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1	Electronic and Magnetic Properties of Carbon-based and Boron-based Nano Materials Gunasinghe, Rosi 22 May 2017 (has links) The structural and electronic properties of covalently and non-covalently functionalized graphene are investigated by means of first-principles density-functional-theory. The electronic characteristics of non-covalently functionalized graphene by a planar covalent organic framework (COF) are investigated. The aromatic central molecule of the COF acts as an electron donor while the linker of the COF acts as an electron acceptor. The concerted interaction of donor acceptor promotes the formation of planar COF networks on graphene. The distinctive electronic properties of covalently functionalized fluorinated epitaxial graphene are attributed to the polar covalent C–F bond. The partial ionic character of the C–F bond results in the hyperconjugation of C–F σ-bonds with an sp2 network of graphene. The implications of resonant-orbital-induced doping for the electronic and magnetic properties of fluorinated epitaxial graphene are discussed. Isolation of single-walled carbon nanotubes (SWNTs) with specific chirality and diameters is critical. Water-soluble poly [(m- phenyleneethynylene)- alt- (p- phenyleneethynylene)], 3, is found to exhibit high selectivity in dispersing SWNT (6,5). The polymer’s ability to sort out SWNT (6,5) appears to be related to the carbon–carbon triple bond, whose free rotation allows a unique assembly. We have also demonstrated the important role of dispersion forces on the structural and electronic stability of parallel displaced and Y-shaped benzene dimer conformations. Long-range dispersive forces play a significant role in determining the relative stability of benzene dimer. The effective dispersion of SWNT depends on the helical pitch length associated with the conformations of linkages as well as π-π stacking configurations. We have revisited the constructing schemes for a large family of stable hollow boron fullerenes with 80 + 8n (n = 0,2,3,...) atoms. In contrast to the hollow pentagon boron fullerenes the stable structures constitute 12 filled pentagons and 12 additional hollow hexagons. Based on results from density-functional calculations, an empirical rule for filled pentagons is proposed along with a revised electron counting scheme. We have also studied the relative stability of various boron fullerene structures and structural and electronic properties of B80 bucky ball and boron nanotubes. Our results reveal that the energy order of fullerenes strongly depends on the exchange-correlation functional employed in the calculation. A systematic study elucidates the importance of incorporating dispersion forces to account for the intricate interplay of two and three centered bonding in boron nanostructures. Density Functional Theory Dispersion-Correction Nano Materials Condensed Matter Physics Materials Chemistry Organic Chemistry Physical Chemistry
2	Going beyond the Random Phase Approximation: A systematic assessment of structural phase transitions and interlayer binding energies Sengupta, Niladri January 2018 (has links) The Random Phase Approximation and beyond Random Phase Approximation methods based on Adiabatic Connection Fluctuation Dissipation Theorem (ACFD) are tested for structural phase transitions of different groups of materials, including metal to metal, metal to semiconductor, semiconductor to semiconductor transitions. Also the performance assessment of semilocal density functionals with or without empirical long range dispersion corrections has been explored for the same cases. We have investigated the structural phase transitions of three broad group of materials, semi- conductor to metal transitions involving two symmetric structures, semiconductor to metal and wide bandgap semiconductor to semiconductor transitions involving at least one lower symmetric structure and lastly special cases comprising metal to metal transitions and transitions between energetically very close structural phases. The first group contains Si (diamond → β-tin), Ge (diamond → β-tin) and SiC (zinc blende → rocksalt), second group contains GaAs (zinc blende → cmcm) and SiO 2 (quartz → stishovite) and third group contains Pb (fcc → hcp), C(graphite → diamond) and BN (cubic → hexagonal) respectively. We have found that the difference in behavior of exchange and correlation in semilocal functionals and ACFD methods is striking. For the former, the exchange potential and energy often comprise the majority of the binding described by density functional approximations, and the addition of the correlation energy and potential often induce only a (relatively) small shift from the exchange- only results. For the ACFD, however, non self-consistent EXX typically underbinds by a considerable degree resulting in wildly inaccurate results. Thus the addition of correlation leads to very large shifts in the exchange-only results, in direct contrast to semilocal correlation. This difference in behavior is directly linked to the non-local nature of the EXX, and even though the exchange-only starting point is often nowhere close to experiment, the non-local correlation from the ACFD corrects this deficiency and yields the missing binding needed to produce accurate results. Thus we find the ACFD approach to be vital in the validation of semilocal results and recommend its use in materials where experimental results cannot be straightforwardly compared to other approximate electronic structure calculations. Utilizing the second-order approximation to Random Phase Approximation renormalized (RPAr) many-body perturbation theory for the interacting density-density response function, we have used a so-called higher-order terms (HOT) approximation for the correlation energy. In combination with the first-order RPAr correction, the HOT method faithfully captures the infinite- order correlation for a given exchange-correlation kernel, yielding errors of the total correlation energy on the order of 1% or less for most systems. For exchange-like kernels, our new method has the further benefit that the coupling-strength integration can be completely eliminated resulting in a modest reduction in computational cost compared to the traditional approach. When the correlation energy is accurately reproduced by the HOT approximation, structural properties and energy differences are also accurately reproduced, as confirmed by finding interlayer binding energies of several periodic solids and compared that to some molecular systems along with some phase transition parameters of SiC. Energy differences involving fragmentation have proved to be challenging for the HOT method, however, due to errors that do not cancel between a composite system and its constituent pieces which has been verified in our work as well. / Physics Computational Physics Dispersion Correction Hot Kernel Correction Rpa Scan Structural Phase Transition
3	Implementação de uma correção de dispersão empírica aos métodos semiempíricos RM1 (Recife Model 1) e PM6 (Parametric method 6) / Implementation of an empirical dispersion correction to semiempirical methods RM1 (Recife Model 1) and PM6 (Parametric method 6) Silva, Danylo Alves da 28 August 2017 (has links) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / In the present study, the implementation and parameterization of the dispersion correction functions, denominated DM1 and DM2, was carried out to the quantum semiempirical methods RM1 and PM6, in the program Mopac2007. The aim of this study is to improve the description of weak interactions by the methods above mentioned with the addition of na energy correction. The DM1 methodology contains 7 parameters while the DM2 model presents 13 parameters for the correction function. Unlike previous work, the correction was used to adjust not only the energy, but also the geometric parameters. The parameterization was performed using a training set composed by 10 structures from S22 database and 24 structures from S66 database. The results show that RM1-DM1 and RM1- DM2 improved the total response function when compared to RM1, the RM1- DM1 is better at describing the geometries of the complexes on the other hand, the RM1-DM2 is more efficient in reproducing the dispersion energy. The PM6- DM1 and PM6-DM2 methods, for the test set, had a smaller response function than PM7 and PM6 and their extensions with correction of dispersion forces. The best response function for PM6-DM1 and PM6-DM2 is related to the description of the geometries of the complexes, with the dispersion energy being slightly higher than that obtained by the PM6-DH2 method. The semiempirical methods discussed here, together with the theory of density functional, with the most popular B3LYP functional, were used to calculate the geometry of cyclodextrin/guest complexes. The results obtained, with semiempirical methods, showed that AM1, PM3, PM6-DM1 and PM6-DM2 presented the lowest values of RMSD and variability for a set of 43 cyclodextrins. The DFT methodology was used to calculate the geometry of a set of 9 cyclodextrins/guest complexes, the result was compared to semiempirical methods. The best DFT result was obtained with the 6-31G base, it is similar to obtained by the RM1 method. For this set, the methods AM1, PM6-DM1 and PM6-DM2 presented the best results in the description of the geometries. / No presente estudo foi realizada a implementação e parametrização das funções de correção de dispersão, denominadas DM1 e DM2, aos métodos semiempíricos quânticos RM1 e PM6, no programa Mopac2007. O estudo tem o como finalidade melhorar a descrição de interações fracas pelos métodos supracitados com a adição de uma correção de energia. A metodologia DM1 contém 7 parâmetros enquanto, o modelo DM2 apresenta 13 parâmetros para a função de correção. Diferente de trabalhos anteriores a correção foi usada para ajustar, não somente, a energia, mas também parâmetros geométricos. A parametrização foi executada usando um conjunto treinamento que usa 10 estruturas do banco de dados S22 e 24 estruturas do banco de dados S66. Os parâmetros obtidos através do conjunto treinamento foram aplicados ao conjunto teste, o qual é formado pelas 54 estruturas que não fizeram parte do conjunto treinamento. Os resultados mostram que RM1-DM1 e RM1-DM2 melhoraram a função resposta total quando comparado ao RM1, sendo o RM1-DM1 melhor em descrever as geometrias dos complexos e RM1-DM2 mais eficiente em reproduzir a energia de dispersão. Os métodos PM6-DM1 e PM6-DM2 para o conjunto teste apresentaram uma função resposta menor do que o PM7 e PM6 e suas extensões com correção das forças de dispersão. A melhor função resposta para PM6-DM1 e PM6-DM2 está relacionada a descrição das geometrias dos complexos, sendo a energia de dispersão um pouco maior do que a obtida pelo método PM6-DH2. Os métodos semiempíricos, aqui abordados, junto com a teoria do funcional da densidade, com o funcional mais popular B3LYP, foram usados para calcular a geometria de complexos ciclodextrina/convidado. Os resultados obtidos com os métodos semiempíricos mostraram que os métodos AM1, PM3, PM6-DM1 e PM6-DM2 apresentam os menores valores de RMSD e variabilidade para um conjunto de 43 ciclodextrinas. A metodologia DFT foi usada para calcular a geometria para um conjunto de 9 complexos ciclodextrinas/convidado, o resultado foi comparado aos métodos semiempíricos. O melhor resultado DFT foi obtido com a base 6-31G, esse é semelhante ao obtido pelo método RM1. Para esse conjunto os métodos AM1, PM6-DM1 e PM6-DM2 apresentaram os melhores resultados na descrição das geometrias. / São Cristóvão, SE Química Densidade Ciclodextrinas Parametrização Correção de dispersão Métodos semiempíricos Teoria do funcional da densidade Parametrization Dispersion correction Semiempirical methods Theory of density functional Cyclodextrins CIENCIAS EXATAS E DA TERRA::QUIMICA
4	Theoretical studies of molecule-substrate interaction at complex gold and silicon oxide surfaces using surface and cluster models Ting, Chao-Ming 11 January 2021 (has links) The formation and patterns of a monolayer are determined by the interplay of two fundamental interactions, adsorbate-substrate and intermolecular interactions. The binding strength between adsorbate and substrate affects the mobility of the adsorbate at the surface and the stability of the complex. The intermolecular interaction plays a significant role in the monolayer patterns on the epitaxial layer of the substrate. A monolayer can be formed either by a spontaneous self-assembly, or by fabrication via atomic-layer deposition (ALD). The physical and chemical properties of the resulting monolayer have a broad array of applications in fabricating functional materials for hydrophobic or hydrophilic surfaces, biological sensors, alternating the properties of the substrate, catalysis and forming ordered layered structures. In this dissertation, the investigation focuses primarily on the influence of the surface topology on the binding behaviour of adsorbate-surface complexes. The state of the art DFT-TS method is used to simulate the sulfur-containing amino acids at complex gold surfaces and examine the relationship between the binding strengths and the binding sites with various nearest neighbouring environments. The same method is also used to determine if a chemical reaction will take place for various catalytic silicon precursors at a silicon oxide surface. Simulating surface chemistry using the DFT-TS method requires intensive com- puting resources, including CPU use and computing time. Another focus of this dissertation is to increase the data generating speed by reducing the size of the sim- ulated systems without altering the outcome. A relatively small gold cluster is used to study the binding behaviours of small organic molecules on the cluster. The same strategy is also used to simulate the chemical reactions between various self-catalying silicon precursors and a water molecule. / Graduate / 2021-10-21 atomic layer deposition (ALD) Basis set superposition error (BSSE) coordination numbers (CNs) cysteine Density-functional theory (DFT) Gaussian simulation program homocysteine methionine SIESTA simulation program surface chemistry
5	Cobalt porphyrins on coinage metal surfaces - adsorption and template properties / Porphyrine de cobalt dans surfaces métalliques - propriété d’adsorption et de template Houwaart, Torsten 08 July 2014 (has links) Cette thèse est une étude théorique sur la interface de porphyrine de cobalt avec des surfaces métalliques avec le code VASP DFT. Le cadre DFT nécessaire a été introduit dans le chapitre 1. La structure de la jBardeen, une programme ecrit en Java, pour la simulation de la STM est expliqué dans le chapitre 2 et le code source est jointe en annexe. Une étude de l'adsorption de CoTPP sur les surfaces métalliques a été entrepris dans le chapitre 3. Différents paramètres de calcul ont été évalués: Le site d'adsorption et de la géométrie à la fois la molécule et la surface ont été étudiés par rapport à la xc-fonctionnel et correction de la dispersion utilisée. Une adsorption site le plus stable est identifié. Par conséquent, ce site plus stable a été étudiée pour sa structure électronique. Calculés images STM avec le code jBardeen ont été comparés avec une experimentation de CoTPP Cu sur une surface (111) avec une couverture sous monocouche. Dans le chapitre 4, un adatome Fe a été présenté à la CoTPP sur Ag système (111). Trois sites de liaison symétrique différentes pour l'atome Fe ont été identifiés sur le macrocycle, marqué les , bi-, brd- et bru-positions. Un moment magnétique pouvait être attestée qui a été principalement situé sur l'atome Fe. Voies possibles entre les quatre, symétriquement équivalentes, sites bi- ont été étudiées avec des méthodes différentes. Simples calculs dans le vacuum et calculs de la “Nudged Elastic Band” (NEB) de l'ensemble du système a révélé une hauteur de barrière légèrement au-dessus de 0,2 eV allant de position bi à la posititon brd. Une analyse de vibration a montré que la commutation de l'atome Fe est susceptible, lorsqu'il est perturbé hors d'équilibre dans les positions brd et bru. / This thesis is a theoretical study on the cobalt porphyrin - coinage metal surface interface with the DFT code VASP. The necessary DFT framework has been introduced in chapter 1. The structure of the Java program jBardeen for STM simulation is explained in chapter 2 and the source code is attached as Appendix. A study of the adsorption of CoTPP on coinage metal surfaces has been undertaken in chapter 3. Different parameters of the calculation have been evaluated: the adsorption site and the geometry of both the molecule and surface have been investigated with respect to the xc-functional and dispersion correction used. A most stable adsorption site -bridge down- is identified. Consequently, this most stable site was investigated for its electronic structure. Calculated STM images with the jBardeen code were compared with an experiment of CoTPP on a Cu(111) surface with sub monolayer coverage. In chapter 4 an Fe adatom was introduced to the CoTPP on Ag(111) system. Three symmetrically different binding sites for the Fe atom were identified on the macrocycle, labelled the bi-, brd- and bru-positions for bisector, bridge down and bridge up respectively. A magnetic moment could be evidenced which was mainly located on the Fe atom. Possible pathways between the four symmetrically equivalent bisector sites were investigated with different methods. Single point calculations in vacuum and Nudged Elastic Band (NEB) of the whole system revealed a barrier height of slightly above 0.2 eV going from bi- to the brd-position. A vibrational analysis showed that switching of the Fe atom is likely, when perturbed out of equilibrium in the brd- and bru- positions. Porphyrine de Cobalt CoTPP Pophyrine Microscope à effet tunnel STM DFT Surfaces métalliques Adsorption Templates Étude théorique Interface métal molécule VASP JBardeen Programme Java Site d'adsorption Géométrie d'adsorption Correction de dispersion Xc-fonctionnel D2 Grimmes potentiel Grimmes D2 Structure électronique Cu(111) Ag(111) Fe adatome Site de liaison Moment magnétique Couplage magnétique Dynamique de commutation NEB Analyse de vibration Analyse de charge Bader PDOS Cobalt-Tetra-Phenyl-Porphyrin CoTPP Porphyrins Scanning Tunneling Microscopy STM Density Functional Theory DFT Coinage metal surfaces Adsorption Templating Theoretical study Molecule metal interface VASP JBardeen Java program Adsorption site Adsorption geometry Xc-functional Dispersion correction D2 Grimmes potential Grimmes D2 Electronic structure Cu(111) Ag(111) Fe adatom Binding site Magnetic moment Magnetic coupling Switching dynamics NEB Nudged Elastic Band Vibrational analysis Bader charge analysis PDOS Projected Density of States

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