Functionalized nanoparticle networks offer a model system for the study of charge transport in low-dimensional systems as well as a potential platform to implement electronic functionalities. The electrical response of a nanoparticle network is expected to sensitively depend on the molecular inter-connects, i.e. on the linker chemistry. If these linkers have complex charge transport properties as is the case of molecular switches with conformational dependent electronic properties or molecular memristors showing hysteretic behavior, then phenomenological models addressing the large scale properties of the network need to be complemented with microscopic calculations of the network building blocks. In this study we investigate the electronic, structural and charge transport properties of functionalized nanoparticle by employing a multi-scale method in which we combine density-functional based approaches, classical molecular dynamics, and charge transport calculations.