A microscopic study of structural and electronic properties of functionalized silicon surfaces based on first-principles

Surface modification of silicon with organic monolayers tethered to the surface by different linkers is an important process in realizing future (opto-)electronic devices. Understanding the role played by the nature of the linking group and the chain length on the adsorption structures and electronic properties of these assemblies is vital to advance this technology. This Thesis is a study of such properties and contributes in particular to a microscopic understanding of induced changes in the work function of experimentally studied functionalized silicon surfaces. Using first-principles density functional theory (DFT), at the first step, we provide predictions for chemical trends in the work function of hydrogenated silicon (111) surfaces modified with various terminations. For nonpolar terminating atomic species such as F, Cl, Br, and I, the change in the work function is directly proportional to the amount of charge transferred from the surface, thus relating to the difference in electronegativity of the adsorbate and silicon atoms. The change is a monotonic function of coverage in this case, and the work function increases with increasing electronegativity. Polar species such as −TeH, −SeH, −SH, −OH, −NH2, −CH3, and −BH2 do not follow this trend due to the interaction of their dipole with the induced electric field at the surface. In this case, the magnitude and sign of the surface dipole moment need to be considered in addition to the bond dipole to generally describe the change in work function. Compared to hydrogenated surfaces, there is slight increase in the work function of H:Si(111)-XH, where X = Te, Se, and S, whereas reduction is observed for surfaces covered with −OH, −CH3, and −NH2. Next, we study the hydrogen passivated Si(111) surface modified with alkyl chains of the general formula H:Si–(CH2)n–CH2 and H:Si–X–(CH2)n–CH3, where X = NH, O, S and n = (0, 1, 3, 5, 7, 9, 11), at half coverage. For (X)–Hexyl and (X)–Dodecyl functionalization, we also examined various coverages up to full monolayer grafting in order to validate the result of half covered surface and the linker effect on the coverage. We find that it is necessary to take into account the van der Waals interaction between the alkyl chains. The strongest binding is for the oxygen linker, followed by S, N, and C, irrespective of chain length. The result revealed that the sequence of the stability is independent of coverage; however, linkers other than carbon can shift the optimum coverage considerably and allow further packing density. For all linkers apart from sulfur, structural properties, in particular, surface-linker-chain angles, saturate to a single value once n > 3. For sulfur, we identify three regimes, namely, n = 0–3, n = 5–7, and n = 9–11, each with its own characteristic adsorption structures. Where possible, our computational results are shown to be consistent with the available experimental data and show how the fundamental structural properties of modified Si surfaces can be controlled by the choice of linking group and chain length. Later we continue by examining the work function tuning of H:Si(111) over a range of 1.73 eV through adsorption of alkyl monolayers with general formula -[Xhead-group]-(CnH2n)-[Xtail-group], X = O(H), S(H), NH(2). The work function is practically converged at 4 carbons (8 for oxygen), for head-group functionalization. For tail-group functionalization and with both head- and tail-groups, there is an odd-even effect in the behavior of the work function, with peak-to-peak amplitudes of up to 1.7 eV in the oscillations. This behavior is explained through the orientation of the terminal-group's dipole. The shift in the work function is largest for NH2-linked and smallest for SH-linked chains and is rationalized in terms of interface dipoles. Our study reveals that the choice of the head- and/or tail-groups effectively changes the impact of the alkyl chain length on the work function tuning using self-assembled monolayers and this is an important advance in utilizing hybrid functionalized Si surfaces. Bringing together the understanding gained from studying single type functionalization of H:Si(111) with different alkyl chains and bearing in mind how to utilize head-group, tail-group or both as well as monolayer coverage, in the final part of this Thesis we study functionalized H:Si(111) with binary SAMs. Aiming at enhancing work function adjustment together with SAM stability and coverage we choose a range of terminations and linker-chains denoted as –X–(Alkyl) with X = CH3, O(H), S(H), NH(2) and investigate the stability and work function of various binary components grafted onto H:Si(111) surface. Using binary functionalization with -[NH(2)/O(H)/S(H)]-[Hexyl/Dodecyl] we show that work function can be tuned within the interval of 3.65-4.94 eV and furthermore, enhance the SAM’s stability. Although direct Si-C grafted SAMs are less favourable compared to their counterparts with O, N or S linkage, regardless of the ratio, binary functionalized alkyl monolayers with X-alkyl (X = NH, O) is always more stable than single type alkyl functionalization with the same coverage. Our results indicate that it is possible to go beyond the optimum coverage of pure alkyl functionalized SAMs (50%) by adding a linker with the correct choice of the linker. This is very important since dense packed monolayers have fewer defects and deliver higher efficiency. Our results indicate that binary anchoring can modify the charge injection and therefore bond stability while preserving the interface electronic structure

FABRICATION AND CHARACTERIZATION OF MOLECULAR SPINTRONICS DEVICES

Fabrication of molecular spin devices with ferromagnetic electrodes coupled with a high spin molecule is an important challenge. This doctoral study concentrated on realizing a novel molecular spin device by the bridging of magnetic molecules between two ferromagnetic metal layers of a ferromagnetic-insulator-ferromagnetic tunnel junction on its exposed pattern edges. At the exposed sides, distance between the two metal electrodes is equal to the insulator film thickness; insulator film thickness can be precisely controlled to match the length of a target molecule. Photolithography and thin-film deposition were utilized to produce a series of tunnel junctions based on molecular electrodes of multilayer edge molecular electrodes (MEME) for the first time. In order to make a microscopic tunnel junction with low leakage current to observe the effect of ~10,000 molecules bridged on the exposed edge of a MEME tunnel barrier, growth conditions were optimized; stability of a ~2nm alumina insulator depended on its ability to withstand process-induced mechanical stresses. The conduction mechanism was primarily 1) tunneling from metal electrode to oranometalic core by tunneling through alkane tether that acts as a tunnel barrier 2) rapid electron transfer within the oranometalic Ni-CN-Fe cube and 3) tunneling through alkane tether to the other electrode. Well defined spin-states in the oranometalic Ni-CN-Fe cube would determine electron spin-conduction and possibly provide a mechanism for coupling. MEME with Co/NiFe/AlOx/NiFe configurations exhibited dramatic changes in the transport and magnetic properties after the bridging of oranometalic molecular clusters with S=6 spin state. The molecular cluster produced a strong antiferromagnetic coupling between two ferromagnetic electrodes to the extent, with a lower bound of 20 erg/cm,2 that properties of individual magnetic layers changed significantly at RT. Magnetization, ferromagnetic resonance and magnetic force microscopy studies were performed. Transport studies of this configuration of MEME exhibited molecule-induced current suppression by ~6 orders by blocking both molecular channels and tunneling between metal leads in the planar 25μm2 tunnel junction area. A variety of control experiments were performed to validate the current suppression observation, especially critical due to observed corrosion in electrochemical functionalization step. The spin devices were found to be sensitive to light radiation, temperature and magnetic fields. Along with the study of molecular spin devices, several interesting ideas such as ~9% energy efficient ultrathin TaOx based photocell, simplified version of MEME fabrication, and chemical switching were realized. This doctoral study heralds a novel molecular spin device fabrication scheme; these molecular electrodes allow the reliable study of molecular components in molecular transport

HDL particles incorporate into lipid bilayers – a combined AFM and single molecule fluorescence microscopy study

abstract: The process, how lipids are removed from the circulation and transferred from high density lipoprotein (HDL) – a main carrier of cholesterol in the blood stream – to cells, is highly complex. HDL particles are captured from the blood stream by the scavenger receptor, class B, type I (SR-BI), the so-called HDL receptor. The details in subsequent lipid-transfer process, however, have not yet been completely understood. The transfer has been proposed to occur directly at the cell surface across an unstirred water layer, via a hydrophobic channel in the receptor, or after HDL endocytosis. The role of the target lipid membrane for the transfer process, however, has largely been overlooked. Here, we studied at the single molecule level how HDL particles interact with synthetic lipid membranes. Using (high-speed) atomic force microscopy and fluorescence correlation spectroscopy (FCS) we found out that, upon contact with the membrane, HDL becomes integrated into the lipid bilayer. Combined force and single molecule fluorescence microscopy allowed us to directly monitor the transfer process of fluorescently labelled amphiphilic lipid probe from HDL particles to the lipid bilayer upon contact.The final version of this article, as published in Scientific Reports, can be viewed online at: https://www.nature.com/articles/s41598-017-15949-

Dynamic Bioactive Stimuli-Responsive Polymeric Surfaces

This dissertation focuses on the design, synthesis, and development of antimicrobial and anticoagulant surfaces of polyethylene (PE), polypropylene (PP), and poly(tetrafluoroethylene) (PTFE) polymers. Aliphatic polymeric surfaces of PE and PP polymers functionalized using click chemistry reactions by the attachment of –COOH groups via microwave plasma reactions followed by functionalization with alkyne moieties. Azide containing ampicillin (AMP) was synthesized and subsequently clicked into the alkyne prepared PE and PP surfaces. Compared to non-functionalized PP and PE surfaces, the AMP clicked surfaces exhibited substantially enhanced antimicrobial activity against Staphylococcus aureus bacteria. To expand the biocompatibility of polymeric surface anticoagulant attributes, PE and PTFE surfaces were functionalized with pH-responsive poly(2-vinyl pyridine) (P2VP) and poly(acrylic acid) (PAA) polyelectrolyte tethers terminated with NH2 and COOH groups. The goal of these studies was to develop switchable stimuli-responsive polymeric surfaces that interact with biological environments and display simultaneous antimicrobial and anticoagulant properties. Antimicrobial AMP was covalently attached to –COOH terminal ends of protected PAA, while anticoagulant heparin (HEP) was attached to terminal –NH2 groups of P2VP. When pH \u3c 2.3, the P2VP segments are protonated and extend, but for pH \u3e 5.5, they collapse while the PAA segments extend. Such surfaces, when exposed to Staphylococcus aureus, inhibit bacterial growth due to the presence of AMP, as well as are effective anticoagulants due to the presence of covalently attached HEP. Comparison of these “dynamic” pH responsive surfaces with “static” surfaces terminated with AMP entities show significant enhancement of longevity and surface activity against microbial film formation. The last portion of this dissertation focuses on the covalent attachment of living T1 and Φ11 bacteriophages (phages) on PE and PTFE surface. This was accomplished by carbodiimide coupling between –COOH groups on PE and PTFE surfaces and –NH2 moieties present on T1 and Φ11 phages. These studies show that covalently attached T1 and Φ11 phages retain their antimicrobial activity manifested by the effective destruction of both Gram negative Escherichia coli (Φ11) phages and Gram positive Staphylococcus aureus bacteria (T1)

Reproducible flaws unveil electrostatic aspects of semiconductor electrochemistry

Predicting or manipulating charge-transfer at semiconductor interfaces, from molecular electronics to energy conversion, relies on knowledge generated from a kinetic analysis of the electrode process, as provided by cyclic voltammetry. Scientists and engineers encountering non-ideal shapes and positions in voltammograms are inclined to reject these as flaws. Here we show that non-idealities of redox probes confined at silicon electrodes, namely full width at half maximum <90.6 mV and anti-thermodynamic inverted peak positions, can be reproduced and are not flawed data. These are the manifestation of electrostatic interactions between dynamic molecular charges and the semiconductor's space-charge barrier. We highlight the interplay between dynamic charges and semiconductor by developing a model to decouple effects on barrier from changes to activities of surface-bound molecules. These findings have immediate general implications for a correct kinetic analysis of charge-transfer at semiconductors as well as aiding the study of electrostatics on chemical reactivity.This work was supported by grants from the Australian Research Council (ARC, DE160100732 (S.C.), DE160101101 (N.D.)). J.G.S. and A.M. greatly appreciate the financial support provided by the Fundación Séneca de la Región de Murcia (Projects 19887/GERM/15 and 18968/JLI/13) and by the Ministerio de Economía y Competitividad (projects CTQ-2015-65243-P and CTQ-2015-71955-REDT Network of excellence “Sensors and Biosensors”). L.Z., M.L.C., and G.G.W. acknowledge funding from the ARC Centre of Excellence Scheme (Project No. CE 140100012). J.J.G. and G.G.W. are under ARC Laureate Fellowships (FL150100060 and FL110100196)

Self assembly of hybrid nanostructures encompassing inorganic, organic and biological applications

The work presented in this thesis will highlight the modification of inorganic and biological materials with organic tethers; the subsequent characterisation of these compounds and the surface studies used to investigate them further. On moving from materials science to cell biology, a variety of techniques are used to demonstrate the chemical modifications and the role the surface has to play in not only visualising the effect of the modification but the surface itself mediating reactions. Described within is the further investigation of Mn Anderson based polyoxometalate clusters .This report documents the grafting of C-16, C-18 alkyl chains and pyrene to hydrophilic Mn Anderson clusters. Solid state studies using scanning electron microscopy and transmission electron microscopy demonstrates the effect of cation exchange from tetrabutyl ammonium (TBA) to dimethyldioctadecyl ammonium (DMDOA) resulting in new POM assemblies. For the C-18 and to some extent the C-16 grafted clusters, uniform, highly ordered assemblies are reported in contrast to the “sea urchin” like structures observed on cation and solvent exchange. The generation of surfactant encapsulated clusters in conjunction with surface grafted clusters has been achieved. For the first time these organically tethered POM‟s have been patterned successfully onto self assembled monolayers (SAMs) using microcontact printing. In addition to this, studies involving human fibroblast cells (hTERT-BJI) are reported. Cells have been found to attach and spread on monolayers terminated in pyrene terminated POM. It has been observed that POMs play a crucial role in the adhesion of cells to surfaces. Solid state techniques scanning electron microscopy (SEM) and atomic force microscopy (AFM) are used in the investigation of not only inorganic compounds but the post translational modification of proteins. Highlighting the importance of these techniques in the further understanding or reactions and the effects the reactions have on the molecules Further the investigation of polyoxometalates herein the development of molybdenum (VI) oxide polyoxometalate cluster, β-[Mo18O54(SO3)2]4-, that canundergo a reversible conversion between two electronic states, upon thermal activation is described. Experiments have uncovered the fact that the two embedded redox agents can be thermally activated and ejected from the sulfite anions and delocalised over the metal oxide cluster. The role of the surface in such a reaction is described detailing its importance in the reaction from a fully oxidised state to a two electron reduced state. This work demonstrates the use of a POM as a potential starting point to create a single molecule device at the nanoscale

Membrane functionalisation using polyrotaxanes with amphiphilic cyclodextrins

This work is aimed at the design and characterisation of a new family of tethered ligands, called sliding tethered ligands (STLs). They are based on topological complexes between polymers and amphiphilic cyclodextrins (CDs), which can be inserted into phospholipid membranes. At first we investigate the membrane insertion properties of amphiphilic cholesteryl CD derivatives, which are suitable membrane anchors for the STLs. With the help of neutron reflectivity it can be demonstrated that the CD residues show a remarkable conformational adaptability and that the CD cavities remain accessible upon insertion into lipid model membranes. We have developed a synthetic pathway to assemble the STLs from polyrotaxanes with a controlled low number of mono-modified azido-α-CDs, threaded on a polyethylene glycol (PEG) chain. Using newly developed in-situ capping methods the polyrotaxanes are endcapped with adamantane ligands, which can be recognized by a β-CD receptor. Furthermore a cholesteryl anchor is attached to the threaded CD in order to enable the STL to insert into membranes. We demonstrate that STLs readily insert into phospholipid (DPPC) model membranes using IR Absorption Reflection Spectroscopy and investigating the film morphology by Brewster Angle Microscopy and Atomic Force Microscopy. Applying neutron reflectivity it is shown, that for sufficiently high polymer densities the STLs form polymer brushes, which follow the scaling laws predicted by the mean field theory. Using the surface force apparatus it is evidenced that model membranes modified with STLs and cholesteryl β-CD receptors give rise to typical tethered ligand - receptor interaction profiles

Profiling to Probing: Atomic force microscopy to characterize nano-engineered implants

Surface modification of implants in the nanoscale or implant nano-engineering has been recognized as a strategy for augmenting implant bioactivity and achieving long-term implant success. Characterizing and optimizing implant characteristics is crucial to achieving desirable effects post-implantation. Modified implant enables tailored, guided and accelerated tissue integration; however, our understanding is limited to multicellular (bulk) interactions. Finding the nanoscale forces experienced by a single cell on nano-engineered implants will aid in predicting implants’ bioactivity and engineering the next generation of bioactive implants. Atomic force microscope (AFM) is a unique tool that enables surface characterization and understanding of the interactions between implant surface and biological tissues. The characterization of surface topography using AFM to gauge nano-engineered implants' characteristics (topographical, mechanical, chemical, electrical and magnetic) and bioactivity (adhesion of cells) is presented. A special focus of the review is to discuss the use of single-cell force spectroscopy (SCFS) employing AFM to investigate the minute forces involved with the adhesion of a single cell (resident tissue cell or bacterium) to the surface of nano-engineered implants. Finally, the research gaps and future perspectives relating to AFM-characterized current and emerging nano-engineered implants are discussed towards achieving desirable bioactivity performances. This review highlights the use of advanced AFM-based characterization of nano-engineered implant surfaces via profiling (investigating implant topography) or probing (using a single cell as a probe to study precise adhesive forces with the implant surface)

Molecular synthesis and modification of surfaces for electronic device applications

This dissertation focuses on the synthesis of molecules and their grafting onto surfaces in order to modify the physical properties and behavior of various substrates and devices. For gold, first presented is the self-assembly of synthesized dipolar molecules onto OFET electrodes, demonstrating a powerful technique to tune the device's work function for electron injection. Discussed next is a multimodal study using SERS analysis of synthesized OPV and OPE molecules self-assembled within single-molecule electrical junctions, providing a rare glimpse of how tunneling electrons affect molecular structure during conduction. Lastly, STM studies are presented for self-assembled supramolecular wires composed of synthesized azobenzene molecules, demonstrating exciting cooperative UV- and bias-driven switching behavior. For silicon electronic studies where current does not pass through molecules, the synthesis and covalent grafting of a unique POM-species is first presented. Next, a combination XPS, UPS, IPS, and Kelvin Probe study is presented for a series of grafted aryl diazonium salts, offering a model for observed changes in the substrate's work function based on grafting-induced changes its surface band bending and electron affinity. Presented last is a powerful method utilizing diazonium salt grafting to impurity dope an FET device from the surface, demonstrating effects on electronic transport that penetrate even a &sim;5 microm-thick device layer. For "through-molecule" electronic studies on silicon, presented is an investigation of C60 films solvent-grafted into nanogap devices, yielding bistable switching behavior possessing ON:OFF ratios >103 . Also presented is the attachment of Au nanoparticles to device surfaces using synthesized molecular tethers. Finally, the grafting of a synthesized alkoxyarylaminyl radical is discussed. For the protection of silicon devices from environmental conditions, the combined use of diazonium salt grafting and alkene thermal hydrosilylation is presented, demonstrating enhanced resistance of the surface to oxidation relative to diazonium grafting alone. Also discussed is a method to increase surface hydrophilicity using alkene hydrosilylation grafting in the presence of dilute HF, effectively protecting MEMS devices from capillary collapse during exposure to liquid water and humidity. For carbon, the functionalization of graphene devices using synthesized aryl diazonium salts is presented, yielding a model for the kinetics of diazonium salt graphene functionalization