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Molecular mechanics calculations were performed using standard MM2 force fields and VDW radii (Chem 3D Ultra software). The thickness of APS films on silicon oxide was estimated from measurements of the energy minimized structure of APTES with fully extended, staggered alkyl chains. The thickness of APS chemically bound to the surface was taken as the center to center distance from the farthest oxygen atom to the outermost hydrogen of the amine projected onto the long axis of the molecule, less the VDW radii of oxygen, plus the VDW radii of hydrogen. The thickness of the noncovalently bound APS was taken as the center to center distance calculated for the chemically bound case plus the VDW radii of hydrogen and oxygen. Calculations were performed at torsional angles of the amine that resulted in the shortest and longest distances upon projection of an amine hydrogen onto the long molecular axis, Complete hydrolysis of the ethoxy groups was assumed in both cases. In addition, a monolayer of water was assumed to be present before and after APS formation, resulting in no net change in the measured thickness.
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