Self-Assembly Mechanisms of Organosilanes and Porphyrins Investigated with Scanning Probe Microscopy

This dissertation details the development of new fabrication strategies for the preparation of spatially selective surfaces by combining techniques of particle lithography and scanning probe microscopy (SPM). This combination of lithography and nanoscale surface characterization was applied to study the mechanisms of molecular level surface-assembly of organosilanes and porphyrin on surfaces of Si(111). Particle lithography was used to investigate the surface assembly of 4-chloromethylphenyltrichlorosilane (CMPS) within exposed sites of nanoholes in selected solvents and at selected temperatures to gain insight into the details of self-polymerization. Nanopillars of CMPS were generated under selected conditions of solvent and temperature and characterized with atomic force microscopy (AFM). CMPS nanopillars were shown to grow taller with more layers at higher reactions temperatures. It was also observed that CMPS nanopillars grown in toluene formed more fractured pillars with multiple domains from a single nanoholes, compared to nanopillars grown in bicyclohexane that were observed to have more structured growth and less diverse morphology. The self-assembly of CMPS was strictly confined to nanoholes with the surrounding matrix showing very little evidence of non-specific adsorption. Surface platforms of nanopatterned CMPS nanopillars were fabricated within a resistive thin film of octadecyltrichlorosilane (OTS) to spatially direct and pattern the addition of 5,10,15,20-Tetra(4-pyridyl)porphyrin. The generation of CMPS-porphyrin heterostructures was studied ex-situ and confirmed by statistically significant changes in nanostructure height before and after the porphyrin addition. The fabrication of CMPS-porphyrin heterostructures from morphologically diverse CMPS nanopillar foundations was studied to provide insight into the mechanisms of CMPS nanopillar self-assembly. The morphology of final stage heterostructures closely resembled the original morphology of the CMPs nanopillars with little evidence of non-specific adsorption across the OTS thin film resist. Particle lithography was used to fabricate silicon porphyrin nanostructures on surfaces of Si(111) via a porphyrin-silane coupling reaction. Previous steps for nanopatterning porphyrin on a surface included an additional step to of an organosilane linker molecular that the porphyrin molecules could bind and assembly from. This new protocol coordinates a silane to each porphyrin macrocycle though a simple single vessel reaction system developed by Kurihara et al.1 Through this coupling reaction porphyrins can be directly assembled on surfaces of silicon and glass. Porphyrin nanostructures of nanoholes, nanorings and nanopillars as well as porphyrin thin films were generated using this technique

Conductance statistics from a large array of sub-10 nm molecular junctions

Devices made of few molecules constitute the miniaturization limit that both inorganic and organic-based electronics aspire to reach. However, integration of millions of molecular junctions with less than 100 molecules each has been a long technological challenge requiring well controlled nanometric electrodes. Here we report molecular junctions fabricated on a large array of sub-10 nm single crystal Au nanodots electrodes, a new approach that allows us to measure the conductance of up to a million of junctions in a single conducting Atomic Force Microscope (C-AFM) image. We observe two peaks of conductance for alkylthiol molecules. Tunneling decay constant (beta) for alkanethiols, is in the same range as previous studies. Energy position of molecular orbitals, obtained by transient voltage spectroscopy, varies from peak to peak, in correlation with conductance values.Comment: ACS Nano (in press

Electromechanical Lifting Actuation of a MEMS Cantilever and Nano-Scale Analysis of Diffusion in Semiconductor Device Dielectrics

This dissertation presents experimental and theoretical studies of physical phenomena in micro- and nano-electronic devices. Firstly, a novel and unproven means of electromechanical actuation in a micro-electro-mechanical system (MEMS) cantilever was investigated. In nearly all MEMS devices, electric forces cause suspended components to move toward the substrate. I demonstrated a design with the unusual and potentially very useful property of having a suspended MEMS cantilever lift away from the substrate. The effect was observed by optical micro-videography, by electrical sensing, and it was quantified by optical interferometry. The results agree with predictions of analytic and numerical calculations. One potential application is infrared sensing in which absorbed radiation changes the temperature of the cantilever, changing the duty cycle of an electrically-driven, repetitively closing micro-relay. Secondly, ultra-thin high-k gate dielectric layers in two 22 nm technology node semiconductor devices were studied. The purpose of the investigation was to characterize the morphology and composition of these layers as a means to verify whether the transmission electron microscope (TEM) with energy dispersive spectroscopy (EDS) could sufficiently resolve the atomic diffusion at such small length scales. Results of analytic and Monte-Carlo numerical calculations were compared to empirical data to validate the ongoing viability of TEM EDS as a tool for nanoscale characterization of semiconductor devices in an era where transistor dimensions will soon be less than 10 nm

Atomic Force Microscopy Tip-enhanced Laser Ablation

In the present work, an apertureless atomic force microscope (AFM) tip-enhanced laser ablation (TELA) system was developed and investigated. An AFM was coupled to an optical parametric oscillator (OPO) wavelength tunable laser for sample ablation with a submicron sampling size. The AFM was used to image the surface and hold the AFM tip 10 nm above the sample surface. The AFM tip is coated with a layer of gold with a thickness of 35 nm. The incident laser wavelength was tuned in the visible and near-infrared (IR) region and focused on the AFM tip. With the tip-enhancement effect, ablation craters on the surface with a submicron size were obtained. The mechanism of TELA was investigated using anthracene and three laser dyes: rhodamine B, methylene blue, and IR 797 chloride. All samples were prepared in thin films and the laser energy was set just below their far-field ablation threshold. The wavelength was tuned from 450 to 1100 nm to cover the visible and near-IR range. It was found that ablation is independent of the absorption of the compounds. The ablation crater volume was measured and found to have a maximum at 500 nm and an approximately linear drop to 800 nm. Craters could not be produced between 800 and 1200 nm and were slightly smaller at 450 nm compared to 500 nm. Apertureless TELA was then performed to sample plasmid DNA with 532 nm, which resulted in a sampling volume of 0.14 μm3 with 12% in variation. The captured DNA was amplified and the amount of sample transferred from each ablation crater was quantitated at 20 ag/spot

Visualization of Recombinant DNA and Protein Complexes Using Atomic Force Microscopy

Atomic force microscopy (AFM) allows for the visualizing of individual proteins, DNA molecules, protein-protein complexes, and DNA-protein complexes. On the end of the microscope's cantilever is a nano-scale probe, which traverses image areas ranging from nanometers to micrometers, measuring the elevation of macromolecules resting on the substrate surface at any given point. Electrostatic forces cause proteins, lipids, and nucleic acids to loosely attach to the substrate in random orientations and permit imaging. The generated data resemble a topographical map, where the macromolecules resolve as three-dimensional particles of discrete sizes (Figure 1) 1,2. Tapping mode AFM involves the repeated oscillation of the cantilever, which permits imaging of relatively soft biomaterials such as DNA and proteins. One of the notable benefits of AFM over other nanoscale microscopy techniques is its relative adaptability to visualize individual proteins and macromolecular complexes in aqueous buffers, including near-physiologic buffered conditions, in real-time, and without staining or coating the sample to be imaged

New Methods for Depositing and Imaging Molecules in Scanning Tunneling Microscopy

Methods and apparatus are described to deposit and image molecules by scanning tunneling microscopy (STM) under an inert atmosphere. Three methods of applying molecules have been evaluated: equilibrium adsorption from the vapor phase, sublimation, and electrospraying. Using these methods, a variety of organic and biopolymer molecules have been deposited and imaged on graphite and on gold (111), grown epitaxially on mica. Compared with alternatives, such as the use of high vacuum apparatus or glove boxes, these procedures offer some important advantages: they are inexpensive, convenient, and more rapid. Mercaptoethanol, ethanolamine, ethanol, acetic acid, and water produce two-dimensional crystalline adlayers on gold substrates, when they are introduced into the scanning cell as vapors. These adlayers are assumed to involve hydrogen bonding of the molecules to an oxide of gold formed on the surface. Electrospraying protein solutions on gold surfaces yielded images of individual protein molecules with lateral dimensions close to those measured by X-ray analysis, and thicknesses of 0.6-1.3 nm. In the case of metallothionein, the known internal domain structure of the molecule was reproducibly observed. No detailed internal structure could be resolved in the other examples examined

Surface and Interfacial Approaches for the Characterization of Biomolecular Interactions and to Optimize Desi-MS Performance

This work involves the surface and interfacial characterization of biomolecular interactions by atomic force microscopy and optimization of desorption electrospray ionization mass spectrometry. In the first part (part I), suitable surface of functionalized porous silicon are created and characterized to enhance Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) capability. DESI-MS is a powerful emerging analytical tool that finds applications in fundamental research and as a diagnostic tool. Enhancement of the performance of this technique will make it superior and improve the scope of its applications. The use of super hydrophobic porous silicon proved to enhance the desorption/ionization mechanism of DESI. It improves the ionization efficiency almost two fold when compared to the traditionally used glass slide and porous polytetraflouroethylene surfaces under the same conditions. The functionalized porous surfaces showed incredible stability, which is suitable for long time and high throughput analysis. We proposed a mechanism whereby the porous silicon acts as a barrier for the spray solvent, and creates a pool of analyte during desorption, leading to greater stability. On the other hand, the super hydrophobic functionality improves the ionization power of the technique by increasing analyte concentration over the area sampled and preventing filing of the pores. The functionalized porous surfaces are also suitable for DESI-imaging of biomolecules and tissue cells. In the second part (part II) of this thesis, Atomic Force Microscopy (AFM) was used to confirm site-specific protein-DNA interaction of the vancomycin resistance associated regulatory protein (VraR) from S. aureus. The protein stoichiometry at the binding site was confirmed as being mostly dimer for VraR, and as oligomers for phosphorylated VraR. In another project, AFM proved to be a very useful technique for the visualization and characterization of RNA. It enable us to visualized for the first time, the three dimensional structural architecture of genomic RNA of tomato bushy stunt virus. AFM allowed us to confirm the proposed long range-RNA-RNA interaction existing within the genome, leading to a more compact structure. Volume analyses enable to confirm the existence of compact structures as visualized in the AFM images. These results are consistent with expected conformations utilized by the TBSV virus for different viral processes. Sub-genomic RNA expressed by the TBSV virus, also exhibited compact structures with different degree of protrusions. All observed RNA and sub-genomic RNA structures from our AFM images were consistent with the selective 2-hydroxyl acylation analyzed by primer extension (SHAPE) predicted structures

bOptimizing atomic force microscopy for characterization of diamond-protein interfaces

Atomic force microscopy (AFM) in contact mode and tapping mode is employed for high resolution studies of soft organic molecules (fetal bovine serum proteins) on hard inorganic diamond substrates in solution and air. Various effects in morphology and phase measurements related to the cantilever spring constant, amplitude of tip oscillations, surface approach, tip shape and condition are demonstrated and discussed based on the proposed schematic models. We show that both diamond and proteins can be mechanically modified by Si AFM cantilever. We propose how to choose suitable cantilever type, optimize scanning parameters, recognize and minimize various artifacts, and obtain reliable AFM data both in solution and in air to reveal microscopic characteristics of protein-diamond interfaces. We also suggest that monocrystalline diamond is well defined substrate that can be applicable for fundamental studies of molecules on surfaces in general