<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.

La croissance de polymères bidimensionnels a été étudiée sous ultra-haut vide sur des surfaces métalliques par microscopie à effet tunnel (STM). La première étude concerne la croissance de réseaux nanoporeux covalents bidimensionnels obtenus par réaction de déshydratation des molécules d'acide 1.4 diboronique (BDBA). Les meilleurs réseaux sont obtenus pour les dépôts à flux élevés sur des substrats d'Argent chauffés à 150°C. La deuxième étude concerne la réaction chimique entre les molécules de 1,2,4,5 tétracyanobenzène (TCNB) et les atomes de Fer. La formation de liaison covalente entre les molécules et les atomes de Fer est thermiquement activée par des recuits à 200°C et permet la formation d'octacyanophtalocyanine de Fer. Ce travail ouvre de nouvelles perspectives pour la fabrication de matériaux 2D originaux obtenus par des réactions chimiques de surface. / The growth of two dimensional polymers has been studied under ultra-high vacuum on metallic surfaces by scanning tunnelling microscopy (STM). The first study relates on the growth of two dimensional covalent nanoporous networks obtained after dehydratation reaction of the 1,4 diboronic acid benzene molecule (BDBA). The best networks have been obtained with high molecular flux on silver metallic substrates maintained at 150°C during deposition. The second study relates on chemical reaction between the 1, 2, 4, 5 tetracyanobenzene molecule (TCNB) and iron atoms. The reaction takes place after an annealing at 200°C. In that case some iron octacyanophthalocyanine have been successfully synthesised at surfaces. This work opens new perspectives for the fabrication of 2D original materials by chemical reactions on surfaces.

La nanostructure et les propriétés électroniques de matériaux modèles pour le photovoltaïque organique, ont été étudiées en utilisant la Microscopie à Force Atomique en mode non contact sous ultra-vide (NC-AFM) et la Microscopie à sonde de Kelvin (KPFM). En utilisant le mode modulation d'amplitude (AM-KPFM), le potentiel de surface photo- généré dans des mélanges donneur-accepteur présentant une ségrégation de phase optimale a pu être visualisé à l'échelle du nanomètre. Afin de préciser la nature des forces mises en jeu dans le processus d'imagerie KPFM, des oligomères π-conjugués auto-assemblés ont ensuite été étudiés. Une transition entre régimes à longue et à courte portée a ainsi été mise en évidence en combinant l'imagerie en haute résolution aux mesures de spectroscopie en distance. Ces mesures ont également démontré que l'influence des forces électrostatiques à courte portée peut être minimisée en travaillant au seuil du contraste de dissipation. Enfin cette procédure a été utilisée, en combinaison avec les mesures de spectroscopie de photoélectrons UV, pour analyser la fonction de sortie locale d'électrodes transparentes à base de nanotubes de carbone fonctionnalisés. / In this thesis, noncontact atomic force microscopy (NC-AFM) and Kelvin probe force microscopy (KPFM) under ultrahigh vacuum have been applied to investigate the nanostructure and electronic surface properties of model materials for organic photovoltaics. First, it has been demonstrated that the surface photovoltage of nanoscale phase segregated donor-acceptor photovoltaic blends can be finely resolved at the nanometer scale by using amplitude modulation KPFM (AM-KPFM). Next, model self-assembled π-conjugated oligomers have been investigated, in order to obtain a deeper insight into the nature of the tip-surface forces involved in the KPFM imaging process. A crossover between long-range (LR) and short-range (SR) regimes has been evidenced by combining high resolution imaging with distance-spectroscopy measurements. It has also been shown that the influence of the SR electrostatic forces can be minimized by working at the onset of the damping contrast. Finally, using this procedure, the local work function of flexible transparent electrodes, comprised of functionalized carbon nanotubes by metallic nanoparticles, has been investigated, and compared to the averaged value deduced from ultraviolet photoelectron spectroscopy.

Dans ce rapport de thèse, nous présentons les résultats obtenus avec la croissance d'assemblages supramoléculaires hautement cristallins et stables à température ambiante sur des surfaces isolantes d'halogénures d'alcalins. L'objectif de cette étude est de caractériser structurellement ces réseaux auto-assemblés et de mettre en évidence l'ensemble des forces d'interaction mises en œuvre dans les processus de croissance et de diffusion, en combinant la microscopie à force atomique en mode non contact (nc-AFM) sous ultravide et des calculs théoriques basés sur la théorie de la fonctionnelle de la densité (DFT) et la dynamique moléculaire. Nous montrons comment des paramètres bien définis concernant le choix de la molécule d'une part tels que sa taille, sa forme, sa symétrie, sa flexibilité et sa fonctionnalité, et le choix du substrat d'autre part, influent sur la morphologie de croissance et permettent de contrôler les propriétés de diffusion des molécules en surface et donc la structure supramoléculaire résultante. / In this thesis, we report the results obtained with the growth of highly crystalline and stable supramolecular assemblies at room temperature on insulating surfaces of bulk alkali halides single crystals. The objective of this study is to structurally characterize these self-assembled networks and understand all the interaction forces involved in the growth and diffusion processes. This is performed by joint non-contact atomic force microscopy (nc-AFM) experiments in ultrahigh vacuum and theoretical calculations based on density functional theory (DFT) and molecular dynamics. We show how well-defined parameters for the choice of the molecule on the one hand such as size, shape, symmetry, flexibility and functionality, and the choice of the substrate on the other hand, influence the morphology growth and serve to steer the structure and diffusion properties of such systems.

Designing novel nanostructures which exploit the self-assembly capabilities of biomolecules yields a promising approach to control matter at the nanoscale. Here, the homochiral molecular self-assemblies of the methionine and tyrosine amino acids on the monocrystalline Ag(111) and Cu(111) surfaces are characterized by means of scanning tunneling microscopy (STM) and spectroscopy (STS), helium atom scattering (HAS), x-ray photoelectron spectroscopy (XPS) and near-edge x-ray absorption fine structure (NEXAFS) in ultrahigh vacuum (UHV). On Ag(111), methionine self-assembles into supramolecular chains following the <110> substrate axis, forming regular nanogratings with tunable periodicity. Within the nanowires, a zwitterionic dimerization scheme is revealed. STS shows that the biomolecular nanostructures act as tunable one-dimensional quantum resonators for the surface state electrons. Zero-dimensional electronic confinement is achieved by positioning single iron atoms in the molecular trenches. This shows a novel approach to control the dimensionality of surface state electrons. The nanogratings were exploited to steer the spontaneous one-dimensional ordering of cobalt and iron atoms. For T > 15 K, the metal species self-align into homogeneously distributed chains in between the biomolecular trenches with ~25 Å interatomic distace. For Co, the dynamics of the self-alignment was monitored, revealing a reduced mobility in comparison with isolated Co atoms on bare Ag(111). On Cu(111), the self-assembly of methionine is influenced by the substrate reactivity and its temperature during molecular deposition. For T < 273 K, the biomolecules assemble in anisotropic extended clusters oriented with a -10° rotation off the <110> substrate orientations, whereas above 283 K a regularly ordered 1D phase arises with a +10° rotation off these high-symmetry axis. XPS reveals a structural transformation triggered by a thermally activated deprotonation of the zwitterionic ammonium group. On Ag(111), tyrosine self-assembles above a critical temperature into linear structures primarily following the substrate crystalline symmetry. A zwitterionic non-covalent molecular dimerization is demonstrated, NEXAFS data providing evidence of a non-flat adsorption of the phenyl ring. This recalls the geometrical pattern of methionine on Ag(111) and supports a universal self-assembling scheme for amino acids on close-packed noble metal surfaces, the different mesoscopic ordering being determined by the side chain reactivity.

Designing novel nanostructures which exploit the self-assembly capabilities of biomolecules yields a promising approach to control matter at the nanoscale. Here, the homochiral molecular self-assemblies of the methionine and tyrosine amino acids on the monocrystalline Ag(111) and Cu(111) surfaces are characterized by means of scanning tunneling microscopy (STM) and spectroscopy (STS), helium atom scattering (HAS), x-ray photoelectron spectroscopy (XPS) and near-edge x-ray absorption fine structure (NEXAFS) in ultrahigh vacuum (UHV). On Ag(111), methionine self-assembles into supramolecular chains following the <110> substrate axis, forming regular nanogratings with tunable periodicity. Within the nanowires, a zwitterionic dimerization scheme is revealed. STS shows that the biomolecular nanostructures act as tunable one-dimensional quantum resonators for the surface state electrons. Zero-dimensional electronic confinement is achieved by positioning single iron atoms in the molecular trenches. This shows a novel approach to control the dimensionality of surface state electrons. The nanogratings were exploited to steer the spontaneous one-dimensional ordering of cobalt and iron atoms. For T > 15 K, the metal species self-align into homogeneously distributed chains in between the biomolecular trenches with ~25 Å interatomic distace. For Co, the dynamics of the self-alignment was monitored, revealing a reduced mobility in comparison with isolated Co atoms on bare Ag(111). On Cu(111), the self-assembly of methionine is influenced by the substrate reactivity and its temperature during molecular deposition. For T < 273 K, the biomolecules assemble in anisotropic extended clusters oriented with a -10° rotation off the <110> substrate orientations, whereas above 283 K a regularly ordered 1D phase arises with a +10° rotation off these high-symmetry axis. XPS reveals a structural transformation triggered by a thermally activated deprotonation of the zwitterionic ammonium group. On Ag(111), tyrosine self-assembles above a critical temperature into linear structures primarily following the substrate crystalline symmetry. A zwitterionic non-covalent molecular dimerization is demonstrated, NEXAFS data providing evidence of a non-flat adsorption of the phenyl ring. This recalls the geometrical pattern of methionine on Ag(111) and supports a universal self-assembling scheme for amino acids on close-packed noble metal surfaces, the different mesoscopic ordering being determined by the side chain reactivity.

Designing novel nanostructures which exploit the self-assembly capabilities of biomolecules yields a promising approach to control matter at the nanoscale. Here, the homochiral molecular self-assemblies of the methionine and tyrosine amino acids on the monocrystalline Ag(111) and Cu(111) surfaces are characterized by means of scanning tunneling microscopy (STM) and spectroscopy (STS), helium atom scattering (HAS), x-ray photoelectron spectroscopy (XPS) and near-edge x-ray absorption fine structure (NEXAFS) in ultrahigh vacuum (UHV). On Ag(111), methionine self-assembles into supramolecular chains following the <110> substrate axis, forming regular nanogratings with tunable periodicity. Within the nanowires, a zwitterionic dimerization scheme is revealed. STS shows that the biomolecular nanostructures act as tunable one-dimensional quantum resonators for the surface state electrons. Zero-dimensional electronic confinement is achieved by positioning single iron atoms in the molecular trenches. This shows a novel approach to control the dimensionality of surface state electrons. The nanogratings were exploited to steer the spontaneous one-dimensional ordering of cobalt and iron atoms. For T > 15 K, the metal species self-align into homogeneously distributed chains in between the biomolecular trenches with ~25 Å interatomic distace. For Co, the dynamics of the self-alignment was monitored, revealing a reduced mobility in comparison with isolated Co atoms on bare Ag(111). On Cu(111), the self-assembly of methionine is influenced by the substrate reactivity and its temperature during molecular deposition. For T < 273 K, the biomolecules assemble in anisotropic extended clusters oriented with a -10° rotation off the <110> substrate orientations, whereas above 283 K a regularly ordered 1D phase arises with a +10° rotation off these high-symmetry axis. XPS reveals a structural transformation triggered by a thermally activated deprotonation of the zwitterionic ammonium group. On Ag(111), tyrosine self-assembles above a critical temperature into linear structures primarily following the substrate crystalline symmetry. A zwitterionic non-covalent molecular dimerization is demonstrated, NEXAFS data providing evidence of a non-flat adsorption of the phenyl ring. This recalls the geometrical pattern of methionine on Ag(111) and supports a universal self-assembling scheme for amino acids on close-packed noble metal surfaces, the different mesoscopic ordering being determined by the side chain reactivity. / Science, Faculty of / Chemistry, Department of / Graduate

No description available.

The ability of RNA bases to self-assemble into larger structures is an important research area relevant to the origins of life. In the RNA helix the bases are arranged on a sugar-phosphate carcass but it has been suggested that the initial ordering could form on a flat surface. This thesis is an attempt to establish experimentally whether the complementary RNA bases, adenine and uracil, have the ability to self-assemble into large ordered structures when adsorbed on metal and mineral surfaces. The Au (111) surface was chosen as a preferred substrate as it is flat, relatively free of defects, chemically inert and reconstructs in a characteristic pattern of corrugation lines, which provide a reference for crystallographic directions. Six of the molecular phases shown were observed for the first time with molecular resolution and the possible two-dimensional arrangements of adenine and uracil molecules for these phases are proposed. The pure adenine and pure uracil structures have chiral unit cells and in the case of pure uracil alternating monochiral domains within the polychiral islands are created. Well-ordered intricate uracil-adenine bimolecular networks were also observed. The self-assembly of both uracil and adenine appears to be weakly influenced by the surface crystallography. The (100) surface of the mineral pyrite (FeS₂) was chosen as the alternative substrate as it is the most common face that occurs naturally in pyrite crystals. The experiments show the formation of small adenine and uracil crystals at the terrace edges. Neither uracil nor adenine were observed to form a monolayer on the surface of the terraces. The results of the experiments described in this thesis are very interesting in terms of establishing the possible mechanisms for creating regular chiral molecular networks and provide a useful insight into the role of surfaces in the processes of self-assembly of RNA bases.