In this paper we report on molecular dynamics simulations of the line shapes of the absorption spectra of perylene.Ar-n, heteroclusters (n=1-45), which rest on the spectral density method. Inhomogeneous semiclassical absorption line shapes were calculated by averaging of microcanonical spectra over the accessible phase space region. We utilized a potential modeling scheme for the excited-state atom-atom potentials, which accounts well for the spectral shifts of small (n=1-6) clusters. The size dependence and the isomer specificity of the spectral shifts and spectral linewidths were elucidated. The analysis of the power spectra of the energy gap correlation function established that the dominating contribution to the line shape and line broadening of the electronic origin at finite temperatures (T greater than or equal to 10 K) originates from the low-frequency diffusive soft mode. For these heteroclusters the soft mode contribution can be described within the stochastic slow modulation limit, being determined by the dispersion of the soft mode and being independent of its damping. Finite-frequency intermolecular motion gives only a minor (less than or equal to 10%) contribution to the line broadening. Our analysis interrelates spectral line broadening and nuclear dynamics.