The cyclic voltammogram of complex 6 shows one successive reversible one-electron redox wave corresponding to the oxidation of the Ruthenium moiety and peak-to-peak separations are smaller than 59 mV(ideal value of one electron transfer with diffusing controlling). In addition, the peak currents are linear to scan rate, i.e., i £\ V. This observation is corresponding to the electrochemical property of SAM, and we would like to suggest that the electron transfer process in the electrochemical measurements is direct controlling. Furthermore, we synthesized a nano-material by using of redox stable Ru(II)-Terpyridyloctanethiol attached to gold cluster (complex 7). The clusters are stable in air, soluble in nonpolar organic solvents and the characters could be examining by traditional chemical instruments such as NMR, UV/Vis, TEM. Finally, complex 7 seif-assembled on gold electrode (complex 8). This observation is corresponding to the electrochemical property of SAM, and we would like to suggest that the electron transfer process in the electrochemical measurements is direct controlling. we would like to suggest that the complex 5 has bi-functionalized property.

Molecular self-assembly through non-covalent interactions is an integral part of countless natural and synthetic materials. The Iverson group specifically focuses on aromatic donor-acceptor interactions and the subsequent self-assembly of molecules containing these functionalities. The work has predominately utilized association between the electron-rich 1,5-dialkoxynaphthalene (DAN) and the electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) to create numerous self-assembled structures through intramolecular or intermolecular aromatic donor-acceptor interactions. The self-assembly and inherent electronic properties of aromatic units have made them attractive candidates for nature-inspired molecules, molecular machines and organic electronic materials. The focus of these D-A interactions now shifts from an aqueous environment as solid state aromatic D-A interactions are promising modes of driven self-assembly for molecular architectures geared towards material applications. Aromatic units have long been applied in areas such as organic electronic materials due to their inherent charge transport properties. NDI has become a molecule of considerable interest among the organic electronics community due its electron transporting properties and ability to self-assemble. Therefore a thorough understanding of NDI and DAN-NDI self-assembly in the solid state should be of importance for the improvement and development of molecular architectures for organic electronic devices. The following dissertation chapters focus on NDI or its aromatic D-Acomplex with DAN. Chapter 2 investigates an unusual thermochromic behavior that occurred in our previous study when several solid state DAN:NDI mixtures lost their characteristic red color while crystallizing from the mesophase. Chapter 3 describes the synthetic progress towards a rigid, non-conjugated DAN-NDI molecule that retains electrostatic complementarity and ultimately led us to explore solid state non-covalent interactions of conjugated aromatic NDI-donor polymers. Chapter 5 describes an approach to synthesize conjugated NDI polymers and a diyne NDI to serve as an important synthetic intermediate. The work in chapter 6 tests the solid state association between neutral aromatic donor and acceptor polymer strands. The work enhances the present understanding of these D-A interactions in different phases. The results also support recent discussions about aromatic stacking dominated by interactions between highly polarized groups on the periphery of aromatic units rather than overall polarization of the aromatic ring itself (i.e. D-A interactions). / text

No / The relationship between molecular self-assembly processes and nucleation during crystallization from solution is an important issue, both in terms of fundamental physical chemistry and for the control and application of crystallization processes in crystal engineering and materials chemistry. This contribution examines the extent to which the occurrence of crystal polymorphism can be used as an indicator of the nature of molecular aggregation processes in supersaturated solutions. For the specific case of 2,6-dihydroxybenzoic acid a combination of solubility, spectroscopic, crystallization, and molecular modeling techniques are used to demonstrate that there is a direct link between the solvent-induced self-assembly of this molecule and the relative occurrence of its two polymorphic forms from toluene and chloroform solutions.

The rational design, synthesis, and characterization of several systems that undergo self-assembly are described. Systems were chosen based on their ability to self-assemble in a highly ordered and predictable fashion that imparts order on the structure such that it is able to perform a given device function. Herein we describe self-assembled multilayered thin films on gold that can behave as molecular wires with tunable length, photocurrent generating films, and surfaces with photoswitchable wettability, and self-assembling peptide nanotubes that can potentially function as long range energy and electron transfer conduits. A non-covalent, modular approach to multilayered thin film fabrication was used to generate three thin film systems that function as molecular scale wires, photocurrent generating devices, and photoswitchable thin films, respectively. These films were based on 4-[(10-mercaptodecyl)oxy]pyridine-2,6-dicarboxylic acid self-assembled monolayers on gold. These monolayers are able to chelate metal (II) ions, and thus multilayers were assembled based on metal-ligand coordination chemistry. The three systems described were characterized by contact angle measurements, electrochemical methods, and grazing angle IR spectroscopy. All three systems emphasize the versatility of a modular approach to thin film construction, and provide proof-of-concept for future studies. A cyclic octapeptide architecture was employed as a scaffold for the predictable self-assembly of photoactive groups within a nanotubular structure. The degree of cyclic peptide aggregation in stacking nanotube systems and non-stacking monomer systems, was studied via fluorescence emission spectroscopy. Based on the spectral results, it was determined that peptide nanotubes can be constructed such that photoactive side chains can be assembled in stacks. Future experiments for the determination of long range energy and/or charge transfer in these systems are also discussed.

<p>Synthetic biology is an emerging technology field whose goal is to use biology as a substrate for engineering. Self-assembly is one of the many methods for fabricating such synthetic biosystems.</p><p>Self-assembly is a process where components spontaneously arrange themselves into organized aggregates by the selective affinity of substructures. DNA is an excellent candidate for making synthetic biological systems using self-assembly because of its modular structure and simple chemistry. This thesis describes several</p><p>techniques which use DNA as a nano-construction material and</p><p>explores the computational capabilities of DNA self-assembly.</p><p>For this dissertation, I set out to build a biomolecular computing device with several</p><p>useful properties, including compactness, robustness, high degrees of complexity, flexibility, scalability and easily characterized yields</p><p>and convergence rates. However, a unified device that satisfies all these properties is still many years away. Instead, this thesis presents designs, simulations,</p><p>and experimental results for several distinct DNA nano-systems, as</p><p>well as experimental protocols, each of which satisfies a subset of the above-mentioned properties. The hope is that the lessons learned from building all these biomolecular computational devices would bring us closer to our ultimate goal and would eventually pave the path for a computing device that satisfies all the properties. We experimentally demonstrate how we can reduce errors in tiling assembly using an optimized set of physical parameters. We propose a novel DNA tile design</p><p>which enforces directionality of growth, reducing assembly errors. We build simulation models to characterize damage in fragile nanostructures under the impact of various external forces. Furthermore, we investigate reversible computation as a means to provide self-repairability to such damaged structures.</p><p>We suggest two modifications of an existing DNA computing device,</p><p>called Whiplash PCR machine, which allow it to operate robustly outside of controlled laboratory conditions and allow it to implement a simple form of inter-device communication. We present analysis techniques which characterize the yields and time convergence of self-assembled DNA nanostructures. We also present an experimental demonstration of a novel DNA nanostructure which is capable of tiling the plane and could prove to be a way of building 3D DNA assemblies.</p> / Dissertation

Kinetically controlled isothermal growth is fundamental to biological development, but it remains challenging to rationally design molecular systems that self-assemble isothermally into complex geometries via prescribed assembly and disassembly pathways. By exploiting the programmable chemistry of base pairing, sophisticated spatial and temporal control have both been demonstrated in DNA self-assembly, but largely as separate pursuits. This dissertation extends a new approach, called developmental self-assembly, that integrates temporal with spatial control by using a prescriptive molecular program to specify the kinetic pathways by which DNA molecules isothermally self-assemble into well-defined three-dimensional geometries. / Chemistry and Chemical Biology

Samouspořádání organických molekul je spontánní proces tvorby nanostruktur, při kterém je výsledná struktura určena mezimolekulárními and molekulárně-substrátovými interakcemi. Pochopení principů samouspořádávání je klíčem k přípravě funkčních nanostruktur s atomární přesností. Tato diplomová práce se zaměřuje na přípravu a studium samouspořádaných molekulárních struktur 4,4’-diphenyl dikarboxylové kyseliny na povrchu grafenu připraveného na Ir(111). Pro studium vlastností molekulárních struktur je využito rastrovací tunelovací mikroskopie a nízkoenergiové elektronové mikroskopie. Tato kombinace umožňuje získat informace z oblastí o velikosti v řádu nanometrů až milimetrů. V práci je popsána molekulární strukuktura stabilní při pokojové teplotě. Vazebný motiv této struktury je dán interakcí karboxylových skupin sousedních molekul.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第19898号 / 工博第4214号 / 新制||工||1651(附属図書館) / 32975 / 京都大学大学院工学研究科材料化学専攻 / (主査)教授 木村 俊作, 教授 瀧川 敏算, 教授 今堀 博 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

Graphene, one-atom-thick planar sheet of carbon atoms densely packed in a honeycomb crystal lattice, has grabbed appreciable attention due to its exceptional electronic, mechanical and optical properties. Chemical functionalization schemes are needed to integrate graphene with the different materials required for potential applications. Molecular self-assembly behavior on graphene is a key method to investigate the mechanism of interaction between molecules and graphene and the promising applications related to molecular devices. In this thesis, we report the molecular self-assembly behavior of phenyl-C61-butyric acid methyl ester (PCBM), C60, perylenetetracarboxylic dianhydride (PTCDA) and Gd3N@C80 on flat and rippled graphene 2D material by the experimental methods of scanning tunneling microscope (STM) and atomic force microscope (AFM) and by the theoretical method of density functional theory (DFT). We found that molecules form ordered structures on flat graphene, while they form disordered structure on rippled graphene. For example, PCBM forms bilayer and monolayer structures, C60 and Gd3N@C80 form hexagonal close packed (hcp) structure on flat graphene and PTCDA forms herringbone structure on flat graphene surface. Although C60 and Gd3N@C80 both form hcp structure, C60 forms a highly ordered hcp structure over large areas with little defects and Gd3N@C80 forms hcp structure only over small areas with many defects. These differences of structure that forms on flat graphene is mainly due to the molecule-molecule interactions and the shape of the molecules. We find that the spherical C60 molecules form a quasi-hexagonal close packed (hcp) structure, while the planar PTCDA molecules form a disordered herringbone structure. From DFT calculations, we found that molecules are more effected by the morphology of rippled graphene than the molecule-molecule interaction, while the molecule-molecule interaction plays a main role during the formation process on flat graphene. The results of this study clearly illustrate significant differences in C60 and PTCDA molecular packing on rippled graphene surfaces. / Doctor of Philosophy / As the first physical isolated two-dimensional (2D) material, graphene has attracted exceptional scientific attention. Due to its impressive properties including high carrier density, flexibility and transparency, graphene has numerous potential applications, such as solar cell, sensors and electronics. 2D molecular self-assembly is an area that focuses on organization and interaction between self-assembly behaviors of molecules on surface. Graphene is an excellent substrate for the study of molecular self-assembly behavior, and study of molecular study is very important for graphene due to potential applications of molecules on graphene. In this thesis, we present investigations of the molecular self-assembly of PCBM, C60, PTCDA and Gd3N@C80 on graphene substrate. First, we report the two types of bilayer PCBM configuration on HOPG with a step height of 1.68 nm and 1.23 nm, as well as two types of monolayer PCBM configuration with a step height of 0.7 nm and 0.88 nm, respectively. On graphene, PCBM forms one type of PCBM bilayer with a step height of 1.37 nm and one type of PCBM monolayer with a step height of 0.87 nm. By building and analyzing the models of PCBM bilayers and monolayers, we believe the main differences between two configurations of PCBM bilayer and monolayer is the tilt angle between PCBM and HOPG, which makes type I configuration the higher molecule density and binding energy. Secondly, we report the investigation of self-assembly behaviors of C60 and PTCDA on flat graphene and rippled graphene by experimental scanning tunneling microscope (STM) and theoretical density functional theory (DFT). On flat graphene, C60 forms hexagon close pack (hcp) structure, while PTCDA forms herringbone structure. On rippled graphene, C60 forms quasi-hcp structure while PTCDA forms disordered herringbone structure. By DFT calculation, we study the effect of graphene curvature on spherical C60 and planar PTCDA. Finally, we report a STM study of a monolayer of Gd3N@C80 on graphene substrate. Gd3N@C80 forms hcp structure in a small domain with a step height of 0.88 nm and lattice constant of 1.15 nm. According to our DFT calculation, for the optimal organization of Gd3N@C80 and graphene, the gap between Gd3N@C80 and graphene is 3.3 Å and the binding energy is 0.95 eV. Besides, the distance between Gd3N@C80 and Gd3N@C80 is 3.5 Å and the binding energy is 0.32 eV.

Le couplage covalent de précurseurs moléculaires spécialement conçus, assisté par une surface métallique, a récemment émergé comme nouvelle voie pour la création de nouvelles architectures moléculaires prometteuses pour l’électronique moléculaire. Les phtalocyanines et leurs dérivés ont attiré beaucoup d’intérêt à cause de leurs propriétés chimiques et optoélectroniques. Dans cette thèse la synthèse de composés de phtalocyanine est présentée. Les composés sont obtenus par une réaction en surface entre précurseurs fonctionnalisés avec quatre groupements carbonitriles et des atomes métalliques. L’étude expérimentale est faite par microscopie à effet tunnel et spectroscopie de photoémission X. Les précurseurs moléculaires de TCN-DBTTF et de PPCN ont été étudiés. Les TCN-DBTTF ont été déposés avec les atomes de Mn, Fe ou Cu sur Ag(111) et Au(111). La réaction de cyclotetramerization a été activée par recuits. Dans le cas le plus favorable (TCN-DBTTF avec Fe sur Ag(111)), la réaction peut être activée à 200°C et permet la synthèse de phtalocyanines individuelles. Un recuit à plus haute température permet de continuer la réaction en 1D (250°C) et en 2D (275°C). Des résultats similaires ont été obtenus pour le dépôt de PPCN avec Mn ou Cu sur Au(111). L’évolution des spectres des niveaux de coeur permet d’obtenir une preuve de la réaction. Les différents facteurs qui influencent la cyclotetramerisation ont été étudiés.L'étude démontre la versatilité de la méthode: la synthèse en surface permet la création de polymères 2D originaux connectés par des macrocycles de phtalocyanine susceptibles d’être étendus à un grand nombre de précurseurs et d’atomes métalliques. / Surface-assisted covalent coupling of suitably designed molecular precursors on metal surfaces has recently emerged as a new route towards the design of novel molecular architectures promising for future applications. Phthalocyanines and their derivatives have been widely studied for their chemical and optoelectronic properties. In this thesis the synthesis of phthalocyanine compounds is presented. The compounds are obtained through an on-surface reaction between tetracarbonitrile-functionalized precursors and metals. The experimental investigation is carried out by means of scanning tunnelling microscopy and X-Ray photoemission spectroscopy. Two molecular precursors, TCN-DBTTF and PPCN, are studied. TCN-DBTTF molecules are deposited with metal atoms (Mn, Fe, or Cu) on Ag(111) and Au(111). Annealing is used to activate the reaction of cyclotetramerization between precursors and metals. In the most favourable case (TCN-DBTTF with Fe on Ag(111)) the reaction can be activated at 200°C and leads to the synthesis of individual phthalocyanines. Increasing the temperature allows the synthesis of polymeric lines, at 250°C, and small 2D domains, at 275°C. Similar results are obtained for PPCN deposition with Mn or Cu on Au(111). In this latter case, the evolution of core level spectra allows a chemical proof of the on-surface reaction. The factors affecting on-surface cyclotetramerization have also been studied. This study demonstrates the versatility of the method: on-surface cyclotetramerization allows creating original 2D polymers connected by phthalocyanine macrocycles, and may work with a wide range of tetracarbonitrile-functionalized precursors and metallic atoms.