Development of nanopatterns on self assembled monolayer (SAM) organic films using scanning probe microscope (SPM) nanolithography techique

Thesis (Master)--Izmir Institute of Technology, Materials Science and Engineering, Izmir, 2006Includes bibliographical references (leaves: 109-112)Text in English; Abstract: Turkish and Englishxiv, 112 leavesPatterning and fabrication of nanostructures on surfaces is a great demand for nanoscale electronic and mechanical devices. Current techniques such as electron beam lithography and photolithography provides limited resolution and they are not capable of reproducible in nanoscale. Among those, Scanning Probe Microscopy (SPM) lithography that uses a nanometer sharpened tip has demonstrated outstanding capabilities for nanometer level patterning on various surfaces. Moreover, SPM techniques offer creating nanopatterns of Self Assembled Monolayers (SAMs) with molecular precision and visualizing surfaces with the highest spatial resolution. In this work, nanoscratches on gold surfaces and oxidation patterns on titanium surface were successfully performed as example of SPM lithography. In the second stage, Octadecylamine-HCl, Octadecanetiol (ODT) and Decylmercaptan (DM) SAM organic films were fabricated on various substrates; i.e., mica, silica, titanium surface deposited on silicon, n and p type silicon, using self assembly film preparation techniques. The film thicknesses were measured with Atomic Force Microscope (AFM). Nanopatterns were fabricated on SAM films using AFM tip by exerting a local high pressure at the contact that causes the displacement of SAM molecules by a high shear force. It was observed that there was no formation of SAMs on n type Si and silica substrates whereas there were organic assemblies on the other substrates. Fabricated nanopatterns were examined and thickness measurement was done. Molecular lengths of the organics were evaluated by using of SPARTAM 02 LINUX-UNIX with the method of PM3 and the measured values were compared with the calculated ones and it was concluded that monolayers were formed on the surfaces

A Computational Study of Small Gold Clusters with H2S, Thiols, H2O, and Alcohols

Alkane thiols, RSH, are commonly used in aqueous solution to stabilize and prevent aggregation of gold clusters, Aun. Initially a RSH-Aun complex is formed and, subsequently, there is hydrogen atom transfer to form a RSAunH complex. We examine the rate of this reaction for small neutral gold clusters, with n=1-2 and short-chain thiols with R = H, CH3, and CH3CH2, using transition state theory. The comparison of DFT (with the functionals, BP86 and M06-2X), and MP2 was performed. A pseudopotential was employed to account for the large relativisitic effects exhibited by gold. Equilibrium geometries and vibrational frequencies of the RSH-Aun and RSAunH complexes were obtained, as well as thermo-chemical values for the transfer of a hydrogen atom from sulphur to gold. The activation energy and rate of hydrogen atom transfer was also determined

Designing surface chemistries for in situ AFM investigations of biomolecular reactions with proteins at the nanoscale

In situ atomic force microscopy (AFM) characterizations and lithography can be applied to investigate the orientation, reactivity and stability of protein molecules adsorbed on nanostructures of self-assembled monolayers at near-physiological conditions. Automated nanografting was used to fabricate regular arrays of nanopatterns of ù-functionalized n-alkanethiols with designated terminal chemistries. After writing nanopatterns, protein binding occurs selectively on carboxylate-terminated nanopatterns via covalent bonds that are formed using N-ethyl-N\u27(dimethylaminoporpyl)-carbodiimide and N-hydroxysuccinimide activation. The amine groups of lysine residues of proteins bond covalently to nanopatterns of carboxylate-terminated alkanethiol self-assembled monolayers, to form a robust surface attachment for sustained contact-mode AFM imaging during biochemical reactions. Staphylococcal protein A (SpA) furnishes a generic foundation for binding immunoglobulins for nanometer scale sandwich assays. The self-assembly of á,ù-alkanedithiols onto Au(111) was investigated using AFM. When SAMs of 1,8-octanedithiol or 1,9-nonanedithiol are grown naturally from solution, different surface orientations are observed in comparison to methyl-terminated n-alkanethiols. Local views from AFM images reveal a layer of mixed orientations in which the majority of á,ù-alkanedithiol molecules adopt an orientation parallel to the surface with both thiol endgroups bound to Au(111). Results from AFM studies reveal that the chemisorption of thiol endgroups of dithiols inhibits the phase transition from a lying-down to a standing orientation during natural self-assembly. Another method for producing protein nanostructures is particle lithography. Monodisperse mesospheres can be applied to rapidly prepare millions of exquisitely uniform nanometer-sized structures of proteins on flat surfaces using conventional benchtop chemistry steps of mixing, centrifuging, evaporation and drying. The natural self-assembly of monodisperse spheres provides a high throughput and efficient route to prepare circular geometries over millimeter scale areas. The spontaneous assembly of silica or latex mesospheres into organized crystalline layers on flat substrates supplies a structural frame to direct the placement of proteins. Nanopatterns of ferritin, apoferritin, immunoglobulin G and bovine serum albumin were produced with particle lithography. The applicability of particle lithography to generate arrays of protein nanostructures on surfaces such as mica(0001), glass and Au(111) was demonstrated. The morphology and diameter of the protein nanostructures can be tailored by selecting the ratios of protein-to-particles and the diameters of spheres

Molecular Tips for Chemically Selective STM

Scanning tunneling microscopy (STM) has been a powerful tool in surface science. STM, however, often lacks chemical selectivity. In this laboratory, it has been demonstrated that the use of molecular tips allows STM to attain the chemical selectivity. The chemical selectivity arises from the facilitation of electron tunneling by chemical interactions between tip molecules and particular chemical species of sample molecules. The available interactions reported so far include hydrogen bond and metal-coordination interactions. In the present study, I showed facilitation of electron tunneling through charge-transfer interaction, which allows us to locate electroactive moieties and to construct a novel intermolecular junction for testing molecular-scale electronic devices. In addition, it was demonstrated that carboxy-terminated single-walled carbon nanotube (SWNT) tips enable high resolution and chemically selective observation. Finally, it was shown that the selective observation of oxygen-containing functional groups can be tailored by controlling the extent of the hydrogen bond acidity or basicity of tip molecules.報告番号: 乙15970 ; 学位授与年月日: 2004-04-08 ; 学位の種別: 論文博士 ; 学位の種類: 博士(理学) ; 学位記番号: 第15970号 ; 研究科・専攻: 理学系研究

Nanobiotechnologie: Werkzeuge für die Proteomik : molekulare Organisation und Manipulation von Proteinen und Proteinkomplexen in Nanodimensionen

First milestone of this Ph.D. thesis was the successful extension of conventional NTA/His-tag technique to self-assembling, multivalent chelator thiols for high-affinity recognition as well as stable and uniform immobilization of His-tagged proteins on chip surfaces. Bis-NTA was linked via an oligoethylene glycol to alkyl thiols by an efficient modular synthesis strategy yielding a novel, multivalent compound for formation of mixed SAMs with anti-adsorptive matrix thiols on gold. Multivalent chelator chips allow a specific, high-affinity, reversible, long-term immobilization of His-tagged proteins. In AFM studies reversibility of the specific protein immobilization process was visualized at single molecule level. The entire control over the orientation of the immobilized protein promotes this chip surface to an optimal platform for studies focusing on research targets at single molecule level and nanobiotechnology. Based on the constructed protein chip platform above and a novel AFM mode (contact oscillation mode, COM) – developed during the current Ph.D. work – protein nanolithography under physiological conditions enabling fabrication of active biomolecular patterns in countless variety has been established. Reversible COM-mediated nanostructuring is exceptionally suitable for multiplexed patterning of protein assemblies in situ. The first selfassembled protein layer acts as a biocompatible and ductile patterning material. Immobilized proteins can be replaced by the AFM tip applying COM, and the generated structures can be erased and refilled with different proteins, which are immobilized in a uniform and functional manner. Multi-protein arrays can be systematically fabricated by iterative erase-and-write processes, and employed for protein-protein interaction analysis. Fabrication of two-dimensionally arranged nanocatalytic centres with biological activity will establish a versatile tool for nanobiotechnology. As an alternative chip fabrication approach, the combined application of methodologies from surface chemistry, semiconductor technology, and chemical biology demonstrated successfully how pre-patterned templates for micro- and nanoarrays for protein chips are fabricated. The surface physical, as well the biophysical experiments, proved the functionality of this technology. The promises of such process technology are fast and economic fabrication of ready-to-use nanostructured biochips at industrial scale. Membrane proteins are complicated in handling and hence require sophisticated solutions for chip technological application. A silicon-on-insulator (SOI) chip substrate with microcavities and nanopores was employed for first technological investigation to construct a protein chip suitable for membrane proteins. The formation of an artificial lipid bilayer using vesicle fusion on oxidized SOI cavity substrates was verified by CLSM. Future AFM experiments will give further insights into the chip architecture and topography. This will provide last evidence of the sealing of the cavity by the lipid bilayer. Transmembrane proteins will be employed for reconstitution experiments on this membrane protein chip platform. Highly integrated microdevices will find application in basic biomedical and pharmaceutical research, whereas robust and portable point-of-care devices will be used in clinical settings.Erster Meilenstein der vorliegenden Arbeit war die erfolgreiche Erweiterung des konventionellen NTA/His-tag-Konzepts auf selbst-assemblierende, multivalente Chelatorthiole für die hochaffine Erkennung und stabile, einheitliche Immobilisierung His-getaggter Proteine auf Chipoberflächen. Mittels einer effizienten, modularen Synthesestrategie wurden Bis-NTA-Module über Oligoethylenglykoleinheiten an Alkylthiole angebunden. Diese Chelatorthiole wurden zusammen mit antiadsorptiven Matrixthiolen zur Ausbildung gemischter selbst-assemblierender Monolagen (SAMs) auf Goldoberflächen eingesetzt. Die multivalenten Chelatorchips erlauben eine spezifische, hochaffine, umkehrbare und langfristige Immobilisierung His-getaggter Proteine. Die Umkehrbarkeit der spezifischen Proteinimmobilisierung wurde in rasterkraftmikroskopischen (AFM) Studien bis zur Einzel-Molekül-Ebene visualisiert. Die vollständige Kontrolle über die Orientierung immobilisierter Proteine qualifiziert diese entwickelte Chipoberfläche zu einer optimalen Plattform für Anwendungsbereiche der Einzelmolekülbiochemie und Nanobiotechnologie. Basierend auf dieser Plattform für Proteinchips und einem – im Rahmen dieser Arbeit – neuentwickelten AFM-Modus (Kontaktoszillationsmodus, COM) wurde die „Protein-Nanolithographie“ etabliert, welche die Fabrikation von aktiven, biomolekularen Strukturen in unzähliger Vielfalt ermöglicht. Die umkehrbare COM-vermittelte Nanolithographie ist insbesondere für die multiplexe Anordnung von Proteinverbänden in situ geeignet. Die erste Schicht immobilisierter Proteine fungiert als ein biokompatibles und verformbares Strukturierungsmaterial. Diese immobilisierten Proteine können nun im Kontaktoszillationsmodus mit der AFM-Spitze lokal entfernt („Löschen“) und gegen andere Proteine – die an die freigelegte Chipoberfläche ebenfalls spezifisch und funktional immobilisieren – ausgetauscht werden („Schreiben“). Arrays, bestehend aus mehreren unterschiedlichen Proteinen können nun systematisch in iterativen Lösch-und-Schreib-Vorgängen fabriziert und für Proteininteraktionsanalysen eingesetzt werden. Die Fabrikation von zwei-dimensional arrangierten nanokatalytischen Zentren mit biologischer Aktivität wird von großem Nutzen für die Nanobiotechnologie sein. Eine alternative Herstellungsmethode aus einer Kombination von Oberflächenchemie, Halbleitertechnologie und chemischer Biologie wurde für die Fabrikation von vorstrukturierten Templaten für Mikro- und Nanoarrays entwickelt. Die Funktionalität dieser Chipplattform wurde anhand oberflächen- und biophysikalischer Experimente erfolgreich gezeigt. Zukünftiges Ziel ist die Anfertigung vorstrukturierter Template in der Dimension weniger Nanometer zur Ausbildung von Bio-Arrays mit einzelnen Molekülen. Ein weiteres Ziel besteht in der kompletten Verlagerung des Herstellungsprozesses in die Gasphase. Eine Produktion in der Gasphase verspricht eine schnelle und wirtschaftliche Erzeugung sofort einsatzbereiter nanostrukturierter Biochips im industriellen Maßstab. Der Umgang mit Membranproteinen verlangt besondere Vorkehrungen im experimentellen Milieu, ebenso speziell sind die Bedürfnisse in den entsprechenden Chip-Anwendungen. Ein Chip mit Mikrokavitäten und Nanoporen, basierend auf der „Silicon-on-Insulator“ (SOI)-Technologie, wurde für erste technologische Studien zum Entwurf eines Proteinchips für Membranproteine eingesetzt. Künstliche Lipidmembranen wurden auf der SOI-Oberfläche mittels Vesikelfusion ausgebildet und mit konfokaler Laser-Scanning-Mikroskopie gezeigt. Zukünftige AFM-Experimente werden weitere Einsichten in die Chiparchitektur und Topographie ermöglichen. Transmembranproteine werden in Rekonstitutionsexperimenten für funktionale Studien der Membranproteinchips eingesetzt. Anwendungsbereiche solcher hochintegrierten Mikrosysteme sind sowohl in der biologischen Grundlagenforschung als auch in mobilen Diagnostikgeräten im klinischen Einsatz zu finden

DESIGN OF HIGHLY STABLE LOW-DENSITY SELF-ASSEMBLED MONOLAYERS USING THIOL-YNE CLICK REACTION FOR THE STUDY OF PROTEIN-SURFACE INTERACTIONS

Protein adsorption on solid surfaces is a common yet complicated phenomenon that is not fully understood. Self-assembled monolayers have been utilized in many studies, as well-defined model systems for studying protein-surface interactions in the atomic level. Various strategies, including the use of single component SAMs[1, 2], combinations of long and short alkanethiolates with methyl- and hydroxyl- terminal groups[3, 4], and using mixtures of alkanethiolates with similar chain length and varying terminal functional group [5] have been used to effectively control the surface wettability and determine the effect of surface composition and wettability on protein adsorption. In this dissertation we report key new findings on the effect of surface density of functional groups on protein adsorption phenomenon. In The first phase of this research, we developed a novel approach for preparation of low-density self-assembled monolayers(LD-SAMs) on gold surfaces, based on radical-initiated thiol-yne click chemistry. This approach provides exceptional adsorbate stability and conformational freedom of interfacial functional groups, and is readily adapted for low-density monolayers of varied functionality. The resulting monolayers have two distinct phases: a highly crystalline head phase adjacent to the gold substrate, and a reduced density tail phase, which is in contact with the environment. First, we investigated the feasibility of the proposed chemistry in solution-phase. In this approach, we synthesized “Y” shaped carboxylate-terminated thiol adsorbates via radical-initiated thiol-yne reaction. The LD-SAMs were then prepared through immersion of gold substrates into the solution of synthesized adsorbate molecules in hexane. The chemical structuring and electrochemical properties of resultant LD-SAMs were analyzed and compared with those of analogous traditional well-packed monolayers, using techniques such as Fourier transform infrared spectroscopy, ellipsometry, electrochemical impedance spectroscopy, reductive desorption, and contact angle goniometry. Characterization results indicated that resulting LD-SAMs have a lower average crystallinity, and higher electrochemical stability compared to well-packed monolayers. In addition, using a three-electrode system, we were able to show a reversible change in LD-SAM surface wettability, in response to an applied voltage. This remodeling capacity confirms the low density of the surface region of LD-SAM coatings. The second area of work was focused on using the developed chemistry in solid-phase. The solid-phase approach minimized the required synthesis steps in solution-phase method, and used the photo-initiated thiol-yne click-reaction for grafting of acid-terminated alkynes to thiol-terminated monolayers on a gold substrate to create similar LD-SAMs as what were prepared through solution-phase process. We characterized the resulting monolayers and compared them to analogous well-packed SAMs and the also low-density monolayers prepared through the solution phase approach. The results confirmed the proposed two-phase structure, with a well-packed phase head phase and a loosely-packed tail phase. In addition, the electrochemical studies, indicated that the resultant monolayers were less stable than the monolayers prepared via solution-phase, but they are yet significantly more stable than typical well-packed monolayers. The less stability of these monolayers were attributed to the partial desorption of adsorbates from the gold substrate due to UV irradiation during the grafting process. Building on the established chemistry, we studied the effect of lateral packing density of functional groups in a monolayer on the adsorption of Bovine serum albumin protein. we used surface plasmon resonance spectroscopy (SPR) and spectroscopic ellipsometry, to evaluate BSA adsorption on carboxylate‑, hydroxyl-, or alkyl- terminated LD-SAMs. It was found that for the LD-SAMs, the magnitude of protein adsorption is consistently higher than that of a pure component, well-packed SAM for all functionalities studied. In addition, it was seen that the magnitude of BSA adsorption the LD-SAMs, was consistently higher than that of a pure component, well-packed SAM for all functionalities studied. The difference of protein adsorption on LD-SAMs and SAMs can not be associated to difference in lateral packing density, unless we eliminate the impact of other contributing factors in protein adsorption such as surface energy. In order to better understand the impact of packing density on protein-surface interactions, we prepared the mixed SAMs of (carboxylate/alkyl) and (hydroxyl/alkyl) with matching surface energy as the carboxylate and hydroxyl terminated LD-SAMs. It was found that the energy-matched mixed SAMs of carboxylate and hydroxyl functionality adsorbed more protein than the LD-SAMs. However, an opposite trend was seen for the alkyl surfaces, where surface energies are comparable for LD-SAMs and pure component SAMs, indicating that BSA proteins have higher affinity for methyl- terminated LD-SAMs than well-packed SAMs

Modulating Surface Dipoles in Fluorinated Thin Films

This dissertation investigates the effect a surface dipole has on the interfacial properties of partially fluorinated self-assembled monolayers (FSAMs). In the first study, the synthesis of a new type of partially fluorinated adsorbate of the form CH3(CF2)6(CH2)nSH where n = 10–13 was performed. On the surface, these adsorbates generate a novel hydrocarbon-fluorocarbon (HC-FC) dipole at the interface of the SAMs that has a profound effect on the wettability of the surfaces with various contacting liquids; specifically, the inverse odd-even effect observed with regard to the wettability of polar protic and aprotic liquids. Additionally, the properties of the HC-FC dipole were compared to those of a FC-HC (fluorocarbon-hydrocarbon) dipole derived from CF3-termianted alkanethiols. In efforts to understand further the effect of the new HC-FC dipole, an additional series of alkyl-terminated alkanethiols of the form H(CH2)n(CF2)6(CH2)11SH, where n = 1–7, was synthesized and used to form SAMs. In this study, the dipole was systematically buried in the film and analyzed with several contacting liquids. The effect of the dipole in these types of FSAMs appears to have a diminished effect after 3 hydrocarbons, after which an odd-even effect in the wettability was observed. The odd-even effects observed in the FSAMs were the opposite of that observed with normal alkanethiols of the same carbon length, which suggests that the orientation of the terminal methyl group is different from the normal alkanethiol. Finally, to explore further the effect of the direction of the FC-HC and HC-FC dipoles, evaporated gold surfaces were electrochemically modified with a monolayer of silver via underpotential deposition (UPD). The monolayer of silver has an effect on the structural features of the films caused by the different binding geometries of the sulfur on gold and silver. The structural difference between the two substrates inverts the odd-even effects for SAMs with a FC-HC dipole. For SAMs possessing a HC-FC dipole, the presence of silver on the gold surface also changes the orientation of the molecules on the different metals, influencing the physical and interfacial properties of the resulting films.Chemistry, Department o

Gold surfaces and nanoparticles are protected by Au(0)-thiyl species and are destroyed when Au(I)-thiolates form

The synthetic chemistry and spectroscopy of sulfur-protected gold surfaces and nanoparticles is analyzed, indicating that the electronic structure of the interface is Au(0)-thiyl, with Au(I)-thiolates identified as high-energy excited surface states. Density-functional theory indicates that it is the noble character of gold and nanoparticle surfaces that destabilizes Au(I)-thiolates. Bonding results from large van der Waals forces, influenced by covalent bonding induced through s-d hybridization and charge polarization effects that perturbatively mix in some Au(I)-thiolate character. A simple method for quantifying these contributions is presented, revealing that a driving force for nanoparticle growth is nobleization, minimizing Au(I)-thiolate involvement. Predictions that Brust-Schiffrin reactions involve thiolate anion intermediates are verified spectroscopically, establishing a key feature needed to understand nanoparticle growth. Mixing of preprepared Au(I) and thiolate reactants always produces Au(I)-thiolate thin films or compounds rather than monolayers. Smooth links to O, Se, Te, C, and N linker chemistry are established

Scanning Probe Investigations of the Surface Self-Assembly of Organothiols and Organosilanes Using Nanoscale Lithography

Particle lithography and scanning probe lithography were applied to study the kinetics and mechanisms of surface self-assembly processes. Organothiols on Au(111) and organosilane on Si(111) were chosen as model systems for investigations at the nanoscale using atomic force microscopy (AFM). Fundamental insight of structure/property interrelationships and understanding the properties of novel materials are critical for developments with molecular devices. Methods using an AFM probe for nanofabrication have been applied successfully to prepare sophisticated molecular architectures with high reproducibility and spatial precision. The established capabilities of AFM-based nanografting were reviewed for inscribing patterns of diverse composition, to generate complicated surface designs with well-defined chemistries. Nanografting provides a versatile tool for generating nanostructures of organic and biological molecules, as well as nanoparticles. Protocols of nanografting are accomplished in liquid media, providing a mechanism for introducing new reagents for successive in situ steps for 3-D fabrication of designed nanopatterns. Because so many chemical reactions can be accomplished in solution, there are rich possibilities for chemists to design studies of other surface reactions. Surface assembly and self-polymerization of chloromethylphenyltrichlorosilane (CMPS) were investigated using test platforms of organosilanes fabricated with particle lithography. A thin film of octadecyltrichlorosilane (OTS) with well-defined nanopores was prepared on Si(111) to spatially confine the surface assembly of CMPS within nanopores of OTS. Time-dependent changes during the self-polymerization of CMPS was visualized ex situ using AFM. Molecular-level details of CMPS nanostructures were obtained from high resolution AFM images to track the growth of organosilanes on Si(111). Measurements of the heights and diameters of CMPS nanostructures provided quantitative information of the kinetics of CMPS self-polymerization. Scanning probe-based methods of nanolithography were applied to investigate the self-assembly of a tridentate organothiol, 1,1,1-tris(mercaptomethyl)heptadecane (TMMH). Multidentate adsorbates can address problems with long-term stability to oxidation observed with monothiolated n-alkylthiols. Multidentate thiol ligands demonstrate improved resistance to oxidation, thermal desorption and UV exposure. Progressive changes in surface morphology for TMMH assembly onto Au(111) was studied in situ with time-lapse AFM, monitoring changes in surface coverage at different time intervals. Nanoshaving and nanografting were used as molecular rulers to evaluate the thickness of films of TMMH

Studying Properties of Nano-Scale Moieties Using Functionalized Self-Assembled Monolayers.

Ph.DDOCTOR OF PHILOSOPH