Multi-functionalization of catalytically-active nanomaterials provides a valuable tool for enhancing reaction yield by shifting reaction equilibrium, and potentially also by adjusting reaction-diffusion kinetics. For example, multi-functionalization of mesoporous silica to make the interior pore surface hydrophobic can enhance yield in dehydration reactions. Detailed molecular-level modeling to describe the pore environment, as well as the reaction and diffusion kinetics is challenging, although we briefly discuss current strategies. Our focus, however, is on coarse-grained stochastic modeling of the overall catalytic process for highly restricted transport within narrow pores (with single-file diffusion), while accounting for a tunable interaction of the pore interior with reaction products. We show that making the pore interior unfavorable to products can significantly enhance yield due to both thermodynamic and kinetics factors.