The recent progress made in devising chemical methods for the synthesis of defect-free one- and two-dimensional organic nanosystems with reproducible properties has prompted an enormous interest in developing a quantitative understanding of the assembly process and the resulting intrinsic properties of the structures as they interact with their environment. In this presentation, I will review examples where theoretical nanoscience and computational sciences can be used to account for experimental findings and to predict emergent properties in a range of systems. Spin-depending electronic transport, thermoelectricity, heterostructures, chemical doping, effects of substrate will be discussed and placed in the perspective of designing materials with tailored properties. In each case, success and failure of atomistic theories, ranging from self-consistent tight-binding, density functional theory, and many-body perturbation theory will be discussed within the context of current developments in their respective fields.