This thesis presents work done investigating methods for constructing patterns on the nanometer scale. Various methods of nanolithography using atomic force microscopes (AFMs) are investigated. The use of AFMs beyond their imaging capabilities is demonstrated in various experiments involving nanografting and surface electrochemical modification. The use of an AFM to manipulate a monolayer of thiols deposited on a gold substrate via nanografting is shown in our work to enable chemical modification of the surface of the substrate by varying the composition of the monolayer deposited on it. This leads to the selective deposition of various polymers on the patterned areas. Conditions for enhancing the selective deposition of the self-assembled polymers are studied. Such conditions include the types of polymers used and the pH of the polyelectrolyte solutions used for polymer deposition. Another method of nanolithography is investigated which involves the electrochemical modification of a monolayer of silanes deposited on a silicon substrate. By applying a potential difference and maintaining the humidity of the ambient environment at a certain level we manage to change the chemical properties of select areas of the silane monolayer and thus manage to establish selective deposition of polymers and gold nanoparticles on the patterned areas. Parameters involved in the patterning process using surface electrochemical modification, such as humidity levels, are investigated. The techniques established are then used to construct circuit elements such as wires. / Ph. D.

Progress in chemomechanical functionalization was made by investigating the binding of molecules and surface coverage on the silicon surface, demonstrating functionalization of silicon with gases by chemomechanical means, analyzing atomic force microscopy probe tip wear in atomic force microscopy (AFM) chemomechanical nanografting, combining chemomechanical functionalization and nanografting to pattern silicon with an atomic force microscope, and extending chemomechanical nanografting to silicon dioxide. Molecular mechanics of alkenes and alkynes bound to Si(001)-2x1 as a model of chemomechanically functionalized surfaces indicated that complete coverage is energetically favorable and becomes more favorable for longer chain species. Scribing a silicon surface in the presence of ethylene and acetylene demonstrated chemomechanical functionalization with gaseous reagents, which simplifies sample cleanup and adds a range of reagents to those possible for chemomechanical functionalization. Thermal desorption spectroscopy was performed on chemomechanically functionalized samples and demonstrated the similarity in binding of molecules to the scribed silicon surface and to the common Si(001)-2x1 and Si(111)-7x7 surfaces. The wearing of atomic force microscope probe tips during chemomechanical functionalization was investigated by correlating change over time and force with widths of created lines to illustrate the detrimental effect of tip wear on mechanically-driven nanopatterning methods. In order to have a starting surface more stable than hydrogen-terminated silicon, silicon reacted with 1-octene was used as a starting surface for AFM chemomechanical functionalization, producing chemomechanical nanografting. Chemomechanical nanografting was then demonstrated on silicon dioxide using silane molecules; the initial passivating layer reduced the tip friction on the surface to allow only partial nanografting of the silane molecules. These studies broadened the scope and understanding of chemomechanical functionalization and nanografting.

Organic molecules such as porphyrins and alkanethiols are currently being investigated for applications such as sensors, light-emitting diodes and single electron transistors. Porphyrins are stable, highly conjugated compounds and the choice of metal ion and substituents bound to the macrocycle as well as other effects such as chemical surrounding and cluster size modulate the electronic and photonic properties of the molecule. Porphyrins and their derivatives are relatively non-toxic and their very rich photo- and electro-chemistry, and small HOMO-LUMO gaps make them outstanding candidates for use in molecularly-enhanced electronic applications. For these studies, self-assembled tri-pyridyl porphyrin thiol derivatives have been fully characterized on Au(111) surfaces. A variety of surface characterization techniques such as Atomic Force Microscopy (AFM), Scanning Tunneling Microscopy (STM), FT-IR spectroscopy and X-ray photoelectron spectroscopy (XPS) have been implemented in order to obtain information regarding the attachment orientation based on the angle and physical height of the molecule, conductivity which is determined based on the apparent height and current-voltage (I-V) measurements of the molecule, conductance switching behavior due to conformational or other effects as well as the stability of the molecular ensembles. Specifically, the transport properties of free base and zinc coordinated tri-pyridyl porphyrin thiol molecular islands inserted into a dodecanethiol matrix on Au(111) were investigated using STM and cross-wire inelastic electron tunneling spectroscopy (IETS). The zinc porphyrin thiol islands observed by STM exhibited reversible bias induced switching at high surface coverage due to the formation of Coulomb islands of ca. 10 nm diameter driven by porphyrin aggregation. Low temperature measurements (~ 4 K) from crossed-wire junctions verified the appearance of a Coulomb staircase and blockade which was not observed for single molecules of this compound or for the analogous free base. Scanning probe lithography via nanografting has been implemented to directly assemble nanoscale patterns of zinc porphyrin thiols and 16-mercapotohexadecanoic acid on Au surfaces. Matrix effects during nanopatterning including solvent and background SAMs have been investigated and ultimately ~ 10 nm islands of zinc porphyrins have been fabricated which is the optimal size for the observed switching effect.