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.

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.

<p>This study is focused on designing and characterizing protein-based building blocks in order to construct self-assembled nano-structured biomaterials. In detail, this research aims to: (1) investigate a new class of proteins that possess nanospring behaviors at a single-molecule level, and utilize these proteins along with currently characterized elastomeric proteins as building blocks for nano-structured biomaterials; (2) develop a new method to accurately measure intermolecular interactions of self-assembling two or more arbitrary (poly)peptides, and select some of them which have appropriate tensile strength for crosslinking the proteins to construct elastomeric biomaterials; (3) construct well-defined protein building blocks which are composed of elastomeric proteins terminated with self-oligomerizing crosslinkers, and characterize self-assembled structures created by the building blocks to determine whether the elasticity of proteins at single-molecule level can be maintained.</p><p>Primary experimental methods of this research are (1) atomic force microscope (AFM) based single-molecule force spectroscopy (SMFS) that allows us to manipulate single molecules and to obtain their mechanical properties such as elasticity, unfolding and refolding properties, and force-induced conformational changes, (2) AFM imaging that permits us to identify topology of single molecules and supramolecular structures, and (3) protein engineering that allows us to genetically connect elastomeric proteins and self-assembling linkers together to construct well-defined protein building blocks.</p><p>Nanospring behavior of á-helical repeat proteins: We revealed that á-helical repeat proteins, composed of tightly packed á-helical repeats that form spiral-shaped protein structures, unfold and refold in near equilibrium, while they are stretched and relaxed during AFM based SMFS measurements. In addition to minimal energy dissipation by the equilibrium process, we also found that these proteins can yield high stretch ratios (>10 times) due to their packed initial forms. Therefore, we, for the first time, recognized a new class of polypeptides with nanospring behaviors. </p><p>Protein-based force probes for gauging molecular interactions: We developed protein-based force probes for simple, robust and general AFM assays to accurately measure intermolecular forces between self-oligomerization of two or more arbitrary polypeptides that potentially can serve as molecular crosslinkers. For demonstration, we genetically connected the force probe to the Strep-tag II and mixed it with its molecular self-assembling partner, the Strep-Tactin. Clearly characterized force fingerprints by the force probe allowed identification of molecular interactions of the single Strep-tag II and Strep-Tactin complex when the complex is stretched by AFM. We found a single energy barrier exists between Strep-tag II and Strep-Tactin in our given loading rates. Based upon our demonstration, the use of the force probe can be expanded to investigate the strength of interactions within many protein complexes composed of homo- and hetero-dimers, and even higher oligomeric forms. Obtained information can be used to choose potential self-assembling crosslinkers which can connect elastomeric proteins with appropriate strength in higher-order structures. </p><p>Self-assembled nano-structured biomaterials with well-defined protein-based building blocks: We constructed well-defined protein building blocks with tailored mechanical properties for self-assembled nano-structured materials. We engineered protein constructs composed of tandem repeats of either a I27-SNase dimer or a I27 domain alone and terminated them with a monomeric streptavidin which is known to form extremely stable tetramers naturally. By using molecular biology and AFM imaging techniques, we found that these protein building blocks transformed into stable tetrameric complexes. By using AFM based SMFS, we measured, to our knowledge for the first time, the mechanical strength of the streptavidin tetramer at a single-molecule level and captured its mechanical anisotropy. Using streptavidin tetramers as crosslinkers offers a unique opportunity to create well-defined protein based self-assembled materials that preserve the molecular properties of their building blocks.</p> / Dissertation

Dans cette thèse, nous avons étudié les propriétés photoniques et vibrationnelles de monocouches moléculaires auto-assemblées sur graphène et la possibilité d'utiliser des multicouches auto-assemblées de pérylène comme milieu à gain pour l'amplification de plasmons. Le graphène, en tant que matériau transparent et conducteur, a permis pour la première fois de corréler la géométrie du réseau de l’auto-assemblage supramoléculaire avec ses propriétés optiques, grâce à la microscopie à effet tunnel et à des mesures de spectroscopiques optiques et Raman. En comparant plusieurs colorants autoassemblés sur le graphène, nous avons mis en lumière les effets des interactions intermoléculaires et des interactions colorant-graphène sur le spectre d'absorption du colorant adsorbé. Le transfert d'énergie rapide des colorants vers la couche degraphène par les mécanismes de Förster et de Dexter empêche toute relaxation radiative du colorant..Néanmoins, nous avons démontré la première fonctionnalisation fluorescente non-covalente du graphène par une monocouche de colorants autoassemblée en mettant en place une stratégie à base d’espaceurs. Nous avons exploité l’extinction rapide de la fluorescence des colorants par le graphène pour étudier les spectres Raman des auto-assemblages moléculaires sur graphène, et nous avons révélé l'apparition d'un mode vibrationnel couplé entre les molécules adsorbées et le substrat de graphène. Nous avons démontré le régime de couplage fort entre un auto-assemblage tri-dimensionnel de pérylène et un plasmon polariton de surface en optimisant l'orientation et l'organisation des molécules de colorant par rapport au champ électrique du mode de plasmon. Nous avons prouvé que les milieux de gain auto-assemblés en agrégats-J peuvent théoriquement conduire à des milieux de gain efficaces pour l'amplification de plasmons. Cependant, nous avons révélé expérimentalement que les recombinaisons exciton-exciton limitent le taux de pompage à des fluences élevées dans ces milieux denses. / In this work, we have studied thephotonic and vibrational properties of selfassembled molecular monolayers on graphene and the possibility to use perylene self-assembled multilayers as a gain medium for plasmon amplification. Graphene, as a transparent and conductive material, has offered for the first time to correlate the self-assembly structure as deduced from scanning tunneling microscopy to photonic properties as analyzed by optical and Raman spectroscopy measurements. By comparing several self-assembled dyes on graphene we have shed lighton how intermolecular and dye-graphene interactions modify the absorption spectrum of the adsorbed dye.Fast Förster and Dexter energy transfer from the adsorbed dyes to the graphene layer prevent any radiative decay of the dye.Nevertheless, we have demonstrated the first fluorescent non-covalent functionalization of graphene by a supramolecular self-assembled monolayer using a spacer approach.We have exploited the fast dye fluorescence quenching by graphene to study Raman spectra of self-assembled dye on graphene, and we have shown the appearance of a coupled vibrational mode between the adsorbed molecules and the graphene substrate. We have demonstrated the strong couplingregime between a three-dimensional perylene self-assembly and a propagating plasmon polariton by optimizing the orientation and the organisation of the dye molecules compared to the electric field of the plasmon mode. We have shown that J-aggregated self-assembled gain media may theoretically lead to efficient gain media for plasmon amplification. However, we experimentally demonstrated that exciton-exciton recombination limits the achievable pumping rate at high fluences in such dense media.