The reaction between (3-aminopropyl)dimethylmethoxysilane (APDMS) with silica and silsesquioxane 3,5,7,9,11,13,15-heptacyclopentylpentacyclo[9.5.1.1(3,9).1(5,15).1(7.13) ]octasiloxan-1-ol was studied in hexane and tetrahydrofuran (THF) using experimental (reaction kinetics, FTIR) and quantum chemistry methods. In hexane at temperatures above 245 K, the reaction rate decreases with increasing temperature due to a reduction of prereaction complex formation at higher temperature. Below 245 K the reaction itself is rate limiting, resulting in a reaction rate decrease with decreasing temperature. The reaction occurs much faster in hexane than in THF in part because of stronger competitive effects of the O-containing polar solvent with the formation of APDMS/silsesquioxane prereaction complexes due to hydrogen bonding. Analysis of the experimental data and computational results suggest that the catalytic reaction is second-order with respect to APDMS, the second APDMS molecule plays the role of catalyst. Estimation of the activation energy using dynamic calculations give results much more in agreement with experiment than nondynamic calculations, since the limiting H+ transfer stage occurs so quickly (similar to 15 fs) that displacements of other atoms are insignificant to the activation energy.