We use multiscale modeling to study how the molecular properties of a protein affect its adsorption and transport in ion exchange chromatography matrices with either open pores or charged polymers grafted into the pore structure. Coarse-grained molecular dynamics (MD) simulations of lysozyme, bovine serum albumin, and immunoglobulin show that higher protein net charge leads to greater partitioning into the polymer-grafted pore space but slower diffusion there due to favorable electrostatic interactions, while larger size decreases both pore space partitioning and diffusion due to steric effects of the polymers. Mass transfer simulations based on the MD results show that the polymer-grafted systems can enhance the adsorption kinetics if pore space partitioning and diffusion are both sufficiently high. The simulations illustrate that to achieve fast adsorption kinetics, there is a tradeoff between favorable binding and rapid diffusion which largely depends on the charge and size of the protein. (c) 2017 American Institute of Chemical Engineers AIChE J, 63: 4564-4575, 2017