Molecular diffusion is the dominant solute transport process in clays and claystones that are considered as sealing materials in the deep geological disposal of radioactive waste. These materials are typically water saturated, but during construction and later, at elevated temperatures or when gas may be produced, unsaturated conditions prevail. Investigating the clay's water retention properties as well as solute transport under unsaturated conditions is therefore mandatory. Here, functional dependencies of these properties were derived from atomistic and pore-scale simulations. In the absence of tomographic maps that resolve all pores in clays, model clay structure maps with different pore size distributions were generated using a previously developed algorithm. Upscaled water retention functions and upscaled diffusion coefficients of unsaturated samples were derived from these maps based on the shifted Young-Laplace equation that considers film adsorption and capillary condensation. Pore-scale parameters (diffusion coefficients, water film thickness) used for the upscaling were taken from molecular dynamics (MD) simulations, thus connecting MD and pore-scale simulations. We focused on effects of the pore size distribution and of the adsorbed water film on upscaled parameters. Samplescale diffusion coefficients were clearly reduced in unsaturated samples compared to the saturated state, with less reduction when including adsorbed water films. The reduction was stronger in samples with a narrow size distribution of the interparticle pores as compared to those with a wide distribution (but equal mean size). The results follow the trends of the experimental data, even though the scale of the simulations is still clearly smaller than that of typical experiments.