Is there any problem with using 0.1%TFA in HPLC mobile phase if the purpose is isolation, structure elucidation by NMR and bioassay?
Although the boiling point of TFA is 72 °C, it does form an azeotrope with water that boils at 105 °C.
Keep in mind that the compound that shows activity may be acid-labile. Don't commit all of your material to a purification step until you know that step works, and submit a sample of material prior to purification both to verify the bio-assay is running properly in the chance that the compound was deactivated, or didn't elute from the column.
Also note that, if your active compound is ionizable, the retention may greatly change from a column run that used no modifier.
In my opinion, there are no problems at all in using TFA in such concentrations. I have used higher concentrations in the isolation of many natural products without any problems.
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