I have a Peptide that consists of 2 Aminoacids, one of them is Boc-Valin. The Peptide was deprotected using TFA. Does anyone have an idea on how to remove excess TFA besides vacuum drying and lyophilisation?
TFA can be removed using rotary evaporator. Add Methanol (5~6 times) and remove methanol by rotary evaporator. Most of the TFA is removed using this procedure and traces can be removed using vacuum.
If you don't want to use vacuum you can also just evaporate the TFA under a gaseous stream, e.g. nitrogen, then do a precipitation in ether as suggested above.
Since you have a short peptide it will not precipitate in ether and anyway this is usually used to get rid of the removed protecting groups and not the TFA. Since TFA is highly volatile you should be able to remove it either under reduced pressure or we also remove it under nitrogen stream under the fume hood.
As Christina Lamers mentioned, a dipeptide will most likely not get precipitated in cold ether. Depending on your scale of synthesis, if its a small scale one, I would suggest using a stream of air/nitrogen under fumehood, applying reduced pressure would be unnecessary. In case you are handling a much larger amount of TFA, try evaporating with a rotavap, apply periodic vacuum with proper precautions, efficient chilling etc. Discard the TFA carefully and thoroughly wash the rotavap assembly with acetone. I carried our several batches of preparation that required removal of 10-15 ml of TFA and it perfectly worked. If you still have any residual TFA try removing it by co-evaporating with toluene (as azeotrope).
@Jonathan...by ether I meant diethyl ether to be precise. My answers/suggestions are based on my 3 years experience on working with peptides with lengths in the range 4-30 mer. A longer peptide will have many polar side chains and naturally diethyl ether would easily precipitate it out. Shorter peptides would lack such benefit and most of the times it just goes into the ether layer and u don't even see any precipitate. In such cases adding an even more non polar solvent won't help you anyway especially when it's a dipeptide and yes I have tried to add pet ether many times but it never really improved things anyway!!
Regarding small molecule synthesis trituration with pet ether is a common practice indeed but we are in the realm of peptides here. Unfortunately, at times we are helpless to stick to common practices like evaporation, lyophilisation etc.
I totally agree with all the points mentioned by Christina lamers and I can totally relate to my experiences as well.
My intention was never to make any universal comment, I merely wanted to suggest the most plausible situation! Maybe it wasn't conveyed the way I wanted it to be. I have revised my statement accordingly for your kind review.
also I never said anything that indicates "peptide chemistry is ruled by different principles than chemistry"
I wanted to rather point out the subtle differences in their 'physical properties' that makes situations a bit tricky, sometimes.
and last but not the least, your first statement "Ether should precipitate out the peptide and hold onto the TFA" come on! A valine containing dipeptide ? Seriously ?
Best way to remove TFA is leave it under fumehood with steam of N2. You also can use reduced pressure. But it's not necessary. Because, TFA is very volatile, so you can easily get rid from it
However, if you have large quantity I'll recommend reduce pressure. Have done that several times for dipeptides. It comes handy. Sometimes it might have trace amount of TFA and it didn't make any issues for my other steps.
Already a lot has been suggested, with my experience on short peptides i also will suggest the rotary evaporation by addition of small amount of methanol three to four times depending upon the amount of TFA.