The effects of ionic liquid nanostructure and long-range Coulomb interactions on the molecular dynamics electrospray simulations are discussed. Bulk structure analysis of EAN, EMIM-BF4, and EtAN is performed in the presence of an electric field and the existence of a bistatic layer is witnessed using molecular dynamics. Mechanisms that both cause and restrict the formation of these long carbon chain lamellar layers, detrimental to ion emissions, are studied using bulk simulations. Molecular dynamics is used to study the dependence of emission currents on the choice of long-range Coulomb model, Coulomb cut-off radius, and the domain periodicity for electrospray simulations of coarse-grained EMIM-BF4. It is observed that for electrospray simulations with a capillary immersed in the domain, the direct assessment of the Coulomb energy without any long-range Coulomb model and non-periodic domains provide the most accurate emission characteristics.