Manipulating Soft Materials Molecules Covalently Coupled On Silicon Surface

Soft materials, such as polymers, nucleic acids, proteins, colloidal suspensions, and liquid crystals are highly flexible. The concept of soft materials is first proposed by a French physicist Pierre Gilles de Gennes in 1991. Their flow properties intermediate between those of a crystalline solid and a liquid, which are characterized by fluidlike disorder on the molecular scale and a high degree of order at longer length scales (from 10 to 10μm). Due to the special noncovalent interactions, such as hydrogen bonds, ionic interactions, van der Waals forces, dipolar interactions, hydrophobic interactions and coordination bonds in ligands and complexes, self-assemblies of soft materials can be exploited to create a great number of nanostructures and nanoscale devices. It is a powerful and scalable method for nanotechnology and then has diverse applications in electronics, biomedicine, new materials and energy.Today, interfacing "top-down" with "bottom-up" methods to fabricate micro-and nano-devices are one target in nanoscience and nanotechnology. It is able to design materials at the nanoscale, whether through "top-down" or through "bottom-up" methods. The bottom-up strategy is to organize the nanometer scale molecular assemblies into larger supramolecular systems in the mesoscopic scale from 10 nm to tens of micrometers. While the top-down strategy is based on patterning on a large scale while reducing the lateral dimensions to the nanoscale. It includes photolithography, focus ion beam lithography and block copolymer lithography and so on. Both the self-assembly of DNA based on the simplicity and tractability of the base-pairing interaction, and the microdomain formation of block copolymer via microphase separation based on thermodynamic incompatibility belong to the bottom-up strategy.In this dissertation, we covalently graft soft materials (DNA nantubes and polymer brushes) onto a patterned silicon surface using photolithography and block-copolymer lithography. The specific research works are summarized as follows:1. Grow DNA nanotubes on functionalized patterns of poly(poly(ethylene glycol) monomethacrylate) brushes (Si-g-Poly(PEGMA)) by photolithography on silicon surface.The fabrication procedure is as follows:first, the passivation silicon oxide layer of the single crystalline silicon was etched by dilute HF solution to generate dangling bonds of Si-Hx; secondly, through surface hydrosilylation reaction, the bromoisobutyryl group as the polymerization initiator was introduced; thirdly, poly(PEGMA) brushes were grown in-situ by Surface Initiated Atom Transfer Radical Polymerization (SI-ATRP); fourthly, the side chains of hydroxyl groups were converted by succinic anhydride to carboxyl groups (Si-g-poly(PEGMA-COOH)); fifthly, photolithography was carried on to generate circular spot arrays exposing poly(PEGMA-COOH) patterns; sixthly, NHS-ester (N-hydroxysuccinimidyl ester) was introduced by EDC/NHS coupling on photolithographied poly(PEGMA) patterns; finally six-helix DNA tubes were immobilized, followed by in-situ growth of DNA tubes on these patterns. Multiple transmission-reflection infrared spectroscopy (MTR-IR), gel electrophoresis, transmission electron microscopy (TEM), and scanning electron microscopy (SEM) were used to monitor and identify the whole process, which confirmed the feasibility of DNA self-assembly on the functionalized patterns of a silicon chip.2. Nano-well arrays etched from a template of PS-P4VP colloidal coatings.We constructed uniform 50～80 run nano-wells on silicon wafers with a dilute HF solution. The basis of this approach is the self-assembly of polystyrene-block-poly-(4-vinyl pyridine) (PS-P4VP) amphiphilic diblock copolymer micelles into uniform films on silicon surface. Etching takes place exclusively beneath the protonated P4VP cores of the polymer micelles. The etching conditions, such as silicon wafer type, HF concentration, etching time, THF vapor, HCl solution, were investigated to control the nano-well morphologies, which were observed by scan electron microscope (SEM) and atomic force microscope (AFM).3. Polymer brushes grown on silicon nano-well arrays.Since the freshly etched nano-wells on silicon are Si-Hx-terminated, we ca n deposit Au or Ag nanoparticles on these nano-wells via galvanic displacemen t. Similarly, the bromoisobutyryl group as the polymerization initiator was intro duced through hydrosilylation. Then, polymer brushes of poly(PEGMA), poly(m ethacrylic acid) (PMAA), and poly(methacrylic acid)-g-poly(N-isopropylacrylami de) (PMAA/PNIPAM) were grafted to the surface by SI-ATRP. As PMAA is polyelectrolyte, it undergoes conformational changes in response to variations in pH. When exposed to an alkaline solution (for example, pH=8), the side chai n of carboxylic acid groups of PMAA will be deprotonated, which leads to th e swelling of the polymer brushes. While exposed to an acid aqueous solution (for example, pH=3), PMAA polymer chains will collapse to the compressed coil conformation. These changes have been observed using AFM both in air a nd in liquid. With the liquid AFM, the force curve of PMAA brushes at pH 8 and 3 were measured, and their corresponding Young’s moduli were calculated. The EDC/NHS activation of PMAA generated only anhydride, probably becau se of the formation of the stable six-membered anhydride ring via intramolecul ar dehydration between two adjacent carboxyl groups in PMAA. While for the polymer blend brushes of PMAA/PNIPAM, both NHS-ester and anhydride wer e obtained. With increasing the NIPAM ratio in the monomer mixture, the pea k intensity of NHS-ester was enhanced.4. EDC/NHS activation mechanisms of PMAA with both products of anhydride and NHS-ester.We have investigated two PMAA-based systems:reiterative EDC/NHS activation and amidation of PMAA, EDC/NHS activation of the polymer blend of PMAA and PNIPAM with blending ratios of 10,20,30,40,50,60,70,80,90,100% PMAA. PMAA and PMAA/PNIPAM brushes were prepared through SI-ATRP on porous silicon by Pt-assisted chemical etching.3-Amino-l-azidopropane (AAP), an infrared probe of the azide tag with a strong stretching band at 2105 cm-1, was used as the amidation reagent. In the above two systems, especially for EDC/NHS activations, we observed the opposite waxing and waning phases of both NHS-ester and anhydride respectively, with increasing the fragmentation degree of methacrylic acid blocks in polymer blends. From infrared measurements and quantitative estimation, we suggest a structure-reactivity relationship for EDC/NHS activation of PMAA:The mathacrylic acid (MAA) monomers next to each other themselves in a polymer chain prefers to form anhydride due to the Thorpe-Ingold effect (gem dialkyl effect), while lonely MAA monomers isolated by other side chains convert to NHS-ester. In addition, we studied the amidation and hydrolysis kinetics of anhydride and NHS-ester, their hydrolysis are both much slower than amidation at pH 8.5. As the hydrolysis and amidation are competitive reactions in solution, this ensures the amidation efficiency.