings have an Rf of 0.4 in 2:1 Hex/EA? Do you still have 4 acetates in the nmr/mass spec? Do you have an OH stretch in the IR?
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gfunk

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Re: Purification of a sugar on chromatography column
« Reply #6 on: March 28, 2009, 07:35:15 PM »

I would try adsorbing your reaction mixture into the silica.  Pour some silica into your worked-up product, use some DCM to make the thing into a slurry, place on vacuum to dry it and fluff it up.  Place it in your column and run.

When I run columns on very polar compounds, I'll start off with 30% EtOAc in hexanes, ramp it up in 20% increments or so, and finish with 2-10% MeOH in EtOAc.  I never use more than 10% MeOH as per what azmanam mentioned above.

If that doesn't work, what about a RP stationary phase?
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Capn Jack

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Re: Purification of a sugar on chromatography column
« Reply #7 on: March 29, 2009, 03:39:21 AM »

Dear all,

I am trying to synthesise a sugar (peracetylated 6-azidofucose) and
have at long last reached the final step of peracetylation. The protocol I am following suggests using Hexane:Ethyl acetate 2:1 but my product gets stuck on top of the silica if I use it (even though it runs at an Rf of about 0,4 on a TLC). <SNIP>


One possibility is that the TLC plates are "old" and have adsorbed water, deactivating the silica on the plates somewhat. To test this theory, try the column with hexane/ethyl acetate pre-saturated with water.
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Captain Sci

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Re: Purification of a sugar on chromatography column
« Reply #8 on: July 21, 2009, 01:57:23 AM »

I realise I joined this thread at a late stage, but I nevertheless have a suggestion for anyone facing similar "technical difficulties".

If your compound elutes well on TLC plates for one reason or another, why not purify it via preparative thin layer chromatography? Nowadays you can get plates with thickness values of up to 2.0 mm, and you should be able to separate well over 1.0 g at a time using a full-size 20 x 20 cm plate. Some of my contacts use 500 micron thick plates and have been able to do 400+ mg of their products at a time - all you do is crape off the silica at the end and wash off your compound.

Still, I am surprised to hear that your compound elutes so well on TLC plates but does not appear immediately amenable to chromatographic purification. The silica gel on your TLC plate is probably much finer than the silica gel in your column - I wonder if this is the reason? Also, what is the pore size and volume of the silica you are using for the column chromatography? If it happens to be significantly different in comparison to the TLC silica gel, then you should try using a different type of silica gel.

Athan
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da692

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Re: Purification of a sugar on chromatography column
« Reply #9 on: July 22, 2009, 04:21:29 PM »

I would first make sure that what you're putting on the column is indeed fully acetylated. Also, are you sure you're not observing decomp on the tlc plate? do a 2d tlc and make sure. have you accounted for mass balance - it may go to crap on the column but are you gettting all of your mass off? have fun, sugars suck
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