Lipophilic nucleosides: studies toward self-assembled functional materials

Molecular self-assembly takes advantage of supramolecular non-covalent interactions (ionic, hydrophobic, van der Waals, hydrogen and coordination bonds) for the construction of organized and tunable systems. In this field, lipophilic guanosines can represent powerful building blocks thanks to their aggregation proprieties in organic solvents, which can be controlled by addition or removal of cations. For example, potassium ion can template the formation of piled G-quartets structures, while in its absence ribbon-like G aggregates are generated in solution. In this thesis we explored the possibility of using guanosines as scaffolds to direct the construction of ordered and self-assembled architectures, one of the main goals of bottom-up approach in nanotechnology. In Chapter III we will describe Langmuir-Blodgett films obtained from guanosines and other lipophilic nucleosides, revealing the “special” behavior of guanine in comparison with the other nucleobases. In Chapter IV we will report the synthesis of several thiophene-functionalized guanosines and the studies towards their possible use in organic electronics: the pre-programmed organization of terthiophene residues in ribbon aggregates could allow charge conduction through π-π stacked oligothiophene functionalities. The construction and the behavior of some simple electronic nanodevices based on these organized thiopehene-guanosine hybrids has been explored.

Stabilizing molecular self-assemblies via on-surface reactions

Für die Realisierung zukünftiger Technologien, wie z.B. molekulare Elektronik, werden Strategien benötigt, um funktionale Strukturen direkt auf Oberflächen zu erzeugen. Für die Bewältigung dieser Aufgabe ist die molekulare Selbstanordnung ein äußerst vielversprechender Bottom-up-Ansatz. Hierbei ist eine der größten Herausforderungen das Zusammenspiel aus intramolekularer Wechselwirkung und der Wechselwirkung zwischen Substrat und Molekülen in ein Gleichgewicht zu bringen. Da jedoch die wirkenden Kräfte der molekularen Selbstanordnung ausschließlich reversibler Natur sind, ist eine langfristige Stabilität fragwürdig. Somit ist die kovalente Verknüpfung der gebildeten Strukturen durch Reaktionen direkt auf der Oberfläche unerlässlich, um die Stabilität der Strukturen weiter zu erhöhen. Hierzu stellt die vorliegende Arbeit eine ausführliche Studie zu molekularer Selbstanordnung und der zielgerichteten Modifikation ebensolcher Strukturen dar. Durch den Einsatz von hochauflösender Rasterkraftmikroskopie im Ultrahochvakuum, welche es erlaubt einzelne Moleküle auf Nichtleitern abzubilden, wurde der maßgebliche Einfluss von Ankerfunktionalitäten auf den Prozess der molekularen Selbstanordnung gezeigt. Des Weiteren konnte die Stabilität der selbst angeordneten Strukturen durch neue Oberflächenreaktionskonzepte entschieden verbessert werden. Der Einfluss von Ankerfunktionen, die elektrostatische Wechselwirkung zwischen Molekül und Substrat vermitteln, auf den Strukturbildungsprozess der molekularen Selbstanordnung wird eingehend durch den Vergleich eines aromatischen Moleküls und seines vierfach chlorierten Derivates gezeigt. Für diese beiden Moleküle wurde ein deutlich unterschiedliches Verhalten der Selbstanordnung beobachtet. Es wird gezeigt, dass die Fähigkeit zur Bildung selbst angeordneter, stabiler Inseln entscheidend durch die Substituenten und die Abmessungen des Moleküls beeinflusst wird. Auch wird in dieser Arbeit die erste photochemische Reaktion organischer Moleküle auf einem Isolator gezeigt. Qualitative und quantitative Ergebnisse liefern ein detailliertes Bild darüber, wie die Abmessungen des Substratgitters die Richtung der Reaktion gezielt beeinflussen. Des Weiteren wird ein allgemeines Konzept zur selektiven Stabilisierung selbstangeordneter Molekülstrukturen durch den kontrollierten Transfer von Elektronen präsentiert. Durch die gezielte Steuerung der Menge an Dotierungsatomen wird die Desorptionstemperatur der molekularen Inseln signifikant erhöht und das Desorptionsverhalten der Inseln entschieden verändert. Diese Arbeit präsentiert somit erfolgreich durchgeführte Strategien um den Prozess der molekularen Selbstanordnung zu steuern, sowie entscheidende Mechanismen um die Stabilisierung und Modifizierung von selbst angeordneten Strukturen zu gewährleisten.

Two-dimensional assembly and local redox-activity of molecular hybrid structures in an electrochemical environment

The self-assembly and redox-properties of two viologen derivatives, N-hexyl-N-(6-thiohexyl)-4,4-bipyridinium bromide (HS-6V6-H) and N,N-bis(6-thiohexyl)-4,4-bipyridinium bromide (HS-6V6-SH), immobilized on Au(111)-(1x1) macro-electrodes were investigated by cyclic voltammetry, surface enhanced infrared spectroscopy (SEIRAS) and in situ scanning tunneling microscopy (STM). Depending on the assembly conditions one could distinguish three different types of adlayers for both viologens: a low coverage disordered and an ordered striped phase of flat oriented molecules as well as a high coverage monolayer composed of tilted viologen moieties. Both molecules, HS-6V6-H and HS-6V6-SH, were successfully immobilized on Au(poly) nano-electrodes, which gave a well-defined redox-response in the lower pA–current range. An in situ STM configuration was employed to explore electron transport properties of single molecule junctions Au(T)|HS-6V6-SH(HS-6V6-H)|Au(S). The observed sigmoidal potential dependence, measured at variable substrate potential ES and at constant bias voltage (ET–ES), was attributed to electronic structure changes of the viologen moiety during the one-electron reduction/re-oxidation process V2+ V+. Tunneling experiments in asymmetric, STM-based junctions Au(T)-S-6V6-H|Au(S) revealed current (iT)–voltage (ET) curves with a maximum located at the equilibrium potential of the redox-process V2+ V+. The experimental iT–ET characteristics of the HS-6V6-H–modified tunneling junction were tentatively attributed to a sequential two-step electron transfer mechanism.

Affinity retardation chromatography: characterization of the method and its application. The description of low affinity laminin self-interactions.

Affinity retardation chromatography (ARC), a method for the examination of low-affinity interactions, is mathematically described in order to characterize the method itself and to estimate binding coefficients of self-assembly domains of basement membrane protein laminin. Affinity retardation was determined by comparing the elutions on a "binding" and on a "nonreacting" column. It depends on the binding coefficient, the concentrations of both ligands, and the nonbinding elution position. Half maximal binding of the NH2-terminal domain of laminin B1-short arm to the A- and/or B2-short arms was estimated to occur at 10-17 microM for noncooperative and at < or = 3 microM for cooperative binding. A model of the laminin polymerization, postulating two levels of cooperative binding behavior, is described.

From supramolecular sheets to fibers and back: establishing the critical parameters that govern the morphology of pyrene-based self-assembled materials

The precise arraying of functional entities in morphologically well-defined shapes remains one of the key challenges in the processing of organic molecules1. Among various π-conjugated species, pyrene exhibits a set of unique properties, which make it an attractive compound for the utilization in materials science2. In this contribution we report on properties of self-assembled structures prepared from amphiphilic pyrene trimers (Py3) consisting of phosphodiester-linked pyrenes. Depending on the geometry of a pyrene core substitution (1.6-, 1.8-, or 2.7- type, see Scheme), the thermally-controlled self-assembly allows the preparation of supramolecular architectures of different morphologies in a bottom-up approach: two-dimensional (2D) nanosheets3 are formed in case of 1.6- and 2.7-substitution4 whereas one-dimensional (1D) fibers are built from 1.8- substituted isomers. The morphologies of the assemblies are established by AFM and TEM, and the results are further correlated with spectroscopic and scattering data. Two-dimensional assemblies consist of an inner layer of hydrophobic pyrenes, sandwiched between a net of phosphates. Due to the repulsion of the negative charges, the 2D assemblies exist mostly as free-standing sheets. An internal alignment of pyrenes leads to strong exciton coupling with an unprecedented observation (simultaneous development of J- and H-bands from two different electronic transitions). Despite the similarity in spectroscopic properties, the structural parameters of the 2D aggregates drastically depend on the preparation procedure. Under certain conditions extra-large sheets (thickness of 2 nm, aspect ratio area/thickness ~107) in aqueous solution are formed4B. Finally, one-dimensional assemblies are formed as micrometer-long and nanometer-thick fibers. Both, planar and linear structures are intriguing objects for the creation of conductive nanowires that may find interest for applications in supramolecular electronics.

From supramolecular sheets to fibers and back: establishing the critical parameters that govern the morphology of pyrene-based self-assembled materials

The precise arraying of functional entities in morphologically well-defined shapes remains one of the key challenges in the processing of organic molecules1. Among various π-conjugated species, pyrene exhibits a set of unique properties, which make it an attractive compound for the utilization in materials science2. In this contribution we report on properties of self-assembled structures prepared from amphiphilic pyrene trimers (Py3) consisting of phosphodiester-linked pyrenes. Depending on the geometry of a pyrene core substitution (1.6-, 1.8-, or 2.7- type, see Scheme), the thermally-controlled self-assembly allows the preparation of supramolecular architectures of different morphologies in a bottom-up approach: two-dimensional (2D) nanosheets3 are formed in case of 1.6- and 2.7-substitution4 whereas one-dimensional (1D) fibers are built from 1.8- substituted isomers. The morphologies of the assemblies are established by AFM and TEM, and the results are further correlated with spectroscopic and scattering data. Two-dimensional assemblies consist of an inner layer of hydrophobic pyrenes, sandwiched between a net of phosphates. Due to the repulsion of the negative charges, the 2D assemblies exist mostly as free-standing sheets. An internal alignment of pyrenes leads to strong exciton coupling with an unprecedented observation (simultaneous development of J- and H-bands from two different electronic transitions). Despite the similarity in spectroscopic properties, the structural parameters of the 2D aggregates drastically depend on the preparation procedure. Under certain conditions extra-large sheets (thickness of 2 nm, aspect ratio area/thickness ~107) in aqueous solution are formed4B. Finally, one-dimensional assemblies are formed as micrometer-long and nanometer-thick fibers. Both, planar and linear structures are intriguing objects for the creation of conductive nanowires that may find interest for applications in supramolecular electronics.

Assembly of τ protein into Alzheimer paired helical filaments depends on a local sequence motif (306VQIVYK311) forming β structure

We have searched for a minimal interaction motif in τ protein that supports the aggregation into Alzheimer-like paired helical filaments. Digestion of the repeat domain with different proteases yields a GluC-induced fragment comprising 43 residues (termed PHF43), which represents the third repeat of τ plus some flanking residues. This fragment self assembles readily into thin filaments without a paired helical appearance, but these filaments are highly competent to nucleate bona fide PHFs from full-length τ. Probing the interactions of PHF43 with overlapping peptides derived from the full τ sequence yields a minimal hexapeptide interaction motif of 306VQIVYK311 at the beginning of the third internal repeat. This motif coincides with the highest predicted β-structure potential in τ. CD and Fourier transform infrared spectroscopy shows that PHF43 acquires pronounced β structure in conditions of self assembly. Point mutations in the hexapeptide region by proline-scanning mutagenesis prevent the aggregation. The data indicate that PHF assembly is initiated by a short fragment containing the minimal interaction motif forming a local β structure embedded in a largely random-coil protein.

Self-assembled monolayers from a designed combinatorial library of de novo β-sheet proteins

A variety of naturally occurring biomaterials owe their unusual structural and mechanical properties to layers of β-sheet proteins laminated between layers of inorganic mineral. To explore the possibility of fabricating novel two-dimensional protein layers, we studied the self-assembly properties of de novo proteins from a designed combinatorial library. Each protein in the library has a distinct 63 amino acid sequence, yet they all share an identical binary pattern of polar and nonpolar residues, which was designed to favor the formation of six-stranded amphiphilic β-sheets. Characterization of proteins isolated from the library demonstrates that (i) they self assemble into monolayers at an air/water interface; (ii) the monolayers are dominated by β-sheet secondary structure, as shown by both circular dichroism and infrared spectroscopies; and (iii) the measured areas (500- 600 Å2) of individual protein molecules in the monolayers match those expected for proteins folded into amphiphilic β-sheets. The finding that similar structures are formed by distinctly different protein sequences suggests that assembly into β-sheet monolayers can be encoded by binary patterning of polar and nonpolar amino acids. Moreover, because the designed binary pattern is compatible with a wide variety of different sequences, it may be possible to fabricate β-sheet monolayers by using combinations of side chains that are explicitly designed to favor particular applications of novel biomaterials.

Nucleator-dependent intercellular assembly of adhesive curli organelles in Escherichia coli.

Bacterial adhesion to other bacteria, to eukaryotic cells, and to extracellular matrix proteins is frequently mediated by cell surface-associated polymers (fimbriae) consisting of one or more subunit proteins. We have found that polymerization of curlin to fimbriae-like structures (curli) on the surface of Escherichia coli markedly differs from the prevailing model for fimbrial assembly in that it occurs extracellularly through a self-assembly process depending on a specific nucleator protein. The cell surface-bound nucleator primes the polymerization of curlin secreted by the nucleator-presenting cell or by adjacent cells. The addition of monomers to the growing filament seems to be driven by mass action and guided only by the diffusion gradient between the source of secreted monomer and the surface of monomer condensation.

Kinetics of self-assembling microtubules: an "inverse problem" in biochemistry.

Experimental time series for a nonequilibrium reaction may in some cases contain sufficient data to determine a unique kinetic model for the reaction by a systematic mathematical analysis. As an example, a kinetic model for the self-assembly of microtubules is derived here from turbidity time series for solutions in which microtubules assemble. The model may be seen as a generalization of Oosawa's classical nucleation-polymerization model. It reproduces the experimental data with a four-stage nucleation process and a critical nucleus of 15 monomers.

Molecular organization of histidine-tagged biomolecules at self-assembled lipid interfaces using a novel class of chelator lipids.

In molecular biology, the expression of fusion proteins is a very useful and well-established technique for the identification and one-step purification of gene products. Even a short fused sequence of five or six histidines enables proteins to bind to an immobilized metal ion chelate complex. By synthesis of a class of chelator lipids, we have transferred this approach to the concept of self-assembly. The specific interaction and lateral organization of a fluorescent fusion molecule containing a C-terminal oligohistidine sequence was studied by film balance techniques in combination with epifluorescence microscopy. Due to the phase behavior of the various lipid mixtures used, the chelator lipids can be laterally structured, generating two-dimensional arrays of histidine-tagged biomolecules. Because of the large variety of fusion proteins already available, this concept represents a powerful technique for orientation and organization of proteins at lipid interfaces with applications in biosensing, biofunctionalization of nanostructured interfaces, two-dimensional crystallization, and studies of lipid-anchored proteins.

Supra-assembly of siliceous vesicles

We report a new approach to produce macroporous (110 nm in diameter) ordered siliceous foams (MOSF) by using block copolymers as templates in the absence of any organic cosolvent. The fine three-dimensional honeycomb structure of MOSF was determined by electron tomography. A formation mechanism of MOSF that spans from the atomic to macroscopic scale is proposed, which involves the cooperative self-assembly of unilamellar vesicles followed by the supra-assembly of vesicles. The fusion of soft vesicles finally leads to MOSF with well-ordered and defined honeycomb structures.

Self-assembled SnO2 micro- and nanosphere-based gas sensor thick films from an alkoxide-derived high purity aqueous colloid precursor

Tin oxide is considered to be one of the most promising semiconductor oxide materials for use as a gas sensor. However, a simple route for the controllable build-up of nanostructured, sufficiently pure and hierarchical SnO2 structures for gas sensor applications is still a challenge. In the current work, an aqueous SnO2 nanoparticulate precursor sol, which is free of organic contaminants and sorbed ions and is fully stable over time, was prepared in a highly reproducible manner from an alkoxide Sn(OR)4 just by mixing it with a large excess of pure neutral water. The precursor is formed as a separate liquid phase. The structure and purity of the precursor is revealed using XRD, SAXS, EXAFS, HRTEM imaging, FTIR, and XRF analysis. An unconventional approach for the estimation of the particle size based on the quantification of the Sn-Sn contacts in the structure was developed using EXAFS spectroscopy and verified using HRTEM. To construct sensors with a hierarchical 3D structure, we employed an unusual emulsification technique not involving any additives or surfactants, using simply the extraction of the liquid phase, water, with the help of dry butanol under ambient conditions. The originally generated crystalline but yet highly reactive nanoparticles form relatively uniform spheres through self-assembly and solidify instantly. The spheres floating in butanol were left to deposit on the surface of quartz plates bearing sputtered gold electrodes, producing ready-for-use gas sensors in the form of ca. 50 μm thick sphere-based-films. The films were dried for 24 h and calcined at 300°C in air before use. The gas sensitivity of the structures was tested in the temperature range of 150-400°C. The materials showed a very quickly emerging and reversible (20-30 times) increase in electrical conductivity as a response to exposure to air containing 100 ppm of H2 or CO and short (10 s) recovery times when the gas flow was stopped.

Stabilization of self-assembled alumina mesophases

An efficient route to stabilize alumina mesophases derived from evaporation-induced self-assembly is reported after investigating various aspects in-depth: influence of the solvent (EtOH, s-BuOH, and t-BuOH) on the textural and structural properties of the mesophases based on aluminum tri-sec-butoxide (ATSB), synthesis reproducibility, role of nonvolatile acids, and the crystallization and thermal stability of the crystalline counterparts. Mesophase specific surface area and pore uniformity depend notably on the solvent; s-BuOH yields the highest surface area and pore uniformity. The optimal mesophase synthesis is reproducible with standard deviations in the textural parameters below 5%. The most pore-uniform mesophases from the three solvents were thermally activated at 1023 K to crystallize them into γ-alumina. The s-BuOH mesophase is remarkably thermally stable, retaining the mesoscopic wormhole order with 300 m2/g (0.45 cm3/g) and an increased acidic site density. These features are not obtained with EtOH or t-BuOH, where agglomerated γ-Al2O3 crystallites are formed with lower surface areas and broader pore size distributions. This was rationalized by the increase of the hydrolysis rate using EtOH and t-BuOH. t-BuOH dehydrates under the synthesis conditions or reacts with HCl, situations that increase the water concentration and rate of hydrolysis. It was found that EtOH exchanges rapidly, producing a highly reactive Al-ethoxide, thus enhancing the hydrolysis rate as well. Particle heterogeneity with random packing of fibrous and wormhole morphologies, attributed to the high hydrolysis rate, was observed for mesophases derived from both solvents. Such a low particle coordination favors coarsening with enlargement of the pore size distribution upon thermal treatment, explaining the lower thermal stability. Controlled hydrolysis and formation of low-polymerized Al species in s-BuOH are possibly responsible for the adequate assembly onto the surfactant. This was verified by the formation of a regular distribution of relatively size-uniform nanoparticles in the mesophase; high particle coordination prevents coarsening, favors densification, and maintains a relatively uniform pore size distribution upon thermal treatment. The acid removal in the evaporation is another key factor to promote network condensation in this route. © 2013 American Chemical Society.

Advancing atomic nanolithography: cold atomic Cs beam exposure of alkanethiol self-assembled monolayers

We report the results of a study into the quality of functionalized surfaces for nanolithographic imaging. Self-assembled monolayer (SAM) coverage, subsequent post-etch pattern definition and minimum feature size all depend on the quality of the Au substrate used in atomic nanolithographic experiments. We find sputtered Au substrates yield much smoother surfaces and a higher density of {111} oriented grains than evaporated Au surfaces. A detailed study of the self-assembly mechanism using molecular resolution AFM and STM has shown that the monolayer is composed of domains with sizes typically of 5-25 nm, and multiple molecular domains can exist within one Au grain. Exposure of the SAM to an optically-cooled atomic Cs beam traversing a two-dimensional array of submicron material masks ans also standing wave optical masks allowed determination of the minimum average Cs dose (2 Cs atoms per SAM molecule) and the realization of < 50 nm structures. The SAM monolayer contains many non-uniformities such as pin-holes, domain boundaries and monoatomic depressions which are present in the Au surface prior to SAM adsorption. These imperfections limit the use of alkanethiols as a resist in atomic nanolithography experiments. These studies have allowed us to realize an Atom Pencil suitable for deposition of precision quantities of material at the microand nanoscale to an active surface.