Molecular mechanics (MM) and molecular dynamics (MD) simulations have been performed to investigate the two-dimensional structure of organosilane self-assembled monolayers (SAMs). Unlike alkanethiol SAMs, the arrangement of molecules in organosilane SAMs is not crystalline, and their molecular structure yet remains undetermined. AMBER 8 is employed with our newly developed Si parameters for the MM/MD simulations. Simulations performed for structures with different bonding networks in the polysiloxane layer shows that the ratio of hydrogen bonds has a profound effect on conformations and strain energies of optimized structures. Our results suggest that alkylsilane SAMs formed on substrates are not perfectly uniform but may have some defects.