This thesis presents the first-principles studies of materials properties within the framework of the density functional theory (DFT). The thesis constitutes three main parts, i. e., pressure-induced phase transitions in solids, data-storage and clean-energy materials. The first part focuses on the predictions of crystal structures and the determinations of electronic properties of Xe-H2, FeB4 and Co3O4. Pressurizing Xe-H2 compound yields the formation of H-rich Xe(H2)8, which can exhibit a metallic feature at comparatively lower pressure than pure hydrogen. Hard superconducting FeB4 gets transformed into a novel transparent phase under pressure owing to the enhanced overlap of atomic cores. Spinel Co3O4 undergoes the phase transition from a cubic to a monoclinic because of the charge transfer between cations via the increased 3d-3d interactions. The second part involves the study of structural and electronic properties of phase-change memory materials (PCMs), i. e., Ge2Sb2Te5 (GST) and Ga-doped In2O3. Van der Waals (vdW) interaction must be considered to obtain accurate crystal structure of layered GST. For Ga-doped In2O3 (GIO), the local structure of amorphous GIO is found to resemble that of amorphous In2O3, except the vicinity of doping atoms. The electronic property of a-GIO is metallic, which considerably differs from the semiconducting feature of the crystalline GIO. This emphasizes the contrast in the conductivity of the crystalline and amorphous upon phase switching of GIO. The third part associates with the search for clean-energy materials, viz., hydrogen production, hydrogen storage and green Mg-ion batteries. For hydrogen production, the role of intrinsic point defects to water adsorption on ZnO(10-10) surface is investigated. The findings show that the Zn and O defect-sites are energetically not favorable for the water adsorption and dissociation. For the purpose of storing hydrogen in a solid phase, silicene, doped by alkaline and alkaline earth metals, is investigated. We find that Li-doped and Na-doped silicene can attain the superior storage capacity. For cathode material of Mg-ion batteries, Mg2Mo6S8, the diffusivity of Mg ions occurs through an available channel in the bulk with the onset temperature of 200 K.

O desafio de encontrar corretamente genes eucarioticos codificadores de proteinas nas sequencias genomicas e um problema em aberto. Neste trabalho, implementamos uma plata- forma, com o objetivo de melhorar a forma com que preditores de genes sao implementados e avaliados. Tres novas ferramentas foram implementadas: ToPS (Toolkit of Probabilistic Models of Sequences) foi o primeiro arcabouco orientado a objetos que fornece ferramentas para implementacao, manipulacao, e combinacao de modelos probabilisticos para representar sequencias de simbolos; MYOP (Make Your Own Predictor) e um sistema que tem como objetivo facilitar a construcao de preditores de genes; e SGEval utiliza grafos de splicing para comparar diferente anotacoes com eventos de splicing alternativos. Utilizamos nossas ferramentas para o desenvolvimentos de preditores de genes em onze genomas distintos: A. thaliana, C. elegans, Z. mays, P. falciparum, D. melanogaster, D. rerio, M. musculus, R. norvegicus, O. sativa, G. max e H. sapiens. Com esse desenvolvimento, estabelecemos um protocolo para implementacao de novos preditores. Alem disso, utilizando a nossa plata- forma, desenvolvemos um fluxo de trabalho para predicao de genes no projeto do genoma da cana de acucar, que ja foi utilizado em 109 sequencias de BAC geradas pelo BIOEN (FAPESP Bioenergy Program). / The challenge of correctly identify eukaryotic protein-coding genes in the genomic se- quences is an open problem. In this work, we implemented a plataform with the aim of improving the way that gene predictors are implemented and evaluated. ToPS (Toolkit of Probabilistic Models of Sequence) was the first object-oriented framework that provides tools for implementation, manipulation, and combination of probabilistic models that represent sequences of symbols. MYOP (Make Your Own Predictor) facilitates the construction of gene predictors. SGEval (Splicing Graph Evaluation) uses splicing graphs to compare dif- ferent annotations with alternative splicing events. We used our plataform to develop gene finders in eleven distinct genomes: A. thaliana, C. elegans, Z. mays, P. falciparum, D. me- lanogaster, D. rerio, M. musculus, R. norvegicus, O. sativa, G. max e H. sapiens. With this development, we established a protocol for implementing new gene predictors. In addi- tion, using our platform, we developed a pipeline to find genes in the 109 sugarcane BAC sequences produced by BIOEN (FAPESP Bioenergy Program).

Au cours de cette thèse, nous avons étudiés théoriquement les propriétés structurelles et électroniques des super-réseaux d'oxyde de manganèse en structure perovskiteö au moyen de calculs ab initio.Les oxydes de manganèse au lanthane, donnés avec la formule générique La(1-x)A(x)MnO(3) (LAMO) (A un élément divalent), constituent une classe importante d'oxydes de manganèse en raison de leurs diverses propriétés, telles que l'effet de magnétorésistance colossale, leur riche diagramme de phase en fonction du dopage, de la température ou de champs externes, et leur grande température Curie. Ces propriétés peuvent être exploitées dans de nombreuses applications technologiques potentielles telles que les valves de spin ou les injecteurs de spin. Le contrôle des propriétés de ces matériaux peut se faire par dépôt sous forme de films minces ou comme blocs de construction dans des super-réseaux. Lorsque x = 1/3, le La(1-x)A(x)MnO(3) massif est ferromagnétique et métallique grâce au mécanisme de double échange dans la electrons 3d de Mn. Lorsque Mn est dans un état de valence mixte, les orbitales eg (dx2-y2 and dz2) sont partiellement occupées et peuvent se délocaliser sur les atomes de Mn voisins, seulement si ceux-ci sont alignés ferromagnétiquement. Dans des films très minces, puisque la direction perpendiculaire au substrat, c, n'a que quelques cellules unitaires d'épaisseur, seules les interactions dans le plan (ab) sont importantes pour les propriétés thermodynamiques. En agissant sur la géométrie de la couche LAMO, on peut ainsi maximiser l'occupation de l'orbitales dx2-y2 et augmenter l'échange magnétique et la température Curie associée.Notre but était donc de concevoir de nouveaux matériaux avec un ordre orbital 3d spécifique afin d'assurer les propriétés magnétiques souhaitées.Dans cette thèse, nous avons travaillé sur deux types de super-réseaux. Le premier était constitué de deux oxydes de manganèse antiferromagnétiques, non dopés, LaMnO(3) et SrMnO(3), c'est-à-dire des super-réseaux [LaMnO(3)]n/[SrMnO(3)]m. Nous avons étudié l'état fondamental magnétique pour différentes valeurs n et m afin d'expliquer les résultats expérimentaux surprenants. Le deuxième type de super-réseaux que nous avons étudiés est composé de couches métalliques LAMO en alternance avec des couches isolantes. En effet, les super-réseaux avec des interfaces métal-isolant ont un grand potentiel dans les applications de valves de spin. Ainsi, nous avons d'abord considéré des super-réseaux entre composés ferromagnétiques-métalliques et ferroélectriques-isolantes [LAMO](3)/[BTiO(3)](3) (A = Sr ou Ba, B = Ba ou Pb). Dans ces super-réseaux, les propriétés magnétiques sont malheuresement réduites en raison de la délocalisation d'électrons dz2 à l'interface entre Mn et Ti. Dans de tels super-réseaux , nous avons clarifié le rôle de la polarisation des couches ferroélectriques et le rôle des mouvements antiferrodistortifs dans les couches de manganite. Enfin, de manierè à 'éviter que la délocalisation ait lieu à l'interface, nous avons conçu un autre super-réseau avec interface métal-isolant dans lequel nous avons remplacé l'isolant (BTiO(3)) par un oxyde simple (BO): [LAMO]n/[BO]p superlattices (A = Sr ou Ba, B = Ba, Sr ou Mg et n = 3 ou 6, p = 6 ou 2). Dans ces nouveaux super-réseaux, nous avons réussi à promouvoir les occupations des orbitales dx2-y2 dans les interfaces assurant un fort moment magnetique à l'interface et a priori une fort temperature de Curie. Nous avons également montré une faible corrélation entre la conductivité électrique et l'ordre orbitaire. / This thesis theoretically studies structural and electronic properties of perovskite manganese oxide superlattices by means of ab-initio calculations.Lanthanum manganese oxides, given with the generic formula La1−xAxMnO3 (LAMO) (A a divalent element), are an important class of perovskite manganese oxides due to their various exotic properties, such as giant and colossal magnetoresistance effect, rich phase diagrams with respect to doping, temperature or external fields, and intinsic large Curie temperature. These properties can be exploited in many potential technological applications such as spin valves or spin injectors. Controlling the properties of these materials can be done through deposition as thin films or as building blocks in superlattices. When x = 1/3, bulk La1−xAxMnO3 is ferromagnetic and metallic due to the double-exchange mechanism in the Mn 3d shell. When Mn is in a mixed valence state, the eg orbitals (dx2-y2 and dz2) are partially occupied, and can delocalize on neighboring Mn atoms only if the latter are ferromagnetically aligned. In very thin films, since the direction perpendicular to the substrate, c, is only a few unit cell thick, only in-plane (ab) interactions are important for the thermodynamic properties. By acting on the LAMO layer geometry, one can thus maximize the dx2-y2 occupancy and increase the magnetic exchange and related Curie temperature.Our aim was thus to design new materials with desired 3d orbital order so that to ensure desired magnetic properties.In this thesis, we worked on two types of superlattices. The first one was made of two undoped antiferromagnetic manganese oxides LaMnO3 and SrMnO3, i.e. [LaMnO3]n/[SrMnO3]m superlattices. We investigated the magnetic ground state for different n and m values in order to explain suprising experimental results. The second type of superlattices is composed of metallic LAMO layers with alternated insulating layers. Indeed, the superlattices with metal-insulator interfaces have a great potential in spin valves applications. Thus, we first considered the ferromagnetic-metallic/ferroelectric-insulating [LAMO]3/[BTiO3]3 superlattices (A= Sr or Ba, B=Ba or Pb) where the magnetic properties are reduced due to delocalization of dz2 electrons at the interface from Mn to Ti. In such superlattices, we clarified the role of the polarization of the ferroelectric layers and the role of the antiferrodistortive motions in the manganite layers. In order to prevent the delocalization taking place at the interface, we designed another superlattice with metallic-insulator interface where we replaced the insulator (BTiO3) with a simple oxide (BO); that is [LAMO]n/[BO]p superlattices (A= Sr or Ba, B=Ba, Sr or Mg and n=3 or 6, p=6 or 2). Within this new superlattice, we successully managed to promote dx2-y2 orbital occupancies at the interfaces which ensures a large magnetic moment at the interfaces and an expected large Curie temperature. We also showed the weak correlation between electrical conductivity and orbital ordering.

Interactions between (bio)molecules, ions and solid surfaces play crucial role in many biological processes as well as in many scientific applications and understanding of this phenomenon on molecular level is a challenging task for today science. Computer simulations can provide detailed view on atomic level if carefully prepared and evaluated models are used. In this thesis, interactions of several types of (bio)molecules with inorganic surfaces are studied by classical and ab initio molecular dynamics. Chemisorbed biomolecules, namely DNA and oligopeptide, covalently attached to graphene and mercury surface, respectively, were studied to make link with DNA chip design and experimental label-free electrochemical measurements, respectively. Quartz (101) surface model applicable to wide range of pH conditions was developed and evaluated against experimental X-ray data. Physisorption of the nucleobases on quartz (101) surface and oxalate dianion on rutile (110) was examined and discussed.

Esta tese tem como objetivo central a descrição teórica rigorosa da estrutura, de propriedades e da espectroscopia de alguns sistemas diatômicos. Como abordagem de cálculo ela se serve da metodologia interação de configurações na sua forma conhecida como excitações simples e duplas a partir de um conjunto de múltiplas referências (MRSD-CI), além de conjuntos base relativamente extensos de funções Gaussianas Cartesianas contraídas. Ela propõe a existência de duas novas espécies moleculares, BeC e BeC+, para as quais um total de 20 estados eletrônicos (13 para o BeC e 7 para o BeC+) foram caracterizados através de suas curvas de potencial e de seus respectivos estados vibro-rotacionais. Constantes espectroscópicas para cada estado foram calculadas e os momentos elétricos das transições eletrônicas mais relevantes foram também estudados. Essas transições foram analisadas tanto em termos de probabilidades de transição calculadas via momento de transição como por meio de fatores de Franck-Condon. Transições vibro-rotacionais dentro de um mesmo estado eletrônico foram ainda examinadas. Para esses vários estados, tempos de vida radiativa foram também calculados. Complementando essa descrição espectroscópica, uma discussão sobre a natureza da ligação química nesses sistemas foi ainda apresentada. Conjugando os resultados obtidos para essas duas espécies, o espectro fotoeletrônico da molécula BeC foi simulado servindo-se da aproximação de Franck-Condon para estimar as intensidades das linhas de cada banda. Além de propriedades eletrônicas como o momento de dipolo, cálculos de gradiente de campo elétrico no átomo de berílio em função da distância internuclear foram também realizados com o propósito de fornecer dados teóricos confiáveis que permitam a determinação experimental do momento quadrupolar do núcleo de 9Be sobre o qual existe certa controvérsia na literatura. Tais cálculos, realizados para os sitemas BeH+ e BeC, além de incluirem o efeito da vibração molecular no gradiente de campo elétrico na forma de uma média vibracional, mostraram que a aproximação de Buckingham usada por alguns grupos não é apropriada para descrever tal efeito. / The aim of this thesis is to describe theoretically the structure, properties, and the spectroscopy of some diatomic species using the multirefence single and double excitations configuration interaction approach, and an extensive atomic basis set of contracted Cartesian Gaussian orbitals. Two new diatomic species are proposed, BeC and BeC+, for which twenty electronic states have been characterized (13 for BeC, and 7 for BeC+) by means of their potential energy curves and vibro-rotational states. Spectroscopic constants for both of them have been computed, as well as electric moments of the most relevant electronic transitions. The transitions have been described by using either transitions probabilities computed with the aid of the theoretical transition moment functions, or by Franck-Condon factors. Vibro-rotational transitions within the same electronic state have also been described. Radiative lifetimes have been computed for several states. Complementing the spectroscopic description, a descussion on the nature of the chemical bonding has also been presented. A combination of the results for the neutral and ionic species allowed the calculation of the vertical and adiabatic ionization potentials and the Franck-Condon distribution spectrum for transitions from the ground state of BeC to selected bound states of BeC+. Besides the electronic properties, as dipole moment, the electric field gradient at the 9Be nucleus has also been computed as a function of the internuclear distance with the purpose of providing reliable theoretical results to help in the spectroscopic determination of the nuclear quadrupole moment of 9Be, since the data reported to date do not seem to be so conclusive. This kind of analysis has been carried out for the species BeH+ and BeC. By taking into account the nuclear motion effects on the electric field gradient as an average over the vibrational wavefunction, it was possible to show that the commom practice of using the Buckingham\'s expression to compute such correction is not recornrnended.

L'avenir de la spintronique repose sur le développement de matériaux ayant des propriétés magnétiques remarquables. L'objectif de cette thèse est de comprendre la physique des deux matériaux fonctionnels proposés pour des applications spintroniques qui utilisent des simulations de la densité fonctionnelle.Nous nous sommes intéressés dans une première partie au ferrite de gallium pour lequel il a été montré que les propriétés dépendaient de la concentration de fer.Les spectres optiques ont été calculés et comparés aux spectres expérimentaux suggérant des niveaux élevés de désordre. Dans la deuxième partie, nous avons montré une polarisation de spin à l’interface hybride formée entre la phthalocyanine de manganèse et la surface de cobalt,en accord avec les expériences de photoémission.La formation de la spinterface a été expliquée par différents mécanismes d'hybridation dans chaque canal de spin.Cette polarisation de spin est coordonnée avec des moments magnétiques induits sur les sites moléculaires. / The future of the spintronics technology requires developing functional materials with remarkable magnetic properties. The aim of this thesis is to understand the physics of functional materials proposed for spintronic applications using ab-initio density functional simulations. We investigated the properties of two different functional materials. We first studied the magnetoelectric gallium ferrite GFO. The dependence of the different properties on the iron concentration has been demonstrated and discussed. The optical spectra were calculated and compared to the experimental once suggesting high levels of iron disorder. In the second part, we demonstrated a highly spin polarized hybrid interface formed between manganese phthalocyanine and cobalt surface in agreement with photoemission experiments. The formation of this spinterface was described by different hybridization mechanisms in each spin channel. This high spin polarization is coordinated with induced magnetic moments on the molecular sites.

Desde sua descoberta por S. Iijima em 1991, os nanotubos de carbono têm sido considerados um dos materiais nanoestruturados mais promissores para o desenvolvimento de novos dispositivos eletrônicos em escala nanoscópica. Devido _a sua alta razão entre a área superficial e o volume, esse material se destaca para aplicações como sensores de gás. No presente trabalho, estudamos através de simulações computacionais, a possibilidade de nanotubos de carbono com defeitos de nitrogênio (os chamados nanotubos CNx), poderem ser usados como sensores de moléculas gasosas. Na primeira parte do trabalho foram realizados cálculos de estrutura eletrônica baseados na Teoria do Funcional da Densidade (DFT) para diferentes sistemas formados pelo nanotubo e pela molécula. Através de cálculos de energia de ligação, foi possível identificar quais gases poderiam ou não serem adsorvidos à superfície do nanotubo. Dentre as moléculas investigadas, o monóxido de carbono e a amônia mostraram ser as mais facilmente adsorvidas ao nanotubo. Na segunda parte, foram realizados cálculos das propriedades de transporte utilizando o formalismo das funções de Green fora do equilíbrio (NEGF) recursivo. Foi possível concluir que os nanotubos estudados poderiam ser usados para detectar o monóxido de carbono e a amônia. Todavia, em relação à seletividade, os resultados indicaram que não parece possível distinguir essas duas moléculas, caso o sistema fosse inserido em um ambiente contendo uma mistura desses gases. Ainda, foram feitas simulações de nanotubos contendo defeitos aleatoriamente distribuídos, de forma a levar em conta os fatores de desordem característicos de sistemas mais realistas. / Since their discovery by S. Iijima in 1991, carbon nanotubes have been considered as one of the most promising nanostructured materials for the development of new nanoscopic electronic devices. Due to its high surface area to volume ratio, this material stands out as a candidate for possible gas sensoring applications. In this thesis, we have studied, by means of computational simulations, the possibility of using carbon nanotubes containing nitrogen defects (the so-called CNx nanotubes) as gas sensors. In the first part, we have performed electronic structure calculations based on Density Functional Theory (DFT) of several systems to address the possible binding of different molecules to the nanotube surface. Our results indicate that, among the molecules which were investigated, carbon monoxide and ammonia adsorb more easily to the nanotube surface. In the second part of this thesis, we have performed calculations of the transport properties by means of non-equilibrium Green\'s function formalism (NEGF). The results have shown that the nitrogen-defect carbon nanotubes could be used to detect, mainly carbon monoxide and ammonia molecules. On the other hand, when dealing with the selectivity of this system, it seems to be not possible to distinguish these gases, in the case of inserting the system in a environment containing a mixture of these molecules. Finally, we have simulated carbon nanotubes with defects randomly distributed along its length, in order to take into account disordering factors usually found in more realistic nanosensors.

Made available in DSpace on 2018-06-27T18:56:30Z (GMT). No. of bitstreams: 2 IURI MEDEIROS JAURIS.pdf: 4071837 bytes, checksum: b9c544072425b0250b8e12d9d9d75d46 (MD5) IURI MEDEIROS JAURIS.pdf.jpg: 3247 bytes, checksum: ed81fc9566ff5a1c9f12acc57ec7b3a5 (MD5) Previous issue date: 2012-08-31 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Dyes are organic compounds used to color or bring shine to other substances, being widely used by the cosmetic industries, pulp, textiles, and many others. However, the complex aromatic structure of these compounds makes them highly stable. In addition, some types of dyes could be toxic to humans or even carcinogenic. Thus, treatment of effluent water contaminated with these dyes is mandatory. Fortunately some recent studies have reported the ability of Carbon Nanotubes (CNTs) to act as adsorbent material for treating aqueous effluents contaminated with dyes. Nevertheless, to the best of our knowledge, so far, none theoretical study focusing mainly in the interaction of CNTs and dyes is available. From this perspective, in this work we have used ab initio simulations based on the densityfunctional theory and implemented on the SIESTA code to evaluate the interaction of tree dyes (Acridine Orange, Alizarin Red S, Methylene blue) and the Anthracene molecule with the pristine (5,5), (8,0) Single Wall Carbon Nanotubes (SWCNTs). Also we have investigate the interaction of those molecules with the pristine (5,5), (8,0) 1-vacancy-SWCNTs. Moreover, to appraise the effects in dye-SWCNT interaction due to SWCNT diameter, we compared the configurations dyes-pristine SWCNTs (5,5); (8,0) with dyes-pristine SWCNTs (16,0); (25,0). Our results show that, in general, the main configurations exhibit an average binding energy around (0.75 eV ≈ 72.36 kJ / mol), characteristic of physical adsorption. This feature could facilitate the eliminations of these dyes after being adsorbed by SWCNTs, enabling the reuse of SWCNTs. Also, the SWCNTs with vacancy have binding energies lower than the CNTs without vacancy, except to the case of methylene blue-SWCNTs. Further, the dyes SWCNTs (5,5) present binding energy greater than dyes SWCNTs (8,0). In most, was not found significant change in molecular structure and electronic character of SWCNTs. Furthermore, dyes-pristine SWCNTs (5,5) and (8,0) present lower binding energy in comparison with dyes-pristine SWCNTs (16,0) and (25,0). / Corantes são compostos orgânicos utilizados para dar cor e/ou conferir brilho a outras substâncias, sendo amplamente empregados nas indústrias de cosméticos, celulose, têxteis, alimentos dentre outros. No entanto, o complexo aromático presente na estrutura destes compostos torna-os altamente estáveis. Além disso, alguns tipos de corantes podem ser tóxicos ou até mesmo carcinogênicos, assim, o tratamento de efluentes aquáticos contaminados por tais compostos é imprescindível. Para tanto, alguns estudos recentes têm relatado a capacidade dos nanotubos de carbono (NTCs) de atuarem como material adsorvente para o tratamento de efluentes aquosos contaminados com tais corantes. Todavia, até o momento, não foi reportado na literatura nenhum estudo teórico com enfoque principalmente na interação entre os nanotubos de carbono e os corantes. Desse modo, a partir desta perspectiva, para avaliar a interação dos corantes: laranja de acridina (LA), vermelho de alizarina S (VAS) e azul de metileno (AM), bem como a molécula de antraceno (AN), com os nanotubos de carbono de parede simples, NTCPS (5,5), (8,0), puros, fez-se uso de cálculos ab initio, baseados na teoria do funcional da densidade, e implementados pelo código SIESTA. Além disso, também se investigou a interação destes corantes com os NTCPS (5,5), (8,0) com uma vacância. Da mesma forma, estudou-se a interação dos NTCPS (16,0) e (25,0) com os corantes LA, VAS e AM, além da molécula de AM, a fim de avaliar a influência do diâmetro dos nanotubos de carbono na interação com tais corantes. Nossos resultados mostram que as configurações principais exibem energia de ligação média em torno de (0,75 eV ≈ 72,36 kJ / mol), características de processos de adsorção física. Energias dessa ordem podem facilitar a dessorção destes corantes, permitindo, assim, a reutilização dos NTCPS. Além disso, na interação corantes-NTCPS, para a maioria das configurações, os NTCPS com uma vacância apresentaram energias de ligação menores do que os NTCPS sem vacância, e os NTCPS (5,5) apresentaram energia de ligação maior do que para os NTCPS (8,0). Mais ainda, não foram encontradas alterações significativas na estrutura molecular e caráter eletrônico dos NTCPS (5,5) e (8,0). Por fim, ressalta-se que, para todas as configurações, a interação corante-NTCPS (8,0) apresentou energia de ligação menor do que a interação corante-NTCPS (16,0) e corante-NTCPS (25,0).

Submitted by MARCIA ROVADOSCHI (marciar@unifra.br) on 2018-08-20T12:07:07Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Tese_MirkosOrtizMartins.pdf: 14740958 bytes, checksum: 7fbd6b5923fb58ef079c134775d7e50d (MD5) / Made available in DSpace on 2018-08-20T12:07:07Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Tese_MirkosOrtizMartins.pdf: 14740958 bytes, checksum: 7fbd6b5923fb58ef079c134775d7e50d (MD5) Previous issue date: 2016-07-22 / In this thesis is studied the interaction between the nitrogenous bases, adenine, cytosine, guanine and thymine with two nanostructures: the graphene and silicene nanoribbons through ab initio calculations based on DFT (Density Functional Theory) using the SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) software. Prior to implementing the software to simulate the behavior at the atomic level of molecules all feature and variants was studied, for computer modeling and simulation; which applications using nanostructures and the best spatial con guration for construction of an initial parameter simulation. The nitrogenous bases as main constitution of the genetic code component, in the form of a double trainer strand of DNA, is the point of interest of this work, along with their behavior when the interaction, by positioning the walking distance - with nanoribbons graphene and silicene. The simulation of the nitrogenous bases and nanoribbons initially obey perpendicular position with the atoms of forming hydrogen bonds in DNA, pointing to the nanostructures. It was calculated, at the end of the simulations, the removal of nitrogenous bases of its current initial position, the di erence in the values of total energy and charge transfer. It has been shown that the interaction energy between nitrogenous bases and graphene nanoribbon are thinner than those found for the interaction with the silicene nanoribbon. When the nitrogenous bases are placed parallel to nanoribbons (both of graphene as silicene) they present chemical bonds, while when they are arranged perpendicularly to the surface of the material, they deviate in the course of its transverse path. It also follows that the silicene nanoribbon is more stable in the adsorption energy than nanoribbon graphene and the interaction of the bases is the energy bands that change xiii subtly, with respect of the gap values. For the graphene nanoribbon, the changes are associated with the position of the Fermi level. These results show, in an original way, di erent con gurations for the nitrogeneous basis on one dimensional carbon and silicon materials. / Nessa tese e estudada a intera c~ao entre as bases nitrogenadas, adenina, citosina, guanina e timina, com duas nanoestruturas: a nano ta de grafeno e a nano ta de siliceno, atrav es de c alculos ab initio baseados na Teoria do Funcional da Densidade (DFT), utilizando o software SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms), esse programa computacional executa c alculos de estrutura eletr^onica e simula c~oes ab initio de din^amica molecular de mol eculas e s olidos. Anterior a execu c~ao do software para simular o comportamento a n vel at^omico das mol eculas, foi estudada a caracter stica e variantes, para modelagem e simula c~ao computacional; quais as aplica c~oes utilizando nanoestruturas e a melhor con gura c~ao espacial para constru c~ao de um par^ametro inicial de simula c~ao. As bases nitrogenadas, sendo componente principal da constitui c~ao do c odigo gen etico, na forma de um duplo lamento formador do DNA (Deoxyribonucleic acid - Acido Desoxiribonucleico), e o ponto de interesse deste trabalho, juntamente com seu comportamento quando na intera c~ao, atrav es do posicionamento a pouca dist^ancia - com as nano tas de grafeno e siliceno. A simula c~ao entre as bases nitrogenadas e as nano tas inicialmente obedecem um posicionamento perpendicular com os atomos formadores das liga c~oes de hidrog^enio, no DNA, apontando para as nanoestruturas. Foi calculado, ao nal das simula c~oes, o afastamento das bases nitrogenadas da sua posi c~ao atual, a diferencia c~ao nos valores de energia total e a respectiva transfer^encia de carga. Foi demonstrado que a energia de adsor c~ao entre as bases nitrogenadas e a nano ta de grafeno s~ao mais t^enues do que aquelas encontradas para a intera c~ao com a nano ta de siliceno. Quando as bases nitrogenadas s~ao colocadas paralelas as nano tas (tanto de grafeno quanto de siliceno) elas fazem liga c~oes qu micas, enquanto se forem dispostas perpendicularmente a superf cie do material, as mesmas se xi afastam no decorrer de seu trajeto transversal. Tamb em se conclui que a nano ta de siliceno e mais est avel no sentido de energia de adsor c~ao do que a nano ta de grafeno e a intera c~ao das bases faz as bandas de energia dessa, alterar de forma sutil, via mudan ca no gap de energia. No caso da adsor c~ao na nano ta de grafeno observam-se altera c~oes na posi c~ao do n vel de Fermi, sem mudan cas nas caracter sticas met alicas do sistema original. Desta forma, este trabalho apresenta, de forma original, diferentes con gura c~oes para a intera c~ao de bases nitrogenadas em sistemas unidimensionais de carbono e sil cio, com aplica c~ao para a detec c~ao individual das bases nitrogenadas formadoras da mol ecula de DNA.

Este projeto tem dois objetivos. Primeiramente estudou-se a aplicabilidade dos splines tricúbicos para a construção de superfícies de energia potencial globais. Um dos obstáculos que este método tem de superar e a escolha de um sistema de coordenadas apropriado, que minimize a influência de pontos não físicos. Para isto, propôs-se o uso do sistema de coordenadas de Pekeris, nunca usado para este fim. Este procedimento foi realizado para três sistemas químicos bem descritos na literatura, [Cl,H2], [F,H,D] e [H,O,Cl], cujas superfícies de energia potencial e propriedades das reações foram usadas como referência. Com base nestes modelos, aplicamos o método proposto variando-se a quantidade e a disposição dos nós das interpolações, a fim de verificar sua influência na qualidade das superfícies interpoladas. Os resultados mostram que as superfícies construídas por este método reproduzem muito bem os cálculos de dinâmica química, tanto por métodos quânticos quanto por métodos clássicos. Para isto, os nós da interpolação devem cobrir as regiões mais importantes da superfície de energia potencial e os valores mais baixos das coordenadas de Pekeris devem ser priorizados. O segundo objetivo consiste na aplicação deste procedimento na construção da superfície de energia potencial [H,S,F]. Com esta superfície, diversas características deste sistema foram analisadas, tais como geometrias dos pontos estacionários, energias relativas e frequências vibracionais. Os valores obtidos estão de acordo com os dados descritos na literatura. A superfície construída também foi usada para a realização de cálculos de dinâmica para a reação F+HS → S+FH. Observamos a existência de dois tipos de mecanismos, um com a formação de um intermediário de longa duração e outro com a abstração direta do átomo de hidrogênio. / This project has two goals. First, we studied the applicability of the tricubic splines to construct global potential energy surfaces. One of the diculties this approach has to overcome is the choice of an appropriate coordinate system that minimises the in uence of non-physical points. For such, we proposed the use of the Pekeris coordinate system, never employed for this purpose. This procedure was carried out for three well described systems, [Cl,H2], [F,H,D] and [H,O,Cl], whose potential energy surfaces and reaction properties were taken as references. Based on these models, we applied the proposed method varying the amount and arrangement of the interpolation knots, to verify their influence on the quality of the interpolated surfaces. The results showed that surfaces constructed by this approach reproduce very well the chemical dynamics calculations, both for the quantum as well as for the classical methods, provided that the interpolation knots cover the most important regions of the potential energy surfaces, and the lower values of the Pekeris coordinates are prioritised. The second goal was the application of this procedure to the construction of the [H,S,F] potential energy surface. With this surface, several characteristics of this system were analysed, such as the geometry of the stationary points, relative energies and vibrational frequencies. The values obtained are in agreement with the data described in the literature. The constructed surface was also used for quantum dynamics calculations on the reaction F + HS → S + FH. We observed two kinds of mechanisms, one of them with the formation of a long-living intermediate and the other with the direct abstraction of the hydrogen atom.