Ab initio and classical molecular dynamics simulations are performed to analyze the structure of the interface between pyrite (100) and one of the possible self-assembled crystalline forms of dilithium phthalocyanine (Li2Pc), a candidate single-ion conductor electrolyte material for rechargeable lithium batteries. A simplified dilithium phthalocyanine model, keeping an anionic matrix structure able to form lithium-ion conducting channels upon self-assembly, is used for an ab initio study of the local interactions with the active sites of a pyrite model cluster. It is found that lithium ions interact strongly with the outmost surface sulfur atoms, whereas the pyrite Fe atoms interact with N atoms of Li2Pc. Ab initio studies provide an estimate of the charge distribution to be used in effective force fields to describe interatomic interactions. Molecular dynamics simulations illustrate that the self-assembly of Li2Pc over a pyrite (100) surface leads to the formation of a crystalline structure where the stacking axis of the Li2Pc molecules is perpendicular to the surface. Ion-conducting channels from the Li2Pc phase are realized through the interface, and transport of lithium ions through these channels into the pyrite phase are observed under an external electric field applied in a direction perpendicular to the interface. (c) 2005 The Electrochemical Society.