Air quality models that generate the concentrations of semi-volatile and other condensable organic compounds using an explicit reaction mechanism require estimates of the physical and thermodynamic properties of the compounds that affect gas/aerosol partitioning: vapour pressure (as a subcooled liquid), and activity coefficients in the aerosol phase. The model of Griffin, Kleeman and co-workers (e.g., Griffin et al., 2003; Kleeman et al., 1999) assumes that aerosol particles consist of an aqueous phase, containing inorganic electrolytes and soluble organic compounds, and a hydrophobic phase containing mainly primary hydrocarbon material. Thirty eight semi-volatile reaction products are grouped into ten surrogate species which partition between the gas phase and both phases in the aerosol. Activity coefficients of the organic compounds are calculated using UNIFAC. In a companion paper (Clegg et al., 2008) we examine the likely uncertainties in the vapour pressures of the semi-volatile compounds and their effects on partitioning over a range of atmospheric relative humidities. In this work a simulation for the South Coast Air Basin surrounding Los Angeles, using lower vapour pressures of the semi-volatile surrogate compounds consistent with estimated uncertainties in the boiling points on which they are based, yields a doubling of the predicted 24-h average secondary organic aerosol concentrations. The dependency of organic compound partitioning on the treatment of inorganic electrolytes in the air quality model, and the performance of this component of the model, are determined by analysing the results of a trajectory calculation using an extended version of the Aerosol Inorganics Model of Wexler and Clegg (2002). Simplifications are identified where substantial efficiency gains can be made, principally: the omission of dissociation of the organic acid surrogates; restriction of aerosol organic compounds to one of the two phases (aqueous or hydrophobic) where equilibrium calculations suggest partitioning strongly in either direction; a single calculation of activity coefficients of the organic compounds for simulations where they are determined by the presence of one component at high concentration in either phase (i.e., water in the aqueous phase, or a hydrocarbon surrogate compound P8 in the hydrophobic phase) and are therefore almost invariant. The implications of the results for the development of aerosol models are discussed.