Designing nanoporous catalysts to destroy chemical warfare agents (CWAs) and environmental contaminants requires consideration of both intrinsic catalytic activity and the mass transfer of molecules in and out of the pores. Polar adsorbates such as CWAs experience a heterogeneous environment in many metal-organic frameworks (MOFs) due to the arrangement of the metal nodes and organic linkers of the MOF. However, quantitative relationships between the pore architecture and the resulting diffusion properties of polar molecules have not been established. We used molecular dynamics simulations to calculate the diffusion coefficients of the CWA simulant dimethyl methyl phosphonate (DMMP) in a diverse set of 776 MOFs with Zr6 nodes. We developed a 4-parameter machine learning model to predict DMMP diffusivities in Zr6 MOFs and found the model to be transferable to the CWA sarin. We then developed a simplified heuristic based on the machine learning model that the node-node distance and accessible surface area should be maximized to find MOFs with rapid CWA diffusion.