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

Investigations of Structure / Property Interrelationships of Organic Thin Films Using Scanning Probe Microscopy and Nanolithography

Studies of the surface assembly and molecular organization of organic thin films were studied using scanning probe microscopy (SPM) and scanning probe lithography (SPL). Systems of organic thin films such as n-alkanethiols and pyridyl functionalized porphyrins were characterized at the molecular level, and measurements of the conductive properties of polythiophenes containing in-chain cobaltabisdicarbollides were accomplished. Understanding the self-organization and mechanisms of self-assembly of organic molecules provides fundamental insight for structure/property interrelationships. Investigations of the surface assembly of 5,10-diphenyl-15,20-di-pyridin-4-yl-porphyrin (DPP) on Au(111) were done using SPL methods of nanoshaving and nanografting. Automated computer designs were developed for nanofabrication to provide local characterizations of the thickness of DPP films and nanostructures. Nanolithography was accomplished using DPP films as either matrix self-assembled monolayers (SAMs) or as molecules for nanofabrication. Results presented in this dissertation demonstrate that DPP forms compact layers on Au(111), which can be used for inscribing nanopatterns of n-alkanethiols. Arrays of DPP nanopatterns with precise geometries and alignment were fabricated within n-alkanethiols by nanografting, demonstrating nanoscale lithography with pyridyl porphyrins can be accomplished to produce an upright surface orientation on Au(111) mediated by nitrogen-gold chemisorption. Beyond research investigations, the applicability of atomic force microscopy (AFM) and advancements with automated SPL were applied for teaching undergraduate chemistry laboratories to introduce the fundamentals of surface chemistry and molecular manipulation. New classroom activities were developed for the Chemistry 3493 Physical Chemistry laboratory to give students “hands-on” training with AFM. Undergraduates were trained to prepare nanopatterns of n-alkanethiols using software to control the position, force and speed of the AFM tip for nanolithography experiments. The sensitivity and nanoscale resolution of current sensing AFM was applied for studies of the conductive properties of electropolymerized thin films of polythiophenes with cobaltabisdicarbollide moieties. Images acquired with AFM furnished views of the morphology of different polymers prepared on gold surfaces. Surface maps of the conductivity of electropolymerized films were acquired with AFM current images. These studies provide new insight of the effects of the bound cobaltabisdicarbollide moiety and coordinated metal centers for the electronic properties of the resulting conducting materials

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

Deterministic Thermal Sculpting of Large-Scale 2D Semiconductor Nanocircuits

Two-dimensional (2D) Transition Metal Dichalcogenide semiconductor (TMDs) nanocircuits are deterministically engineered over large-scale substrates. The original approach combines large-area physical growth of 2D TMDs layer with high resolution thermal - Scanning Probe Lithography (t-SPL), to reshape the ultra-thin semiconducting layers at the nanoscale level. We demonstrate the additive nanofabrication of few-layer MoS2 nanostructures, grown in the 2H-semiconducting TMD phase, as shown by their Raman vibrational fingerprints and by their optoelectronic response. The electronic signatures of the MoS2 nanostructures are locally identified by Kelvin probe force microscopy providing chemical and compositional contrast at the nanometer scale. Finally, the potential role of the 2D TMD nanocircuits as building blocks of deterministic 2D semiconducting interconnections is demonstrated by high-resolution local conductivity maps showing the competitive transport properties of these large-area nanolayers. This work thus provides a powerful approach to scalable nanofabrication of 2D nano-interconnects and van der Waals heterostructures, and to their integration in real-world ultra-compact electronic and photonic nanodevices.Comment: 17 pages, 4 figure

Achieving precision and reproducibility for writing patterns of n-alkanethiol self-assembled monolayers with automated nanografting

Nanografting is a high-precision approach for scanning probe lithography, which provides unique advantages and capabilities for rapidly writing arrays of nanopatterns of thiol self-assembled monolayers (SAMs). Nanografting is accomplished by force-induced displacement of molecules of a matrix SAM, followed immediately by the self-assembly of n-alkanethiol ink molecules from solution. The feedback loop used to control the atomic force microscope tip position and displacement enables exquisite control of forces applied to the surface, ranging from pico to nanonewtons. To achieve high-resolution writing at the nanoscale, the writing speed, direction, and applied force need to be optimized. There are strategies for programing the tip translation, which will improve the uniformity, alignment, and geometries of nanopatterns written using open-loop feedback control. This article addresses the mechanics of automated nanografting and demonstrates results for various writing strategies when nanografting patterns of n-alkanethiol SAMs. © 2008 Wiley Periodicals, Inc

Tip- and laser-based 3D nanofabrication in extended macroscopic working areas

The field of optical lithography is subject to intense research and has gained enormous improvement. However, the effort necessary for creating structures at the size of 20 nm and below is considerable using conventional technologies. This effort and the resulting financial requirements can only be tackled by few global companies and thus a paradigm change for the semiconductor industry is conceivable: custom design and solutions for specific applications will dominate future development (Fritze in: Panning EM, Liddle JA (eds) Novel patterning technologies. International society for optics and photonics. SPIE, Bellingham, 2021. https://doi.org/10.1117/12.2593229). For this reason, new aspects arise for future lithography, which is why enormous effort has been directed to the development of alternative fabrication technologies. Yet, the technologies emerging from this process, which are promising for coping with the current resolution and accuracy challenges, are only demonstrated as a proof-of-concept on a lab scale of several square micrometers. Such scale is not adequate for the requirements of modern lithography; therefore, there is the need for new and alternative cross-scale solutions to further advance the possibilities of unconventional nanotechnologies. Similar challenges arise because of the technical progress in various other fields, realizing new and unique functionalities based on nanoscale effects, e.g., in nanophotonics, quantum computing, energy harvesting, and life sciences. Experimental platforms for basic research in the field of scale-spanning nanomeasuring and nanofabrication are necessary for these tasks, which are available at the Technische Universität Ilmenau in the form of nanopositioning and nanomeasuring (NPM) machines. With this equipment, the limits of technical structurability are explored for high-performance tip-based and laser-based processes for enabling real 3D nanofabrication with the highest precision in an adequate working range of several thousand cubic millimeters