Answer:
Lyophilize. Freeze drying preserves the phytochemicals quite well. Enzymes are inactive, no microbes can grow, there is no heat, and hydrolytically-unstable compounds remain stable. We freeze dry all leaf, stem, bark, root, and cell culture tissue before analysis. It works great. The dried material can be stored in a freezer for years without significant degradation of phytochemicals. Oily materials, like seeds, do not freeze dry. Also, you are will lose a certain fraction of volatile compounds to evaporation.
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