Typically, amino acid salts are "freebased" using ion exchange columns such as Dowex50 and eluting the amino acid with dilute pyridine solution. The
eluate containing the amino acid-pyridine salt is then free dried under high vacuum which removes the water and pyridine leaving behind the free amino
acid. It is otherwise very difficult to obtain free amino acids from solution. Sometimes they will separate or crystallize at the isoelectric point
for the particular amino acid but this is not easy to do.
In the case of lysine hydrochloride, using sodium bicarbonate to neutralize the hydochloride will not work as the terminal amino group of lysine is a
stronger base than bicarbonate. You would need to carefully titrate the HCl with hydroxide but because of the great solubilty of the zwitterion,
isolation of the lysine free base will be very difficult if even possible. In fact, lysine is always isolated as its hydrochloride not as its
"freebase." If you can find it, see Greenstein and Winitz, "Chemistry of the Amino Acids," vol 3 which contains a chapter on lysine.
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