I will try to dry a 50% ethanol solution to obtain my dry extract. When I tried to have a 3rd party remove the solvent from my 20mL sample using purely the rotavap, they told me there was difficulty in drying it so I was thinking of only removing the ethanol such that I can safely lyophilize it. I was thinking of concentrating the sample to around 10% of its initial volume such that even if there's still some ethanol in it, I can simply dilute the extract with water to avoid any problems in the freeze dryer.
Ethanol and water - as I am sure you know, form an azeotrope so it is not possible to remove "all" the EtOH via evaporation. A second issue is that if you remove all the EtOH and "just" have your sample in water, it is possible (probable, even?) that some parts of your sample will crash out as not soluble in only water. This will mean that you get a heterogenious result when freeze drying, which is not likely helpful to downstream processing.
If possible, don't use EtOH in the extract - use something that freeze dries more easily, such as tertiary butanol. If this is not possible, then try and remove as much EtOH as possible in rotary evaoporator - essentially wait until you reach a constant volume, then add some tertiary butanol and mix well to help ensure that you have a homogenious sample. This will then freeze dry well.
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