Nanocomposites consisting of polymers reinforced with filler particles are important for a wide variety of industries and processes, but although they exhibit unique viscoelastic properties and as such are widely applied in e.g. tires, the precise mechanism of their reinforcement is at best incompletely understood at present. In order to understand it at a fundamental level, and ultimately control it in practice, it is essential to determine the impact of interactions between filler particles and polymer matrix on the nanocomposite microstructure and its macroscopic dynamic mechanical properties. To this end, we performed experiments on two model systems as well as molecular dynamics simulations, aiming to determine to what extent widely used shear-distortion models of the reinforcement are applicable as well as the role played by molecular interactions on the enhancement of the mechanical properties. In both experiments and simulations a linear dependence of the reinforcement on the inverse radius of the nanoparticles was obtained. Deformation simulations of a linearly increasing strain showed an overall increase of 50% in the linear modulus when fillers were added to the polymer matrix, regardless of the use of direct interactions among the nanoparticles. Furthermore, the use of attractive nanoparticle interactions resulted in a higher matrix densification at the interfaces and to a sharp increase in the reinforcement.