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Multiscale molecular modeling (M3) is applied in many fields of material science, but it is particularly important in the polymer science, due to the wide range of phenomena occurring at different scales which influence the ultimate properties of the materials. In this context, M3 plays a crucial role in the design of new materials whose properties are infiuenced by the structure at nanoscale. In this work we present the application of a multiscale molecular modeling procedure to characterize polymer/clay nanocomposites obtained with full/partial dispersion of nanofillers in a polymer. This approach relies on a step-by step message-passing technique from atomistic to mesoscale to finite element level; thus, computer simulations at all scales are completely integrated and the calculated results are compared to available experimental evidences. In details, nine polymer nanocomposite systems have been studied by different molecular modeling methods, such as atomistic Molecular Mechanics and Molecular Dynamics, the mesoscale Dissipative Particles Dynamics and the macroscale Finite Element Method. The entire computational procedure has been applied to a number of diverse polymer nanocomposite systems based on montmorillonite as clay and different clay surface modifiers, and their mechanical, thermal and barrier properties have been predicted in agreement with the available experimental data.