Atomic-scale characterization of diamond surfaces and fullerene self-assembly

In this thesis, elemental research towards the implantation of a diamond-based molecular quantum computer is presented. The approach followed requires linear alignment of endohedral fullerenes on the diamond C(100) surface in the vicinity of subsurface NV-centers. From this, four fundamental experimental challenges arise: 1) The well-controlled deposition of endohedral fullerenes on a diamond surface. 2) The creation of NV-centers in diamond close to the surface. 3) Preparation and characterization of atomically-flat diamondsurfaces. 4) Assembly of linear chains of endohedral fullerenes. First steps to overcome all these challenges were taken in the framework of this thesis. Therefore, a so-called “pulse injection” technique was implemented and tested in a UHV chamber that was custom-designed for this and further tasks. Pulse injection in principle allows for the deposition of molecules from solution onto a substrate and can therefore be used to deposit molecular species that are not stable to sublimation under UHV conditions, such as the endohedral fullerenes needed for a quantum register. Regarding the targeted creation of NV-centers, FIB experiments were carried out in cooperation with the group of Prof. Schmidt-Kaler (AG Quantum, Physics Department, Johannes Gutenberg-Universität Mainz). As an entry into this challenging task, argon cations were implanted into (111) surface-oriented CaF2 crystals. The resulting implantation spots on the surface were imaged and characterized using AFM. In this context, general relations between the impact of the ions on the surface and their valency or kinetic energy, respectively, could be established. The main part of this thesis, however, is constituted by NCAFM studies on both, bare and hydrogen-terminated diamond C(100) surfaces. In cooperation with the group of Prof. Dujardin (Molecular Nanoscience Group, ISMO, Université de Paris XI), clean and atomically-flat diamond surfaces were prepared by exposure of the substrate to a microwave hydrogen plasma. Subsequently, both surface modifications were imaged in high resolution with NC-AFM. In the process, both hydrogen atoms in the unit cell of the hydrogenated surface were resolved individually, which was not achieved in previous STM studies of this surface. The NC-AFM images also reveal, for the first time, atomic-resolution contrast on the clean, insulating diamond surface and provide real-space experimental evidence for a (2×1) surface reconstruction. With regard to the quantum computing concept, high-resolution NC-AFM imaging was also used to study the adsorption and self-assembly potential of two different kinds of fullerenes (C60 and C60F48) on aforementioned diamond surfaces. In case of the hydrogenated surface, particular attention was paid to the influence of charge transfer doping on the fullerene-substrate interaction and the morphology emerging from self-assembly. Finally, self-assembled C60 islands on the hydrogen-terminated diamond surface were subject to active manipulation by an NC-AFM tip. Two different kinds of tip-induced island growth modes have been induced and were presented. In conclusion, the results obtained provide fundamental informations mandatory for the realization of a molecular quantum computer. In the process it was shown that NC-AFM is, under proper circumstances, a very capable tool for imaging diamond surfaces with highest resolution, surpassing even what has been achieved with STM up to now. Particular attention was paid to the influence of transfer doping on the morphology of fullerenes on the hydrogenated diamond surface, revealing new possibilities for tailoring the self-assembly of molecules that have a high electron affinity.

Photoactive nanodevices for potential biological applications

Biological systems are complex and highly organized architectures governed by noncovalent interactions, which are responsible for molecular recognition, self-assembly, self-organization, adaptation and evolution processes. These systems provided the inspiration for the development of supramolecular chemistry, that aimed at the design of artificial multicomponent molecular assemblies, namely supramolecular systems, properly designed to perform different operations: each constituting unit performs a single act, whereas the entire supramolecular system is able to execute a more complex function, resulting from the cooperation of the constituting components. Supramolecular chemistry deals with the development of molecular systems able to mimic naturally occurring events, for example complexation and self-assembly through the establishment of noncovalent interactions. Moreover, the application of external stimuli, such as light, allows to perform these operations in a time- and space-controlled manner. These systems can interact with biological systems and, thus, can be applied for bioimaging, therapeutic and drug delivery purposes. In this work the study of biocompatible supramolecular species able to interact with light is presented. The first part deals with the photophysical, photochemical and electrochemical characterization of water-soluble blue emitting triazoloquinolinium and triazolopyridinium salts. Moreover, their interaction with DNA has been explored, in the perspective of developing water-soluble systems for bioimaging applications. In the second part, the effect exerted by the presence of azobenzene-bearing supramolecular species in liposomes, inserted both in the phospholipid bilayer and in the in the aqueous core of vesicles has been studied, in order to develop systems able to deliver small molecules and ions in a photocontrolled manner. Moreover, the versatility of azobenzene and its broad range of applications have been highlighted, since conjugated oligoazobenzene derivatives proved not to be adequate to be inserted in the phospholipid bilayer of liposomes, but their electrochemical properties made them interesting candidates as electron acceptor materials for photovoltaic applications.

Self-sufficient control of urate homeostasis in mice by a synthetic circuit

Synthetic biology has shown that the metabolic behavior of mammalian cells can be altered by genetic devices such as epigenetic and hysteretic switches, timers and oscillators, biocomputers, hormone systems and heterologous metabolic shunts. To explore the potential of such devices for therapeutic strategies, we designed a synthetic mammalian circuit to maintain uric acid homeostasis in the bloodstream, disturbance of which is associated with tumor lysis syndrome and gout. This synthetic device consists of a modified Deinococcus radiodurans-derived protein that senses uric acids levels and triggers dose-dependent derepression of a secretion-engineered Aspergillus flavus urate oxidase that eliminates uric acid. In urate oxidase-deficient mice, which develop acute hyperuricemia, the synthetic circuit decreased blood urate concentration to stable sub-pathologic levels in a dose-dependent manner and reduced uric acid crystal deposits in the kidney. Synthetic gene-network devices providing self-sufficient control of pathologic metabolites represent molecular prostheses, which may foster advances in future gene- and cell-based therapies.

Self-assembly of focal point oligo-catechol ethylene glycol dendrons on titanium oxide surfaces: adsorption kinetics, surface characterization, and nonfouling properties

This work covers the synthesis of second-generation, ethylene glycol dendrons covalently linked to a surface anchor that contains two, three, or four catechol groups, the molecular assembly in aqueous buffer on titanium oxide surfaces, and the evaluation of the resistance of the monomolecular adlayers against nonspecific protein adsorption in contact with full blood serum. The results were compared to those of a linear poly(ethylene glycol) (PEG) analogue with the same molecular weight. The adsorption kinetics as well as resulting surface coverages were monitored by ex situ spectroscopic ellipsometry (VASE), in situ optical waveguide lightmode spectroscopy (OWLS), and quartz crystal microbalance with dissipation (QCM-D) investigations. The expected compositions of the macromolecular films were verified by X-ray photoelectron spectroscopy (XPS). The results of the adsorption study, performed in a high ionic strength ("cloud-point") buffer at room temperature, demonstrate that the adsorption kinetics increase with increasing number of catechol binding moieties and exceed the values found for the linear PEG analogue. This is attributed to the comparatively smaller and more confined molecular volume of the dendritic macromolecules in solution, the improved presentation of the catechol anchor, and/or their much lower cloud-point in the chosen buffer (close to room temperature). Interestingly, in terms of mechanistic aspects of "nonfouling" surface properties, the dendron films were found to be much stiffer and considerably less hydrated in comparison to the linear PEG brush surface, closer in their physicochemical properties to oligo(ethylene glycol) alkanethiol self-assembled monolayers than to conventional brush surfaces. Despite these differences, both types of polymer architectures at saturation coverage proved to be highly resistant toward protein adsorption. Although associated with higher synthesis costs, dendritic macromolecules are considered to be an attractive alternative to linear polymers for surface (bio)functionalization in view of their spontaneous formation of ultrathin, confluent, and nonfouling monolayers at room temperature and their outstanding ability to present functional ligands (coupled to the termini of the dendritic structure) at high surface densities.

Molecular Charge-Transfer Cross Sections and Their Correlation with Reactant Ion Structures

Charge-transfer cross sections have been obtained by using time-of-flight techniques, and results correlated with reaction energetics and theoretical structures computed by self-consistent field-molecular orbital methods. Ion recombination energies, structures, heats of formation, reaction energy defects, and 3.0-keV charge-transfer cross sections are presented for reactions of molecular and fragment ions produced by electron bombardment ionization of CH30CH, and CH$l molecules. Relationships between experimental cross sections and reaction energetics involving different ion structures are discussed.

Orientation dependent molecular friction on organic layer compound crystals

High resolution friction force maps of the benzylammonium terminated crystalline surface of a layer compound are presented. The lateral force map acquired with an atomic force microscope, reveals a significant contrast between different molecular orientations yielding molecular rows which differ from their neighboring ones. The single crystals are formed by stacks of copper oxalate sheets sandwiched between stereoregular organic cations, resulting in highly organized surface structures. Single molecular defects are observed at small loads. The experimental results are compared with numerical calculations which indicate a transition from an unperturbed state at small loads to a distorted state at higher loads. (C) 2011 American Institute of Physics.

Molecular cloning and characterization of equine thymic stromal lymphopoietin

Thymic stromal lymphopoietin (TSLP) is a novel cytokine that plays a central role in T helper 2 (Th2) cell differentiation and allergic inflammation. It is predominantly expressed by epithelial cells, and its expression is increased in patients with atopic dermatitis and asthma. Mice overexpressing TSLP in the skin develop allergic dermatitis and mice overexpressing TSLP in lungs develop asthma-like disease. However, it is not known whether TSLP plays an important role in equine allergies. Therefore, we cloned and sequenced the complete translated region of equine TSLP gene and measured its expression in various tissues. The equine TSLP gene is organized in 4 exons and encodes a protein of 143 amino acids, which has 62% amino acid identity with human TSLP.

Phosphatidylethanolamine in Trypanosoma brucei is organized in two separate pools and is synthesized exclusively by the Kennedy pathway

Phosphatidylethanolamine is a major phospholipid class of all eukaryotic cells. It can be synthesized via the CDP-ethanolamine branch of the Kennedy pathway, by decarboxylation of phosphatidylserine, or by base exchange with phosphatidylserine. The contributions of these pathways to total phosphatidylethanolamine synthesis have remained unclear. Although Trypanosoma brucei, the causative agent of human and animal trypanosomiasis, has served as a model organism to elucidate the entire reaction sequence for glycosylphosphatidylinositol biosynthesis, the pathways for the synthesis of the major phospholipid classes have received little attention. We now show that disruption of the CDP-ethanolamine branch of the Kennedy pathway using RNA interference results in dramatic changes in phosphatidylethanolamine, phosphatidylserine, and phosphatidylcholine. By targeting individual enzymes of the pathway, we demonstrate that de novo phosphatidylethanolamine synthesis in T. brucei procyclic forms is strictly dependent on the CDP-ethanolamine route. Interestingly, the last step in the Kennedy pathway can be mediated by two separate activities leading to two distinct pools of phosphatidylethanolamine, consisting of predominantly alk-1-enyl-acyl- or diacyl-type molecular species. In addition, we show that phosphatidylserine in T. brucei procyclic forms is synthesized exclusively by base exchange with phosphatidylethanolamine.

Growth, modification and integration of carbon nanotubes into molecular electronics

Molecules are the smallest possible elements for electronic devices, with active elements for such devices typically a few Angstroms in footprint area. Owing to the possibility of producing ultrahigh density devices, tremendous effort has been invested in producing electronic junctions by using various types of molecules. The major issues for molecular electronics include (1) developing an effective scheme to connect molecules with the present micro- and nano-technology, (2) increasing the lifetime and stabilities of the devices, and (3) increasing their performance in comparison to the state-of-the-art devices. In this work, we attempt to use carbon nanotubes (CNTs) as the interconnecting nanoelectrodes between molecules and microelectrodes. The ultimate goal is to use two individual CNTs to sandwich molecules in a cross-bar configuration while having these CNTs connected with microelectrodes such that the junction displays the electronic character of the molecule chosen. We have successfully developed an effective scheme to connect molecules with CNTs, which is scalable to arrays of molecular electronic devices. To realize this far reaching goal, the following technical topics have been investigated. 1. Synthesis of multi-walled carbon nanotubes (MWCNTs) by thermal chemical vapor deposition (T-CVD) and plasma-enhanced chemical vapor deposition (PECVD) techniques (Chapter 3). We have evaluated the potential use of tubular and bamboo-like MWCNTs grown by T-CVD and PE-CVD in terms of their structural properties. 2. Horizontal dispersion of MWCNTs with and without surfactants, and the integration of MWCNTs to microelectrodes using deposition by dielectrophoresis (DEP) (Chapter 4). We have systematically studied the use of surfactant molecules to disperse and horizontally align MWCNTs on substrates. In addition, DEP is shown to produce impurityfree placement of MWCNTs, forming connections between microelectrodes. We demonstrate the deposition density is tunable by both AC field strength and AC field frequency. 3. Etching of MWCNTs for the impurity-free nanoelectrodes (Chapter 5). We show that the residual Ni catalyst on MWCNTs can be removed by acid etching; the tip removal and collapsing of tubes into pyramids enhances the stability of field emission from the tube arrays. The acid-etching process can be used to functionalize the MWCNTs, which was used to make our initial CNT-nanoelectrode glucose sensors. Finally, lessons learned trying to perform spectroscopic analysis of the functionalized MWCNTs were vital for designing our final devices. 4. Molecular junction design and electrochemical synthesis of biphenyl molecules on carbon microelectrodes for all-carbon molecular devices (Chapter 6). Utilizing the experience gained on the work done so far, our final device design is described. We demonstrate the capability of preparing patterned glassy carbon films to serve as the bottom electrode in the new geometry. However, the molecular switching behavior of biphenyl was not observed by scanning tunneling microscopy (STM), mercury drop or fabricated glassy carbon/biphenyl/MWCNT junctions. Either the density of these molecules is not optimum for effective integration of devices using MWCNTs as the nanoelectrodes, or an electroactive contaminant was reduced instead of the ionic biphenyl species. 5. Self-assembly of octadecanethiol (ODT) molecules on gold microelectrodes for functional molecular devices (Chapter 7). We have realized an effective scheme to produce Au/ODT/MWCNT junctions by spanning MWCNTs across ODT-functionalized microelectrodes. A percentage of the resulting junctions retain the expected character of an ODT monolayer. While the process is not yet optimized, our successful junctions show that molecular electronic devices can be fabricated using simple processes such as photolithography, self-assembled monolayers and dielectrophoresis.

Quantum transport in a single molecular junction

The craze for faster and smaller electronic devices has never gone down and this has always kept researchers on their toes. Following Moore’s law, which states that the number of transistors in a single chip will double in every 18 months, today “30 million transistors can fit into the head of a 1.5 mm diameter pin”. But this miniaturization cannot continue indefinitely due to the ‘quantum leakage’ limit in the thickness of the insulating layer between the gate electrode and the current carrying channel. To bypass this limitation, scientists came up with the idea of using vastly available organic molecules as components in an electronic device. One of the primary challenges in this field was the ability to perform conductance measurements across single molecular junctions. Once that was achieved the focus shifted to a deeper understanding of the underlying physics behind the electron transport across these molecular scale devices. Our initial theoretical approach is based on the conventional Non-Equilibrium Green Function(NEGF) formulation, but the self-energy of the leads is modified to include a weighting factor that ensures negligible current in the absence of a molecular pathway as observed in a Mechanically Controlled Break Junction (MCBJ) experiment. The formulation is then made parameter free by a more careful estimation of the self-energy of the leads. The calculated conductance turns out to be atleast an order more than the experimental values which is probably due to a strong chemical bond at the metal-molecule junction unlike in the experiments. The focus is then shifted to a comparative study of charge transport in molecular wires of different lengths within the same formalism. The molecular wires, composed of a series of organic molecules, are sanwiched between two gold electrodes to make a two terminal device. The length of the wire is increased by sequentially increasing the number of molecules in the wire from 1 to 3. In the low bias regime all the molecular devices are found to exhibit Ohmic behavior. However, the magnitude of conductance decreases exponentially with increase in length of the wire. In the next study, the relative contribution of the ‘in-phase’ and the ‘out-of-phase’ components of the total electronic current under the influence of an external bias is estimated for the wires of three different lengths. In the low bias regime, the ‘out-of-phase’ contribution to the total current is minimal and the ‘in-phase’ elastic tunneling of the electrons is responsible for the net electronic current. This is true irrespective of the length of the molecular spacer. In this regime, the current-voltage characteristics follow Ohm’s law and the conductance of the wires is found to decrease exponentially with increase in length which is in agreement with experimental results. However, after a certain ‘off-set’ voltage, the current increases non-linearly with bias and the ‘out-of-phase’ tunneling of electrons reduces the net current substantially. Subsequently, the interaction of conduction electrons with the vibrational modes as a function of external bias in the three different oligomers is studied since they are one of the main sources of phase-breaking scattering. The number of vibrational modes that couple strongly with the frontier molecular orbitals are found to increase with length of the spacer and the external field. This is consistent with the existence of lowest ‘off-set’ voltage for the longest wire under study.

Electron transport in molecular systems

The remarkable advances in nanoscience and nanotechnology over the last two decades allow one to manipulate individuals atoms, molecules and nanostructures, make it possible to build devices with only a few nanometers, and enhance the nano-bio fusion in tackling biological and medical problems. It complies with the ever-increasing need for device miniaturization, from magnetic storage devices, electronic building blocks for computers, to chemical and biological sensors. Despite the continuing efforts based on conventional methods, they are likely to reach the fundamental limit of miniaturization in the next decade, when feature lengths shrink below 100 nm. On the one hand, quantum mechanical efforts of the underlying material structure dominate device characteristics. On the other hand, one faces the technical difficulty in fabricating uniform devices. This has posed a great challenge for both the scientific and the technical communities. The proposal of using a single or a few organic molecules in electronic devices has not only opened an alternative way of miniaturization in electronics, but also brought up brand-new concepts and physical working mechanisms in electronic devices. This thesis work stands as one of the efforts in understanding and building of electronic functional units at the molecular and atomic levels. We have explored the possibility of having molecules working in a wide spectrum of electronic devices, ranging from molecular wires, spin valves/switches, diodes, transistors, and sensors. More specifically, we have observed significant magnetoresistive effect in a spin-valve structure where the non-magnetic spacer sandwiched between two magnetic conducting materials is replaced by a self-assembled monolayer of organic molecules or a single molecule (like a carbon fullerene). The diode behavior in donor(D)-bridge(B)-acceptor(A) type of single molecules is then discussed and a unimolecular transistor is designed. Lastly, we have proposed and primarily tested the idea of using functionalized electrodes for rapid nanopore DNA sequencing. In these studies, the fundamental roles of molecules and molecule-electrode interfaces on quantum electron transport have been investigated based on first-principles calculations of the electronic structure. Both the intrinsic properties of molecules themselves and the detailed interfacial features are found to play critical roles in electron transport at the molecular scale. The flexibility and tailorability of the properties of molecules have opened great opportunity in a purpose-driven design of electronic devices from the bottom up. The results that we gained from this work have helped in understanding the underlying physics, developing the fundamental mechanism and providing guidance for future experimental efforts.

Stem cell-related "self-renewal" signature and high epidermal growth factor receptor expression associated with resistance to concomitant chemoradiotherapy in glioblastoma

PURPOSE: Glioblastomas are notorious for resistance to therapy, which has been attributed to DNA-repair proficiency, a multitude of deregulated molecular pathways, and, more recently, to the particular biologic behavior of tumor stem-like cells. Here, we aimed to identify molecular profiles specific for treatment resistance to the current standard of care of concomitant chemoradiotherapy with the alkylating agent temozolomide. PATIENTS AND METHODS: Gene expression profiles of 80 glioblastomas were interrogated for associations with resistance to therapy. Patients were treated within clinical trials testing the addition of concomitant and adjuvant temozolomide to radiotherapy. RESULTS: An expression signature dominated by HOX genes, which comprises Prominin-1 (CD133), emerged as a predictor for poor survival in patients treated with concomitant chemoradiotherapy (n = 42; hazard ratio = 2.69; 95% CI, 1.38 to 5.26; P = .004). This association could be validated in an independent data set. Provocatively, the HOX cluster was reminiscent of a "self-renewal" signature (P = .008; Gene Set Enrichment Analysis) recently characterized in a mouse leukemia model. The HOX signature and EGFR expression were independent prognostic factors in multivariate analysis, adjusted for the O-6-methylguanine-DNA methyltransferase (MGMT) methylation status, a known predictive factor for benefit from temozolomide, and age. Better outcome was associated with gene clusters characterizing features of tumor-host interaction including tumor vascularization and cell adhesion, and innate immune response. CONCLUSION: This study provides first clinical evidence for the implication of a "glioma stem cell" or "self-renewal" phenotype in treatment resistance of glioblastoma. Biologic mechanisms identified here to be relevant for resistance will guide future targeted therapies and respective marker development for individualized treatment and patient selection.

Self-assembling cannabinomimetics: supramolecular structures of N-alkyl amides

Certain fatty acid N-alkyl amides from the medicinal plant Echinacea activate cannabinoid type-2 (CB2) receptors. In this study we show that the CB2-binding Echinacea constituents dodeca-2E,4E-dienoic acid isobutylamide (1) and dodeca-2E,4E,8Z,10Z-tetraenoic acid isobutylamide (2) form micelles in aqueous medium. In contrast, micelle formation is not observed for undeca-2E-ene-8,10-diynoic acid isobutylamide (3), which does not bind to CB2, or structurally related endogenous cannabinoids, such as arachidonoyl ethanolamine (anandamide). The critical micelle concentration (CMC) range of 1 and 2 was determined by fluorescence spectroscopy as 200-300 and 7400-10000 nM, respectively. The size of premicelle aggregates, micelles, and supermicelles was studied by dynamic light scattering. Microscopy images show that compound 1, but not 2, forms globular and rod-like supermicelles with radii of approximately 75 nm. The self-assembling N-alkyl amides partition between themselves and the CB2 receptor, and aggregation of N-alkyl amides thus determines their in vitro pharmacological effects. Molecular mechanics by Monte Carlo simulations of the aggregation process support the experimental data, suggesting that both 1 and 2 can readily aggregate into premicelles, but only 1 spontaneously assembles into larger aggregates. These findings have important implications for biological studies with this class of compounds.

Supramolecular Organization of Heptapyrenotide Oligomers—An in Depth Investigation by Molecular Dynamics Simulations

We present a molecular modeling study based on ab initio and classical molecular dynamics calculations, for the investigation of the tridimensional structure and supramolecular assembly formation of heptapyrenotide oligomers in water solution. Our calculations show that free oligomers self-assemble in helical structures characterized by an inner core formed by π- stacked pyrene units, and external grooves formed by the linker moieties. The coiling of the linkers has high ordering, dominated by hydrogen-bond interactions among the phosphate and amide groups. Our models support a mechanism of longitudinal supramolecular oligomerization based on interstrand pyrene intercalation. Only a minimal number of pyrene units intercalate at one end, favoring formation of very extended longitudinal chains, as also detected by AFM experiment. Our results provide a structural explanation of the mechanism of chirality amplification in 1:1 mixtures of standard heptapyrenotides and modified oligomers with covalently linked deoxycytidine, based on selective molecular recognition and binding of the nucleotide to the groove of the left-wound helix.

Self-Absorption and Luminescence Quantum Yields of Dye-Zeolite L Composites

Electronic absorption and fluorescence spectra based on transmission measurements of thin layers obtained from new perylene−zeolite L composites and new dye1,dye2−zeolite L sandwich composites, the latter acting as antenna systems, have been investigated and analyzed. The influence of extra- and intraparticle self-absorption on the spectral shape and fluorescence quantum yield is discussed in detail. Due to its intraparticle origin, self-absorption and re-emission can often not be avoided in organized systems such as dye−zeolite L composites where a high density of chromophores is a prerequisite for obtaining the desired photophysical properties. We show, however, that it can be avoided or at least minimized by preparing dye1,dye2−zeolite L sandwich composites where donors are present in a much larger amount than the acceptors because they act as antenna systems.