Design of self-assembled layers with biological activity on the Si(001) surfaces

DESIGN OF SELF-ASSEMBLED LAYERS WITH BIOLOGICAL ACTIVITY ONTHE Si(001) SURFACES(Ph. D. Thesis)GÖKHAN DEMİRELGAZI UNIVERSITYINSTITUTE OF SCIENCE AND TECHNOLOGYOctober 2006ABSTRACTIn this study, two different amino-terminated self-assembled layers (SALs)composed of 3-aminopropyltrimethoxysilane (APTS) and 12-hydroxydodecanoic acid (HDA) 2,2?-(ethylenedioxy)diethylamine (EDA) onthe Si(100) surfaces were prepared. Chemical compositions of designedsurfaces were characterized by X-ray photoelectron spectroscopy (XPS).The N 1s and C 1s peaks in the XPS spectrum for the SAMs canqualitatively account for the existence of APTS, HDA and EDA moleculeson the silicon surface. Average thicknesses of APTS, HDA and HDA-EDAoverlayers as estimated by spectroscopic ellipsometry analysis were as6.3, 4.8 and 6.7 nm, respectively. The surface topographies of the APTS-and HDA-EDA-SALs observed by atomic force microscopy (AFM) areconsiderably different from the hydroxylated silicon surface and they havemany additional islands of various heights over the substrate. The watercontact angles of APTS-, HDA- and HDA-EDA-SALs were determined to beas 57°, 38o and 34o, respectively, whereas that of the hydroxylated siliconwas 0.3o, indicating that the difference in their surface hydrophobicility.Furthermore, protein adsorption studies on the amino-terminated SAMswere carried out by using biotin, streptavidin and fluorescein-labeledprotein-A molecules. The fluorescence images obtained by fluorescencemicroscopy showed the formation of the amino terminated SALs on theSi(100) surface. Interactions between antigen and antibody molecules onthe surfaces were also observed by using ellipsometry. In the second partof this study, binding mechanisms of APTS and HDA molecules on theSi(001)-(2x2) surfaces were theoretically investigated by Viena ab initiosimulation package (VASP). Firstly, two possible models for thechemisorption location of the APTS molecule are considered on thehydroxylated Si(001)-(2x2) surface: (i) an above-pedestal position and (ii)an above-hollow position. The first case is found to be energetically morefavorable than the latter by 1.04 eV. Secondly, we assume two differentorientations of HDA molecule on the hydroxylated surface: (i) a linear, and(ii) an angular situation on the above pedestal position. Within eachorientations, we consider two different end groups of the molecule on thesurface, i.e., hydroxyl and carboxylic acid group. Upon their relaxations,linear bonding model with hydroxyl end group of HDA molecule on thehydroxylated Si(001) surface is found to be more energetically favorablethan the other cases by 0.34 eV per HDA molecule. The electronic bandstructure of APTS and HDA chemisorbed surface have been alsocompared with that of the bare-Si(001)-(2x2) surface. It is observed that thechemisorption of APTS and HDA have considerably changed the surfaceelectronic structure of the Si(001)-(2x2) surface.Science Code : 201Key Words : Nanotechnology, self-assembled monolayers,protein chip, density functional theory.Page Number : 117Advisers : Assoc. Prof. Dr. Tuncer ÇAYKARAAssoc. Prof. Dr. Mehmet ÇAKMAK