The purpose of this study is to provide a quantitative characterization of the thermal behavior of amorphous organic pharmaceutical compounds across their glass transition temperature, and to assess their molecular mobility as a function of temperature and time by combining theoretical simulations with experimental measurements using differential scanning calorimetry. A computational approach built on the Boltzmann superposition principle of nonexponential decay and the Adam-Gibbs theory of entropic-dependent structural relaxation is presented. The heat capacities of the crystalline and amorphous forms are incorporated into the simulation in order to accurately assess the entropic fictive temperature as functions of temperature and time under any arbitrary set of experimental conditions. Using this method, we evaluated properties of the glass former, D and To, and the nonexponentiality index beta, for amorphous salicin, felodipine, and nifedipine, by fitting the simulated glass transition profile with the experimentally determined heat capacity across the glass transition region. From this fit, the evolution of the relaxation time of the model compounds following any thermal cycle, including heating, cooling, and isothermal holds can then be estimated a priori. This study reveals the profound and inextricable effect of thermal history on the molecular mobility of the amorphous materials, and the ability of the glass to undergo fast changes in its molecular motions over an aging process even at low temperatures.