Aerosols can influence tropospheric chemistry through deep convection by: (a) serving as CCN or IN and then impacting on cloud development and associated aqueous and gaseous reactions; and (b) serving as platforms for heterogeneous reactions that change the removal rates of certain chemical species. Deep convection is also one of the major sinks of atmospheric aerosols, while at the same time deep convection actually supplies a vast portion of aerosols to the upper troposphere. These processes are determined not only by surface properties of aerosols but also cloud dynamics and microphysics. It is very important for atmospheric chemistry and global change studies to understand these direct and indirect effects of aerosols on tropospheric chemistry as well as the interactions between aerosols and deep convection. To address these issues, we have used a 3D cloud-resolving model including interactive dynamics, cloud and aerosol microphysics, gaseous and aqueous chemistry, heterogeneous chemistry, and radiation. In this study the model is initialized with analyzed data from the ECMWF over a 500 by 500 by 25 km domain. Simulated values of various chemical compounds (e.g. CO, O3) and aerosol number and ice crystal density have been compared with in-situ aircraft observations. A number of simulations with different settings in physics and chemistry as well as aerosol profiles have been carried out. The sensitivities of deep convection related physics and chemistry and its impact on tropospheric chemistry is presented and discussed. Finally, we propose a scheme for calculating the wet removal of aerosols in large-scale models.