Filled elastomers acquire their mechanical strength through fillers forming spanning branched networks throughout the rubber matrix. Here we study one reversibly breakable filler aggregate-to-filler aggregate contact within a network branch and its contribution to dissipative loss using molecular dynamics simulations. Our model system consists of a pair of spherical silica particles embedded in cis-1,4-polyisoprene. Variable chemical options include silanes attached to the particle surfaces at varying density and surface distribution and cross-links between polymer chains as well as Chemical bonding of the polymer chains to the silica particles via silanes. We validate key properties of the pure polymer, including density, thermal expansion, and characteristic ratio as well as the dependence of the polymer network density on sulfur content. On the basis of force-vs-inter particle separation curves for cyclic loading, we obtain the energy dissipation in the contact depending on the aforementioned chemical parameters and temperature. We track the segmental relaxation peak in our model system along the temperature axis while moving the filler particle relative to one another at different speeds. From this we are able to show that the peaks in the loss-vs-temperature diagram correspond to the experimental segment relaxation in pure polyisoprene at the attendant frequencies. This in turn allows to relate the high frequency results of our atomistic simulations to the technically relevant frequency range. Finally, we investigate the structure and mobility of the polymer in the vicinity of the particles.