This research line is devoted to the prediction of structural, electronic and chemical properties of functional materials, including organic soft matter, biological systems and catalysts, through computer simulations (Molecular Dynamics, Metropolis and Kinetic Monte Carlo) methods, quantum chemistry calculations and network analysis. Particular attention is devoted to the comparison with experiments and the quantitative accuracy of the results, achieved by: i) careful modeling and testing of classical intermolecular potentials at various levels of resolution ii) adequate statistics provided by large system sizes and long simulations; iii) development of software tools for the calculation of observables directly or indirectly measurable with experimental techniques; iv) simulating thermodynamic equilibrium and non-equilibrium processes in realistic conditions. This array of techniques is applied to the molecular design of advanced materials possessing liquid crystalline, organic semiconducting, catalytic and light emitting properties and to characterization of complex phenomena, like chemical signaling in proteins.