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In the framework of this thesis molecular nanostructures have been engineered on surfaces and are characterized using a variety of techniques. Two types of molecules have been used: carbon nanotubes (CNT) and 4-[trans-2-(pyrid-4-yl-vinyl)] benzoic acid (PVBA), which is especially designed for nonlinear optical (NLO) applications and to facilitate self-assembly by formation of strong H-bonds. Supramolecular NLO thin films of PVBA have been grown on amorphous glass substrates using Oblique Incidence Organic Molecular Beam Deposition (OI-OMBD) and molecular self-assembly. The molecular orientation in the films has been investigated by studying the macroscopic NLO response of the thin films. When deposited on an atomically clean Cu(100) surface, PVBA molecules assemble into 2D supramolecular arrangements. The obtained 2D structures have been studied in situ by Scanning Tunneling Microscopy (STM). For the growth of vertically aligned CNT structures, first microcontact printing (μCP) has been used to create patterned substrates with ferritin catalyst material, followed by the catalytic growth of CNTs using Chemical Vapor Deposition (CVD). The CNT related structures have been studied by electron microscopy. OI-OMBD is a new approach that delivers noncentrosymmetric organic thin films on amorphous substrates. We studied how the incidence angle of the molecular beam influences the noncentrosymmetric ordering of molecules within the PVBA thin films. An optimum incidence angle was found that lies between 40° and 60° from the substrate normal. These deposition angles result in films with an optimized NLO coefficient that is independent of the film thickness. Moreover, these films have lower absorption and a better mechanical stability than films grown at other deposition angles. By investigating the second harmonic light generation of the PVBA thin films, we found that there is a first thin layer near the substrate where the molecules are oriented perpendicular to the substrate, whereas the molecules in the bulk of the film have a preferential orientation parallel to the substrate. The oblique molecular beam acts as a small symmetry breaking force, giving the molecules – within the plane of the film – a preferential orientation that is a small trend above an equiprobable distribution of orientations. The present optimization is an important step toward the development of optimized NLO thin films, by applying the same deposition technique to molecules with a higher hyperpolarizability. The two-dimensional structures that are formed by PVBA deposited on a Cu(100) substrate result in two distinct phases: the "Square Structure" (SQS) for low molecular coverage and the "Butterfly Structure" (BFS) near saturation coverage. In both phases the carboxylic acid group of the molecules is deprotonated, as demonstrated by XPS measurements. For the SQS, chiral separation of the PVBA 2D enantiomers takes place to form two distinguishable enantiomerically pure domain types. A detailed structural analysis suggests H-bonding between two pyridyl groups and H-bonding involving the carboxylate group. Each carboxylate group binds to the favored or to the unfavored side of a perpendicularly oriented molecule, in a ratio that decreases with molecular coverage. In this way the surface density of characteristic open squares in the SQS can be tuned. For the BFS, the molecular ordering is fundamentally different from the SQS. In the BFS H-bonding does take place between carboxylate groups and the sides of molecules, but four pyridyl groups are pushed together at the center of each 'butterfly' unit instead of forming appreciable H-bonding. Furthermore chiral separation is suppressed, leading to racemic BFS domains. The transition from SQS to the closer packed BFS is driven by space limitations at high molecular coverages. Finally, we report the growth of vertically aligned multi-walled CNT structures on Si/SiO2 substrates, using ferritin as catalyst. The CNTs can be grown at large scale without encapsulated particles or attached amorphous carbon. They have a very narrow diameter distribution and their lengths can be controlled by the growth conditions, to several hundreds of microns and longer. Activation of the ferritin catalyst by oxygen exposure has proven to be indispensable for the growth of aligned CNTs. The oxygen pressure and the CVD temperature determine the growth rate, and the CVD duration determines the final CNT length. Nickel and gold coatings sputtered on CNTs have been studied at different temperatures. Nickel shows a stronger interaction with the CNT walls than gold, resulting in more homogeneous coatings at ambient temperature. Surface diffusion at 660°C leads to the formation of larger clusters, which in case of nickel have a larger contact area with the CNT surface than in case of gold. Inter-CNT connections have been made by growing CNTs directly on the walls of primary CNTs, using the formed nickel clusters or ferritin as catalyst. Field emission measurements performed on CNT samples with secondary CNTs showed clearly improved emission characteristics compared to samples with only primary CNTs.