Molecular dynamics simulations have been performed for precursor molecules used for organic/inorganic polymer hybrid preparation. The initial stage of the sol-gel process was simulated with the components at various water concentrations. Analyses of structural properties of the equilibrium configurations were performed via radial distribution functions. It was concluded that water concentration plays an important role in the agglomeration of the clusters due to the hydrophobic effect. Low water concentration leads to less pronounced hydrophobic interactions between the components resulting in structural instability.