The creation of novel materials with targeted functionalities is the ultimate goal in several scientific and technological fields, ranging from chemistry and pharmaco-chemistry to molecular electronics and renewable energies. Molecular modelling and simulation are vital components of the scientific investigation of materials, as well as essential tools to engineer novel materials with improved performances. Future advances in this field should systematically address the challenge of bridging the gap between simulations and experiments. To this end, a unifying theme of this research is the development of a modelling framework for the investigation of materials. Through the creative synthesis of traditional all-atom simulations, electronic structure methods, and rare events techniques, we apply a multiscale approach to the study of materials and nanostructures.