We studied effect of molecular interactions on the physical properties of binary freeze-dried solids and frozen aqueous solutions using model chemicals containing various functional groups (amino, carboxyl, hydroxyl). Thermal analysis of frozen solutions containing alkyl diamines and hydroxy di- or tricarboxylic acids showed thermal transitions (T(g)': glass transition of maximally freeze-concentrated phase) at temperatures higher than those of the individual solutes. A binary frozen solution containing 80 mM 1,3-diamino-2-hydroxypropane (single-solute T(g)'<-60 degrees C) and 120 mM citric acid (single-solute T(g)': -55.0 degrees C) made the transition at -30.8 degrees C. The molecular weight of the solutes had smaller effects on the transition temperatures of the frozen mixture component solutions. Lyophilization of some high T(g)' mixture frozen solutions (e.g., 1,3-diamino-2-hydroxypropane and citric acid) resulted in cake-structure amorphous solids with glass transition temperatures (T(g)) higher than those of the individual components. Networking of intense hydrogen-bondings and electrostatic interactions between the heterogeneous molecules through the multiple functional groups was suggested to reduce the component mobility in the amorphous freeze-concentrated phase and the freeze-dried solids. Controlling the interactions should be a key to optimizing the physical properties of multi-component amorphous freeze-dried pharmaceutical formulations.