The Laboratory for Computational Molecular Design at ISIC devises original and accurate methodologies to establish, in silico, key structure property relationships of large chemical systems with particular emphasis on those associated with pi-conjugated framework. Herein, we discuss two specific focuses of our activities: i) the development of accurate formalisms based on Kohn-Sham density functional theory to achieve quantitative results for the energies and geometries of extended systems featuring weak interactions and ii) the introduction of schemes to probe and tune the effect of intra- and intermolecular charge transfer on molecular properties. The proposed methodologies are ideally designed to tackle and resolve some of today's relevant aspects associated with the properties of pi-conjugated molecules, such as identifying relationships resulting in high stacking capacities, proposing more stable alternative topologies to large acenes, and analyzing the course of reaction involving assemblies of pi-conjugated molecules.