This dissertation describes the synthesis of molecular machines designed to operate on surfaces (nanocars) or in the solution phase (nanosubmarines), and the study of their diffusion using fluorescence techniques. The design of these molecular machines is aimed to facilitate monitoring of their movement and incorporation of a source of energy for propulsion. To complement previous scanning tunneling microscopy studies of the translation of nanocars on surfaces, chapter 1 describes the synthesis of a family of fluorescently tagged nanocars. The nanocars were functionalized with a tetramethylrhodamine isothiocyanate (TRITC) fluorescent dye. Single-molecule fluorescence microscopy (SMFM) studies of one of these nanocars revealed that 25% of the nanocars moved on glass. The SMFM results also suggested that the dye hindered the mobility of the nanocars. Seeking to improve the mobility, chapter 2 presents the synthesis of a new set of fluorescent nanocars, featuring a 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) dye embedded in their axles. The mobility of these inherently fluorescent nanocars on glass was nearly double than that of their TRITC-tagged predecessors. Their diffusion was also studied on reactive-ion-etched glass, and amino-functionalized glass. The results showed that the mobility is affected by the substrate. To equip the nanocars with an energy input for propulsion, two nanocars functionalized with an olefin metathesis catalyst were synthesized, as described in chapter 3. The catalytic activity of these nanocars toward ring-opening metathesis polymerization (ROMP) in solution was similar to that of their parent catalysts. As an alternative approach to investigate if chemical propulsion through a ROMP process can be achieved at the molecular level, chapter 4 presents the synthesis of a fluorescent ROMP catalyst, termed a nanosubmarine, and the study of its diffusion using fluorescence correlation spectroscopy (FCS). FCS results showed an increase of 20 ± 7% in the diffusion constant of this nanosubmarine in presence of its fuel, cis,cis-1,5-cyclooctadiene. Overall, the work accomplished in this dissertation constitutes a step forward toward development of easily tracked and highly mobile nanocars, and paves the way for the synthesis of truly nanosized chemically propelled molecular machines that operate in the solution phase.

Multi-scale ordering of the components is of utmost importance for the preparation of any functional system. This is particularly interesting for the assembly of plamonic nanoparticles which show drastic differences in their optical properties compared to the individual counterparts, giving rise to the unique opportunity to perform enhanced spectroscopies, sensing, and transporting optical information below the diffraction limitation of light. The control over ordering of nanoscale materials is therefore of paramount importance. Template based bottom up approaches such as using nematic liquid crystals promise a long range, reversible ordering of nanomaterials. It also promises active control over plasmonic properties of metal nanoparticles due to the electric field induced reorientation of liquid crystals, resulting in a change of the local refractive index. This thesis discusses the possibility of ordering anisotropic metal nanoparticles and performing active modulaton of the plasmonics response using a nematic liquid crystals. While long polymer chains can be solvated and aligned in liquid crystal solvents, anisotropic metal nanoparticles could not be dissolved in the nematic liquid crystal phase because of their poor solubility. Here, I show that appropriate surface functionalization can increase the otherwise low solubility of plasmonic nanoparticles in a nematic liquid crystal matrix. I also show that it is possible to reversibly modulate the polarized scattering of individual gold nanorods through an electric field induced phase transition of the liquid crystal. In this thesis, I also studied the motion of a molecular machine, commonly known as nanocars, over different solid surface. I show that individual nanocars, which consist of four carborane wheels attached to an aromatic backbone chassis, can move up to several micrometers over a glass surface at ambient temperature. Their movement is consistent with the rolling of the carborane wheels and can be controlled by tuning the interaction between the surface and the wheels.

This dissertation presents the results of interdisciplinary research, at the crossing of chemistry and physics. Rational design strategies have been developed towards the synthesis of novel molecular machines able to produce a mechanical output at the nanoscale. LT-UHV STM measurements have been performed to manipulate these molecules using electrical voltage pulses as input. Two classes of molecule with different properties have been chosen as core of the designs; azulene due to the high dipole moment when an appropriate substitution pattern is selected and DMBI (1,3 dimethyl 2 phenyl 2,3 dihydro 1 H benzoimidazol) because of the zwitterionic nature. One can assume that these two distinct key features might facilitate a distinct and controllable molecule response to the external electrical field of the STM tip.

Molecular machines are essential components of living organisms. They are highly efficient and robust, much more than their macroscopic analogs. This stimulated growing interest in construction of artificial molecular machines with a set of functions which may be controlled in a specific way. Such man-made molecular complexes are designed as the building blocks for future nanotechnological devices. During the last decades many new molecular machines have been synthesized and characterized by various experimental techniques. This significantly increased our knowledge about systems of such kind and their functioning. However, there are only a few real applications of molecular machines. This is because the fundamental principles of operation of such single-molecule systems are not well understood. Existing theoretical studies, although very helpful, are still very sparse. This is because the molecular machines are very complex systems, comprising up to thousands atoms. Thus the progress in our understanding of nanoscale materials is tightly related to development of efficient computational and theoretical methodologies. In this work we studied two large classes of molecular machines: surface-moving nanocars and molecular rotors/motors, working on the surfaces and in crystalline state. In particular we studied the role of the internal interactions of these machines as well as their interactions with the environment. This included the flexibility of the molecules, including the rotation of the nanocars' wheels, effects of surface and rotors symmetry, charge transfer effects as well as many other factors. We have found out relations which determine the properties of studied classes of molecular machines. The development of computational and theoretical methods was another essential part of this work. In particular we have developed a family of the surface-molecule interaction potentials, aimed to performing long time scale and molecular simulations of complex systems. We also developed a physics-based model of the charge transfer happening between metals and the nanocars. This opened new ways to control such molecular machines. We also developed a theoretical framework to predict response of molecular rotors on various types of driving. Finally, we developed new and improved existing rigid-body molecular dynamics methods and extensively used them in our studies of molecular machines. / Only volume 2 has been digitized.

Orientador: Douglas Soares Galvão / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin / Made available in DSpace on 2018-08-21T12:28:55Z (GMT). No. of bitstreams: 1 Flores_MarceloZimmerSampaio_D.pdf: 28191936 bytes, checksum: a826e249d2e059d0606b87a2936ae425 (MD5) Previous issue date: 2012 / Resumo: Simulações computacionais de sistemas atômico-moleculares despertam enorme interesse em grande parte por ajudar na interpretação de resultados obtidos experimentalmente, pois permitem o acesso de todos os estados estruturais, eletrônicos e dinâmicos, além de permitir estudo de sistemas modelo hipotéticos. É comum existirem dois extremos de complexidade quando se tenta resolver o problema de moléculas e sólidos. De um lado, pode-se optar por um tratamento puramente quântico, por outro, existe a possibilidade de buscar simplificar o problema através da incorporação dos efeitos eletrônicos por um campo de força e seguir com um tratamento clássico restrito às proximidades do equilíbrio. Na presente tese, serão empregadas técnicas abrangendo os dois casos supramencionados, com ênfase em simulações de primeiros princípios baseados em DFT (Density Functional Theory) e de campos de força clássicos com potencial reativo. O principal elemento de interesse é o carbono, que apresenta uma estrutura eletrônica que lhe confere bastante versatilidade para fazer ligações, através de hibridizações dos tipos sp, sp2 e sp3. Tais estados apresentam características eletrônicas peculiares e permitem a formação de uma grande quantidade de estruturas moleculares. Em busca de ajudar na compreensão de estruturas baseadas em cada um dos tipos de hibridização acima descritos, nesta tese são apresentados estudos que não só auxiliam a interpretação experimental, como também propõem estruturas hipotéticas, mas que apresentam viabilidade de síntese experimental. Dessa forma, a presente tese apresenta basicamente cinco trabalhos, a dizer: (i) formação do grafano através da incorporação de hidrogênio em folhas de grafeno (sp2 ?sp3); (ii) nanotubos de carbono de camadas simples (sp2), em busca de uma estrutura com seção reta transversal quadrada; (iii) criação de cadeias atômicas lineares através do estiramento de folhas de grafeno (sp2 ?sp); (iv) receptores moleculares, em que é analisada a dinâmica de incorporação de fulereno (C60) ao chamado buckycatcher (sp2); por fim, (v) simulações em moléculas funcionais conhecidas como nanocarros (sp2 e sp3) / Abstract: Computer simulations for atomic and molecular systems play an important role in interpreting experimental results, because they can easily access simultaneously structural, electronic and dynamic states that are experimentally inaccessible. Additionally, simulations can be used to foresee the existence of hipothetic molecular structures. It is often usual to have to deal between two opposites on electronic strucutre approximations when dealing with molecular structures. In one hand, one can apply pure quantum methods, on the other hand on may adopt a more simplified problem by applying classical force fields when dealing with near-to-equilibrium systems. In the present thesis, most of the aforementioned range of simulation techniques will be covered, with emphasis on ab initio simulations based on the density functional theory (DFT) and classical reactive force fields. Carbon is the element that plays a central role in this work, mainly due to its versatile electronic structure which gives it the ability to perform several bond types based on sp, sp2 and sp3hybridization types. Such states present singular electronic features allowing the formation of a myriad of molecular systems. The present thesis presents several studies that have the privilege of being part of both as a helpful guidance on experimental interpretation and the suggestion of hypothetic carbon-based molecular structures. This way, the following research is presented: (i) graphane formation via hydrogen incoporation on graphene sheets (sp2 ?sp3); (ii) single wall carbon nanotubes (sp2) and its yet to be experimentally achieved square cross section representative; (iii) linear atomic chain formation obtained by graphene sheets stretching (sp2 ?sp); (iv) molecular receptors, where the dynamics of fullerene (C60) incoporation on the so-called buckycatcher is analysed (sp2); (v) simulation on functional molecules named nanocars (sp2 and sp3) / Doutorado / Física / Doutor em Ciências