The (110) crystal plane of SnO2 was found by X-ray diffraction, atomic force microscopy and X-ray photoelectron spectroscopy to grow preferentially in the direction of short-chain sulfonate self-assembled monolayer (SAM) formed from in situ oxidation of 3-mercaptopropyltrimethoxysilane (MPS) treated Si substrates. Molecular simulations were performed to study the optimal packing structure of MPS SAMs on Si (100) surface as well as its induced deposition mechanism to the SnO2 crystal. Molecular mechanics calculations showed that the MPS molecules self-assembled on Si (100) surfaces with a coverage ratio of 50% and a zigzag-like packing pattern. Molecular dynamics calculations reflected that oxidation of the -SH of MPS contributed to uniform -SO3H-terminated SAMs with narrower distribution of dihedral angles. Density functional theory calculations suggested the existence of strong interactions between the -SO3H groups of SAMs and SnO2 (110) plane, which was due to the structural and electrical match between the -SO3H group and the unsaturated atoms on SnO2 (110) plane. These results consistently confirmed that the ordered SAMs with -SO3H terminal group are beneficial to the epitaxial growth of crystal SnO2. (C) 2007 American Institute of Chemical Engineers.