Academic literature on the topic 'Density Functional Theory; SIESTA; Instability'

In this study, the interaction energies between aromatic organic molecules (AOMs) and cellulose are explored using density functional theory (DFT) through the software SIESTA and the exchange-correlational functional VDW-DRSLL. Three AOMs will be modelled: benzene, benzamide and benzoic acid. Firstly, the interaction energies of the dimers of the AOMs are determined. Then, the obtained interaction energies of the cellulose-AOM complexes are compared to the former in order to decide which interaction is stronger. It is found that the studied AOMs are more likely to interact with cellulose than with another identical monomer; benzamide has the highest propensity to interact, followed by benzoic acid and benzene. Furthermore, for all interaction energy calculations a counterpoise correction term will be introduced as an addition to the SIESTA optimisation and it will be shown that without this correction the acquired energy minima will deviate significantly from accepted values from previous studies.

Submitted by MARCIA ROVADOSCHI (marciar@unifra.br) on 2018-08-17T19:58:30Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertação_CristianMafraLedur.pdf: 6580375 bytes, checksum: be466f19cd474caaa7ecaa4004ef38ba (MD5)<br>Made available in DSpace on 2018-08-17T19:58:30Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertação_CristianMafraLedur.pdf: 6580375 bytes, checksum: be466f19cd474caaa7ecaa4004ef38ba (MD5) Previous issue date: 2017-08-15<br>The two-dimensional (2D) materials display many interesting properties, which are not found in bulk structure because the original electronic structure is substantially altered from its three-dimensional (3D) characteristics. Black and blue phosphorene are 2D materials which are attracting many fields interest because of their electronic and magnetic properties, making them possible materials for spintronics devices application. These nanomaterials display some characteristics that allow their use on sensors, thus, this work aims to evaluate the changes in black and blue phosphorenes’ electronic and magnetic properties, before and after the chemical groups functionalizations. We utilized the amide, amine, carboxyl and hydroxyl chemical groups because they are into many living organisms, directing the results for possible systems of molecules adsorption with chemical and/or biological interest application. First-principles calculations based on Density Functional Theory with the Local Density Approximation (LDA) were performed using the SIESTA code. Blue phosphorene systems show a higher structure disturbance level when functionalized, so as atoms displacement, when compared with black phosphorene respective systems. Its binding energy also presents higher values when compared to black phosphorene systems. Both configurations 1-2, show the more stable systems for carboxyl groups functionalized on black and blue phosphorenes, presenting a 2.34 and 2.72 eV binding energy, respectively. The configuration 1-2 take on this post because reestablish the systems' symmetry. The symmetry reestablishment effect occurs in every kind of chemical group. These results imply in a promising black and blue phosphorenes application in systems of molecules adsorption with chemical and/or biological interest.<br>Diversas estruturas bidimensionais (2D) vêm apresentando propriedades interessantes, pois as mesmas são substancialmente alteradas quando comparadas às suas formas tridimensionais (3D). As estruturas de fosforeno negro e azul são materiais 2D que atraíram o interesse de muitas áreas pelo fato de suas propriedades eletrônicas e magnéticas indicarem o seu possível uso em dispositivos spintrônicos. Esses nanomateriais possuem características que permitem sua utilização em sensores, desta forma, este trabalho visa avaliar as mudanças nas propriedades eletrônicas e estruturais dos fosforenos causadas pelas funcionalizações dos grupos químicos amida, amina, carboxila e hidroxila, os quais compõem grande parte das moléculas biológicas presentes em organismos vivos para possível aplicação em sistemas de adsorção de moléculas de interesse biológico. Para desenvolver este trabalho fez-se uso de simulação computacional com cálculos de primeiros princípios, utilizando a Teoria do Funcional da Densidade (DFT), e Aproximação Local da Densidade (LDA) implementada no código computacional SIESTA. Este estudo demonstra que a estrutura de fosforeno azul apresenta maiores perturbações estruturais, como a modificação da posição inicial dos átomos de fósforo, devido às funcionalizações dos grupos químicos, se comparado aos sistemas funcionalizados com o fosforeno negro. Outro fator que chama a atenção são os valores de energia de ligação, onde todos os sistemas de fosforeno azul apresentam módulos maiores neste parâmetro para as respectivas configurações de funcionalização de grupos químicos. Os sistemas mais estáveis de fosforeno negro e azul funcionalizados com dois grupos carboxílicos apresentaram 2,34 e 2,72 eV, respectivamente, para a energia de ligação. Estes sistemas apresentam maior estabilidade devido ao fato de que restabelecem a simetria do sistema, em comparação com as outras configurações. Efeitos semelhantes ocorrem para todos os grupos químicos funcionalizados. Estes resultados indicam uma promissora aplicação das estruturas de fosforeno negro e azul como sistemas de adsorção de moléculas de interesse químico e/ou biológico.

In this thesis, quantum-mechanical calculations within density-functional theory on metallic systems are presented. The overarching goal has been to investigate effects of disorder. In particular, one of the properties investigated is the bindingenergy shifts for core electrons in binary alloys using different theoretical methods. These methods are compared with each other and with experimental results. One such method, the so-called Slater-Janak transition state method relies on the assumption that the single-particle eigenvalues within density-functional theory are linear functions of their respective occupation number. This assumption is investigated and it is found that while the eigenvalues to a first approximation show linear behavior, there are also nonlinearities which can influence the core-level binding energy shifts. Another area of investigation has been iron based alloys at pressures corresponding to those in the Earth’s inner core. This has been done for the hexagonal close packed and face entered cubic structures. The effects of alloying iron with magnesium and nickel on the equation of state as well on the elastic properties have been investigated. The calculations have shown that the hexagonal close packed structure in FeNi is more isotropic than the face-centered cubic structure, and that adding Mg to Fe has a large impact on the elastic properties. Finally, the effects of disorder due to thermal motion of the atoms have been investigated through ab-initio molecular dynamics simulations. Within the limits of this method and the setup, it is found that the face-centered cubic structure of molybdenum can be dynamically stabilized at high temperature, leading to a metastable structure, on the average. The dynamical stabilization of face-centered cubic molybdenum also rendered it possible to accurately calculate the lattice stability relative to the body-centered cubic phase. Inclusion of temperature effects for the lattice stability using ab-initio molecular dynamics simulations resolves the disagreement between ab-initio calculations and thermochemical methods.

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.<br>Graduate<br>2021-10-21