The chemisorption and reaction of 3-aminopropyltrimethoxysilane (APTS) molecule on the Si(111)-(root 3 x root 3) surface are investigated by first principles density-functional calculations within the generalized gradient approximation. Before studying the chemisorption of APTS molecule on the surface, we have firstly put three-OH groups on the silicon surface, but considering six different locations for H and O atoms. Upon their relaxations, model 11, which is assumed to be crosswise for initial orientation of -OH groups, was found to be energetically more favorable than the others. In model 11, after the relaxation, its conformation was transformed to skewed structure due to the repulsive forces between -OH groups. Isolated APTS molecule was also investigated in order to obtain its most stable molecular geometry, for which the HOMO-LUMO gap was found to be 4.41 eV. In addition to these, after the energetically most favorable hydroxylated Si(111) surface was calculated, APTS molecule was chemisorbed on the surface by means of liberating its methoxy groups. In our model for the binding of APTS molecule on the Si(111) surface, the silicon atom in the APTS forms three bonds to hydroxyl groups at the surface. (c) 2007 Elsevier B.V. All rights reserved.