We analyze spin-charge separation in molecular wires using a combination of real-time density-functional simulations and model Hamiltonian calculations. By considering the ab initio electron dynamics of positively charged ͑C 50 H 52 + ͒ and negatively charged ͑C 50 H 52 − ͒ polyacetylene chains under a chemical potential bias, we are able to extract information about the mobility of electrons, holes, and spins in these molecules. Our results indicate that charges move more rapidly than spins in these molecules. We further supplement our ab initio data with empirical calculations employing the Pariser-Parr-Pople ͑PPP͒ model Hamiltonian. Our modeling indicates that the degree of spin-charge separation responds very strongly to the nonlocal exchange interaction, while showing little sensitivity to Coulombic forces. In particular, in order to reproduce the B3LYP results within the PPP model, it is necessary to reduce the strength of the exchange interaction by ca. 50% in the latter. We therefore conclude that many of the features present in the B3LYP spin current response are a direct result of self-interaction error in the functional.