Polymeric chemically amplified resists (CARs) are critical materials for high-throughput lithographic processes. A photoactivated acid-anion catalyst changes the polymer's solubility via a deprotection reaction, which enables pattern development through selective dissolution. To capture observed reaction kinetics, reaction-diffusion models employ a catalyst diffusivity that is accelerated by reaction. However, the microscopic origin and factors contributing to this phenomena remain unclear. Herein, we employ detailed atomistic molecular dynamics simulations to examine the impact of protecting group removal and material relaxation on catalyst mobility. We report data on polymer density, catalyst dispersion, excess free volume, and segmental dynamics with increasing time/extent of deprotection. We then propose simple kinetic Monte Carlo algorithms that can describe both molecular dynamics simulations of deprotection reactions and experimental data.