Air quality models that generate the concentrations of semi-volatile and other condensable organic compounds using an explicit reaction mechanism require estimates of the vapour pressures of the organic compounds that partition between the aerosol and gas phases. The model of Griffin, Kleeman and co-workers (e.g., Griffin et al., 2005) 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. In Part 1 of this work (Clegg et al., 2008) the thermodynamic elements of the gas/aerosol partitioning calculation are examined, and the effects of uncertainties and approximations assessed, using a simulation for the South Coast Air Basin around Los Angeles as an example. Here we compare several different methods of predicting vapour pressures of organic compounds, and use the results to determine the likely uncertainties in the vapour pressures of the semi-volatile surrogate species in the model. These are typically an order of magnitude or greater, and are further increased when the fact that each compound represents a range of reaction products (for which vapour pressures can be independently estimated) is taken into account. The effects of the vapour pressure uncertainties associated with the water-soluble semi-volatile species are determined over a wide range of atmospheric liquid water contents. The vapour pressures of the eight primary hydrocarbon surrogate species present in the model, which are normally assumed to be involatile, are also predicted. The results suggest that they have vapour pressures high enough to exist in both the aerosol and gas phases under typical atmospheric conditions.