Nanometer-scale silicon shows extraordinary electronic and optical properties that are not available for bulk silicon, and many investigations toward applications in optoelectronic devices are being pursued. Silicon nanoparticle films made from solution are a promising candidate for low-cost solar cells. However, controlling the properties of silicon nanoparticles is quite a challenge, in particular shape and size distribution, which effect device performance. At present, none of the solar cells made from silicon nanoparticle films have an efficiency exceeding the efficiency of those based on crystalline silicon. To address the challenge of controlling silicon nanoparticle properties, both theoretical and experimental investigations are needed. In this thesis, we investigate silicon nanoparticle properties via quantum mechanical modeling of silicon nanoparticles and synthesis of silicon nanoparticle films via colloidal grinding. Silicon nanoparticles with shapes including cubic, rectangular, ellipsoidal and flat disk are modeled using semi-empirical methods and configuration interaction. Their electronic properties with different surface passivation were also studied. The results showed that silicon nanoparticles with hydrogen passivation have higher HOMOLUMO gaps, and also the HOMO-LUMO gap depends on the size and the shape of the particle. In contrast, silicon nanoparticles with oxygen passivation have a lower HOMO-LUMO gap. Raman spectroscopy calculation of silicon nanoparticles show peak shift and asymmetric broadening similar to what has been observed in experiment. Silicon nanoparticle synthesis via colloidal grinding was demonstrated as a straightforward and inexpensive approach for thin film solar cells. Data analysis of silicon particles via SEM images demonstrated that colloidal grinding is effective in reducing the Si particle size to sub-micron in a short grinding time. Further increases in grinding time, followed by filtration demonstrated a narrowing of the Si particle size and size-distribution to an average size of 70 nm. Raman spectroscopy and EDS data demonstrated that the Si nanoparticles contain oxygen due to exposure to air during grinding. I-V characterization of the milled Si nanoparticles showed an ohmic behaviour with low current at low biases then Schottky diode behaviour or a symmetric curve at large biases. / Graduate / 0794 / 0544 / zahraalbu@hotmail.com

Nanometer-scale silicon shows extraordinary electronic and optical properties that are not available for bulk silicon, and many investigations toward applications in optoelectronic devices are being pursued. Silicon nanoparticle films made from solution are a promising candidate for low-cost solar cells. However, controlling the properties of silicon nanoparticles is quite a challenge, in particular shape and size distribution, which effect device performance. At present, none of the solar cells made from silicon nanoparticle films have an efficiency exceeding the efficiency of those based on crystalline silicon. To address the challenge of controlling silicon nanoparticle properties, both theoretical and experimental investigations are needed. In this thesis, we investigate silicon nanoparticle properties via quantum mechanical modeling of silicon nanoparticles and synthesis of silicon nanoparticle films via colloidal grinding. Silicon nanoparticles with shapes including cubic, rectangular, ellipsoidal and flat disk are modeled using semi-empirical methods and configuration interaction. Their electronic properties with different surface passivation were also studied. The results showed that silicon nanoparticles with hydrogen passivation have higher HOMOLUMO gaps, and also the HOMO-LUMO gap depends on the size and the shape of the particle. In contrast, silicon nanoparticles with oxygen passivation have a lower HOMO-LUMO gap. Raman spectroscopy calculation of silicon nanoparticles show peak shift and asymmetric broadening similar to what has been observed in experiment. Silicon nanoparticle synthesis via colloidal grinding was demonstrated as a straightforward and inexpensive approach for thin film solar cells. Data analysis of silicon particles via SEM images demonstrated that colloidal grinding is effective in reducing the Si particle size to sub-micron in a short grinding time. Further increases in grinding time, followed by filtration demonstrated a narrowing of the Si particle size and size-distribution to an average size of 70 nm. Raman spectroscopy and EDS data demonstrated that the Si nanoparticles contain oxygen due to exposure to air during grinding. I-V characterization of the milled Si nanoparticles showed an ohmic behaviour with low current at low biases then Schottky diode behaviour or a symmetric curve at large biases. / Graduate / 0794 / 0544 / zahraalbu@hotmail.com

Submitted by Nelson Bretanha (physikosmos@gmail.com) on 2016-01-01T12:55:20Z No. of bitstreams: 1 Métodos Semi-Empíricos (Princípios Básicos e Aplicações).pdf: 4755970 bytes, checksum: 0e2d74ff6ffd8de112da824ec714d84e (MD5) / Approved for entry into archive by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br) on 2016-01-05T18:04:11Z (GMT) No. of bitstreams: 1 bretanhaneto_ne_me_rcla.pdf: 4755970 bytes, checksum: 0e2d74ff6ffd8de112da824ec714d84e (MD5) / Made available in DSpace on 2016-01-05T18:04:11Z (GMT). No. of bitstreams: 1 bretanhaneto_ne_me_rcla.pdf: 4755970 bytes, checksum: 0e2d74ff6ffd8de112da824ec714d84e (MD5) Previous issue date: 2015-12-18 / Neste trabalho investigamos os efeitos decorrentes da presença de heteroátomos numa folha de “supercoroneno” (molécula C58H18 utilizada como uma primeira aproximação para o grafeno). Mais especificamente, utilizando método semi-empírico PM6, implementado no pacote computacional MOPAC2012®, estudamos as diferentes curvas de energia (calor de formação). As curvas estudadas foram obtidas pela passagem de um átomo de carbono sobre uma folha de supercoroneno na qual existe um heteroátomo (foram utilizadas três diferentes estruturas: C57H18Si, C57H18Ge e C57H18Sn). Nesse contexto, estudamos também o efeito destes heteroátomos sobre a densidade eletrônica e os orbitais HOMO e LUMO das diferentes estruturas. / In this work we investigate the effects of the presence of heteroatoms on a “supercoronene” sheet (C58H18 molecule used as a molecular model for graphene). Specifically, we used the semiempirical method PM6 as implemented in MOPAC2012® software to study several (formation) energy curves. The energy curves were obtained by positioning a carbon atom over a “supercoronene” sheet in which there is a heteroatom (this was done for three different structures: C57H18Si, C57H18Ge and C57H18Sn). In this context, the effect of these heteroatoms on the electronic density distributions, as well as their effect on HOMO and LUMO orbitals were also investigated.

Esta tesis analiza los métodos estáticos, los cuales comprenden los métodos analíticos y semi empíricos que son utilizados para determinar la capacidad de carga teórica en pilotes, y los compara con las pruebas de carga dinámica, las cuales brindan el resultado real de la capacidad de carga de un pilote. El análisis realizado recopila las teorías de Therzaghi, Hansen, Meyerhof y Bowles, en cuanto a los modelos analíticos, y las teorías de Aoki Velloso, Decourt Quaresma, Pedro Paulo Velloso y Texeira, por parte de las teorías semi empíricas. / This thesis analyzes the static methods, which include the analytical and semi-empirical methods that are used to determine the theoretical load capacity in piles, and compares them with the dynamic load tests, which provide the real result of the load capacity of a pile. The analysis compiles the theories of Therzaghi, Hansen, Meyerhof and Bowles, regarding the analytical models, and the theories of Aoki Velloso, Decourt Quaresma, Pedro Paulo Velloso and Texeira, by the semi-empirical theories. / Tesis

Orientador: Douglas Soares Galvão / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin / Made available in DSpace on 2018-09-27T13:47:49Z (GMT). No. of bitstreams: 1 Troche_KarlaSouza_M.pdf: 1255427 bytes, checksum: 17251baf9cd0c68ce5c4f8e8adefec0b (MD5) Previous issue date: 2003 / Resumo: Neste trabalho apresentamos estudos de estrutura-atividade realizados para 81 hidrocarbonetos policíclicos aromáticos (PAHs) tentando identificar compostos carcinogênicos. Em particular, empregamos uma nova metodologia desenvolvida para tratar o problema da correlação estrutura geométrica com atividade biológica, denominada Metodologia de Índices Eletrônicos (MIE). Utilizamos três métodos semi-empíricos para estudar a dependência entre a qualidade dos resultados obtidos pela MIE e o Hamiltoniano utilizado. Para validarmos os descritores utilizados pela MIE, investigamos a relação entre a atividade experimental dos PAHs e descritores teóricos através de cinco metodologias de reconhecimento de padrões: a Análise de Componentes Principais (PCA), Análise Hierárquica de Agrupamentos (HCA), K-ésimo vizinho mais próximo (KNN), Soft Independent Modeling of Class Analogies (SIMCA) e as Redes Neurais Artificiais (NN). Para estas investigações distintas pudemos correlacionar a atividade dos PAHs estudados com parâmetros teóricos, em sua maioria eletrônicos, onde os parâmetros utilizados na MIE foram selecionados pelos diferentes métodos. Este estudo valida estatisticamente a MIE como uma nova metodologia capaz de identificar compostos biologicamente ativos, e com um custo computacional menor que técnicas convencionais de Relação estrutura-atividade (SAR) e apresentando um desempenho, em geral superior / Abstract: In this work we present the study structure-activity realized for 81 polycyclic aromatic hydrocarbons (PAHs) trying to identify carcinogenic compounds. Particularly, we used a new methodology developed to deal with the problem of correlation between geometrical structure and biological activity, the Electronic Indices Methodology (EIM). We used three semi-empirical methods to analyze the dependence between the quality of results obtained through EIM and the Hamiltonian used. In order to validate the descriptors used in EIM, we investigated the relationship between the experimental activity of PAHs and the theorical descriptors through five methodologies of pattern recognition: Principal Component Analysis (PCA), Hierarchical Cluster Analysis (HCA), Kth Nearest Neighbor (KNN), Soft Independent Modeling of Class Analogies (SIMCA) and Neural Networks (NN). From these different investigations, we could correlate the activity of PAHs studied with theorical parameters, almost all electronic, where the used parameters on EIM were selected with the different methods. These studies validate the statistical value of electronic parameters derived from EIM analysis and their ability to identify active compounds. The EIM out performed more standard Structure-Activity Relationship (SAR) methodologies / Mestrado / Física da Matéria Condensada / Mestre em Física

Orientador: Douglas Soares Galvão / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin / Made available in DSpace on 2018-08-09T02:37:49Z (GMT). No. of bitstreams: 1 Autreto_PedroAlvesdaSilva_M.pdf: 14908796 bytes, checksum: 389f8f28e3d38fbfe32aeab511893f6e (MD5) Previous issue date: 2007 / Resumo: As melaninas constituem uma classe de pigmentos biológicos de destaque devido, sobretudo, a sua predominante presença nos tecidos dos mamíferos. Há fortes evidências que sugerem que a pigmentação por melanina tem por objetivo proteger a pele contra efeitos prejudiciais da radiação ultravioleta. Além deste papel de fotoproteção, outras funções biológicas são especuladas em razão da presença do pigmento em regiões não iluminadas do corpo como por exemplo no cérebro em que há uma aparente destruição preferencial das células que contém melanina quando ocorrem doenças como o mal de Parkinson. Apesar de décadas de investigações, nenhuma amostra de melanina foi estruturalmente bem caracterizada. Dentre os diversos obstáculos que são responsáveis pelo lento progresso que marca a pesquisa deste pigmento, o maior deles é que as melaninas naturais são altamente insolúveis e de presumido alto peso molecular. Pesquisas recentes desenvolvem sínteses alternativas para as melaninas utilizando outros solventes e demonstram que até 20 % da estrutura desta pode ser composta por água. Assim, neste trabalho investigamos, por métodos quânticos, a geometria e estrutura eletrônica das moléculas 5,6 indolquinona, suas formas reduzidas (semiquinona e hidroquinona) e 27 dímeros obtidos a partir destas, em seus estados neutros e iônicos ( ± 1 e ± 2), no vácuo e nos solventes DMF(dimetilformamida), DMSO (dimetilsulfóxido) e água. Verificamos como o solvente altera as propriedades eletrônicas e espectroscópicas destas estruturas e como este pode ser fundamental para a determinação de suas geometrias. Utilizamos dois modelos para simular o solvente: um modelo contínuo, COSMO (Conductor-like Screening Model) e um discreto, que considera explicitamente cada molécula do solvente e é baseado em simulações Monte Carlo. Notamos que o solvente altera a propriedade de aceitador de dois elétrons de diversas estruturas, fato até então não observado e de importante consequência biológica, visto as eumelaninas poderem ser base de um mecanismo de defesa celular contra radicais livres. Os picos dos espectros de absorção, de um modo geral, são deslocados para o vermelho e, em alguns casos, tem um alargamento. Isto poderia contribuir para a constrção da larga banda característica das eumelaninas. Diversos outros aspectos importantes, em excelente acordo com dados experimentais, são também apresentados ao se considerar o solvente. Um dos mais relevantes mostra que o solvente tem forte influência na geometria da molécula com o menor custo de dimerização, o que nos leva a concluir que esta pode ser de fato a semente de "nucleação" para a formação do polímero de melanina. / Abstract: Melanins belong to an important class of biological pigments due to its abundant presence in mamal tissues. There are strong evidences that suggest that the pigmentation due to melanin would protect the skin against the biochemical devastation induced by solar exposure. Besides the photo-protection feature, other biological functions have been speculated to melanin due to its presence in non-illuminated areas of the body and the apparent preferential destruction of melanin-containing cells in the substancia nigra of the brain in Parkinsonism. Unfortunately, in what concerns structural and chemical composition, no melanin sample has been fully and unambiguously characterized yet, despite the enormous amount of experimental work done so far. The main difficulty for that is that melanin is insoluble in most organic solvents and has high molecular weight. A new synthetic route for melanins, using organic solvents, has been recently achieved and it was demonstrated that about 20 % of the structure of the pigment is composed by water. In this work we have investigated using quantum methods the geometries and electronic structure of 5,6 indolquinone, their redox forms (semiquinone and hidroquinone) and 27 dimers associated, in their neutral and ionic states ( ± 1 e ± 2). The calculation were carried in vacuum and in the solvents dimethyl sulfoxide (DMSO), N,N-dimethyl formamide (DMF) and water. We study the effect of the solvent on the electronic and spectroscopic properties and its importance to determine eumelanin structure. Two models for solvents were used. The first was a continuum model, COSMO (Conductor-like Screening Model), and the second one (based on Monte Carlo simulations) explicitly considers each molecule of the solvent. The results showed that the solvents affected the electron accepton properties allowing the acceptance of two electrons. These aspects have been not been observed before from vacuum calculations and it is of important biological consequence because the melanins can be the base of mechanism of cellular defense against free radicals. The peaks of absorption spectra of the solvated structure are dislocated from red and broadened. This could contribute to the characteristic broad band of eumelanins. Many others important aspects are in better agreement with experimental data when solvent aspects are explicitly taken into account. One of most important results was the observation that solvent effects can alter the order of the lowest energy dimer configuration in relation to the structures in vacuum. This dimer was suggested to be the nucleation seed for the polymer formation. / Mestrado / Física Atômica e Molecular / Mestre em Física

Spin-orbit coupling (SOC) is a relativistic effect whose origin lies in the Dirac’s equation – a relativistic analogue of Schrödinger’s equation. SOC corrects the electronic states of a quantum mechanical system up to ~1 eV in case of semiconductors and ~ 2 – 3.6 eV in case of actinides and heavy elements by considering not only the coordinates but also the spin of the electrons in the system. Most of the applications of the present day technology are based on manipulating the electronic structure of a system with very high accuracy and precision. This demands availability of correct electronic structure of a material or molecule within a feasible computational time. Some direct consequences of SOC in materials can be noticed in analyzing the charge-transport properties of a semiconductor, evaluating the candidature of transition metal dichalcogenides (TMDCs) for spintronic, twistronic and valleytronic applications, and in the origin of topological properties of a material. Not only in materials but also in molecules the SOC effects can be observed. Fine-structure of atomic spectra was explained on the account of SOC. Several additional peaks and wavelength shift in UV-vis spectroscopy of Gold Superatoms can only be explained by correctly considering the energy level splittings caused by SOC. SOC allows intersystem and reverse intersystem crossing by mixing the spin states, ultimately opening various chemical reaction pathways which were spin forbidden before. Current advancements in computational power enrich us to work shoulder to shoulder with experiments where one can simulate the synthesized structures containing thousands of atoms using semi-empirical methods as in DFTB, GFN-XTB. These methods so far considered SOC effects but only as case studies in testing the implementation of SOC Hamiltonian rather than a systemic extension of SOC parameters to most part of the periodic table and studying SOC effects for different categories of materials and molecules. This motivated us to implement the SOC either in the form of highly accurate parameters throughout the periodic table or as addition in hamiltonian in such methods. Twisted van der Waals 2D materials as in twisted TMDC bilayers shows exciting electronic and optoelectronic properties and depending on the twist angle and chemical composition they can have thousands of atoms in their superlattices. A correct electronic analysis of such structures with SOC corrected DFT is computationally very expensive but is feasible at semi-empirical level. Here, we have applied our implementation on TMDC homo and heterobilayer twisted superlattices and studied the effect of SOC on the excitonic properties of the system. Therefore, this work opens the way for realizing various exotic applications of present day materials as well as molecules.:Table of Contents Abstract 4 1 Introduction 8 1.1 Quantum Chemistry: 8 1.2 HF based Semi-Empirical Methods 9 1.3 DFT based Semi-Empirical Methods 11 1.3.1 Density Functional based Tight-Binding Method (DFTB) 11 1.3.2 Geometry, Frequency, Non-Covalent, extended Tight Binding (GFN-xTB) 12 1.4 Spin-Orbit Coupling (SOC) 14 1.4.1 SOC in Materials 18 1.4.2 SOC in Molecular Structures 22 1.5 Theoretical Models for Accounting SOC 24 1.6 Motivation, Objective and Outline of thesis 26 2 Methodology 29 2.1 Quantum Chemistry 30 2.1.1 Schrödinger equation 30 2.2 Density Functional Theory 33 2.2.1 Generalized Gradient Approximations 39 2.3 Spin-orbit Coupling (SOC) 41 2.3.1 Classical Picture of SOC in LS model 42 2.3.2 Quantum Picture of SOC in LS model: 43 2.3.3 Calculation of SOC Paramentes 45 2.4 Density Functional Based Semi-empirical Quantum Mechanical Methods 48 2.4.1 Self-Consistent Charge Density Functional Based Tight Binding Method (SCC-DFTB) 48 2.4.2 Extended Tight-Binding (GFN1-xTB) 51 2.4.3 Addition of Spin-Orbit Coupling Hamiltonian in DFTB and GFN-xTB 54 3 Benchmarking Spin-Orbit Coupling Parameters for DFTB 56 3.1 Introduction 58 3.2 Computational Details of the DFT benchmark calculations 60 3.3 Benchmarking Spin-Orbit Coupling Parameters 60 3.3.1 III-V Bulk Semiconductor 61 3.3.2 Transition Metal Dichalcogenide 2D Crystals 65 3.3.3 Topological Insulators 68 3.4 Conclusions 70 4 Spin-Orbit Coupling Corrections for the GFN-xTB method 71 4.1.1 Introduction 73 4.2 Computational Details of The Benchmark Calculations 75 4.3 Results & Discussion 76 4.3.1 Geometries 76 4.3.2 Effect of SOC on Charge Transport Properties of Chromophores in MOFs 77 4.3.3 Superatoms 82 4.3.4 Effect of SOC on Binding of O2 on Ferrous Deoxyheme 85 4.4 Conclusions 86 5 Spin Orbit Coupling Effects on The Excitonic Properties of Twisted Moiré Transition Metal Dichalcogenides 88 5.1 Introduction 90 5.2 Computational Details 92 5.3 Results & Discussions 93 5.4 Excitons in Twisted Moiré Homobilayers 93 5.5 Excitons in Twisted Moiré Heterobilayers 102 5.6 Conclusions 109 6 Summary 112 A. Acronym 116 B. Appendices 120 SOC Parameters 120 7 References 147 C. Acknowledgement 173

Dans la recherche de nouveaux traitements des maladies broncho-pulmonaires comme l'asthme et la broncho-pneumopathie chronique obstructive, les inhibiteurs de PDE4 sont des cibles intéressantes. Dans cette voie, notre laboratoire s'intéresse à la synthèse d'une nouvelle famille d'inhibiteurs à base pyridazinone. Pour cela, cette thèse couple la modélisation moléculaire (docking : développement méthodologique et application), la synthèse organique ainsi que des tests biologiques.Dans un premier temps, le développement du logiciel d'amarrage moléculaire AlgoGen a été poursuivi. AlgoGen (créé initialement à l'université de Lorraine en 2009) est un logiciel qui couple un algorithme génétique pour la recherche conformationnelle à une évaluation de l'énergie protéine-ligand à un niveau quantique semi-empirique alors que les autres logiciels existant effectuent ce calcul à un niveau classique en général. Le calcul d'une énergie à un niveau quantique est très coûteux en temps. C'est pourquoi, nous avons apporté de nombreuses modifications à ce logiciel afin d'accroître son efficacité dans la recherche conformationnelle. Ce logiciel a ensuite été utilisé sur un jeu de 22 dimères (typiques des reconnaissances moléculaires biologiques) et à huit systèmes protéine-ligand.Dans un deuxième temps, huit inhibiteurs ont été synthétisés et testés in vitro sur la cible PDE4. Pour compléter ce volet expérimental, une étude de structure-activité a été effectuée grâce au docking moléculaire (AlgoGen, Autodock, Glide) pour rationaliser les activités mesurées (IC50). Pour terminer, des pharmaco-modulations guidées par docking ont été réalisées afin de proposer de nouveaux inhibiteurs de plus grandes affinités avec la protéine PDE4D. / For the research of new treatment of bronchopulmonary diseases such as asthma and chronic obstructive pulmonary disease (COPD), the PDE4 inhibitors are an attractive target. Our laboratory is interested in a new PDE4 inhibitors family based on the pyridazinone pattern. For this purpose, this thesis couples molecular modeling (docking: methodological development and application), organic synthesis and biological tests.First, the development of the molecular docking software AlgoGen was continued. AlgoGen (initially created at university of Lorraine in 2009) is a program which couples a genetic algorithm for the conformational research and a protein-ligand energy evaluation at the quantum semi-empirical level while other software do this evaluation at a classical level. Quantum energy calculations are very time consuming. That is the reason why some modifications have been made to improve its efficiency for the conformational search. This software was then used for calculations on a set of 22 dimers (typical in biological molecular recognition) as well on 8 ligand-protein complexes.Secondly, eight inhibitors were synthesized and tested in vitro on the PDE4 target. To complete the experimental part, a structure-activity relationship study was carried out through a molecular docking to rationalize the measured activity (IC50). Finally, pharmaco-modulations guided by docking were made to propose new inhibitors with more affinity with the protein.

<p>The absorption spectra of a recently designed low-bandgap conjugated polymer has been studied using the semi-empirical method ZINDO and TDDFT/B3LYP/6-31G. The vertical excitation energies have been calculated for monomer up to hexamer. Two main absorption peaks can be seen, the one largest in wavelength corresponding to a HOMO to LUMO transition, and one involving higher order excitations. TDDFT results are red-shifted compared to the ZINDO results. Comparison with experiment yields that short conjugation lengths are dominating. This is possibly due to steric interactions between polymer chains, breaking the conjugation length. Such effects are also studied.</p>

The absorption spectra of a recently designed low-bandgap conjugated polymer has been studied using the semi-empirical method ZINDO and TDDFT/B3LYP/6-31G. The vertical excitation energies have been calculated for monomer up to hexamer. Two main absorption peaks can be seen, the one largest in wavelength corresponding to a HOMO to LUMO transition, and one involving higher order excitations. TDDFT results are red-shifted compared to the ZINDO results. Comparison with experiment yields that short conjugation lengths are dominating. This is possibly due to steric interactions between polymer chains, breaking the conjugation length. Such effects are also studied.