Using a combination of atomistic molecular dynamics (MD) simulations and density functional theory (DFT) calculations, the four steps of hydrolysis of aminopropyl-, thiolpropyl-, and butyltrimethoxysilane have been studied. Large box MD simulations at constant pressure and temperature yield appropriate pair distribution functions--which allows us to quantify the number of surrounding water molecules--as well as the density of the systems. These densities serve as input for small box DFT calculations, which allow further geometry optimization and calculation of the electronic structure of the systems. The periodic DFT calculations are compared with gas-phase simulations. In all cases, the first step of hydrolysis is exothermic with the extent depending on the type of silane as well as on the number of hydrogen bonds in the initial stage.