Dissertations / Theses on the topic 'Ab Initio Molecular Dyamics'
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1
Northey, Thomas. "Ab initio molecular diffraction." Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/28772.
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In 1915, Debye derived his well-known equation for the X-ray scattering from a sample of randomly orientated gas-phase molecules. He approximated the molecular scattering by adding the contributions of isolated atomic constituents. This is known as the Independent Atom Model (IAM). However, it omits the redistribution of valence electrons due to bonding, and is limited to the electronic ground state. The main proposition of this thesis is that it is worthwhile going beyond the IAM when interpreting X-ray scattering data. In part, this is motivated by the arrival of new X-ray sources called X-ray Free-Electron Lasers (XFELs). A new method called Ab Initio X-ray Diffraction (AIXRD) is introduced. It calculates the elastic X-ray molecular scattering factor directly from wave functions calculated by ab initio electronic structure theory, for instance Hartree-Fock or multiconfigurational self-consistent field. In this way, the valence electrons are correctly taken into account, and calculations based on electronically excited wave functions become possible. The wave functions must be constructed from spatial orbitals made up of Gaussian-Type Orbitals (GTOs), giving an analytical solution to the Fourier transform integrals involved, and is key to computationally efficient and accurate results. This is compared to a fast Fourier transform (FFT) method, where the electron density is computed on a 3D grid and an FFT algorithm is used to obtain the elastic X-ray molecular scattering factor. Inspired by post-crystallography experiments such as serial femtosecond crystallography and single-particle imaging at XFELs, the AIXRD method is expanded to allow accurate X-ray diffraction calculations from large molecules such as proteins. To make the underlying ab initio problem tractable, the molecule is split into fragments. In other words, the electron density is constructed by a sum of fragment contributions, as is the corresponding molecular form-factor. In this way, it is analogous to the IAM approach except that instead of isolated atoms, there are isolated fragments. A pairwise summation of fragment contributions is also used to account for fragment-fragment interactions. Various fragment definitions are compared based on their effect on the X-ray diffraction signal, and are compared to the IAM method. Finally, X-ray diffraction from molecules in specific quantum states is calculated, revealing a distinct quantum fingerprint in the X-ray diffraction, and a comparison to experiment is made. In particular, the elastic X-ray diffraction is calculated from gas-phase H2 pumped to various electronic, vibrational, and electronic states. This is expanded upon for polyatomic molecules using the harmonic approximation for the vibrational states.
2
Wetzel, Thiele Lee. "Ab initio computational studies." Thesis, Georgia Institute of Technology, 1993. http://hdl.handle.net/1853/26023.
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Somasundram, K. "Ab initio calculation of molecular properties." Thesis, University of Cambridge, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.383905.
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Su, Ming-Der. "Ab initio calculation of molecular surfaces." Thesis, University of Cambridge, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.239130.
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Mohamed, Fawzi Roberto. "Advanced methods in Ab-initio molecular dynamics /." Zürich : ETH, 2006. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=16893.
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Marzari, Nicola. "Ab-initio molecular dynamics for metallic systems." Thesis, University of Cambridge, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285270.
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Prasongkit, Jariyanee. "Molecular Electronics : Insight from Ab-Initio Transport Simulations." Doctoral thesis, Uppsala universitet, Materialteori, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-160474.
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This thesis presents the theoretical studies of electronic transport in molecular electronic devices. Such devices have been proposed and investigated as a promising new approach that complements conventional silicon-based electronics. To design and fabricate future nanoelectronic devices, it is essential to understand the conduction mechanism at a molecular or atomic level. Our approach is based on the non-equilibrium Green's function method (NEGF) combined with density functional theory (DFT). We apply the method to study the electronic transport properties of two-probe systems consisting of molecules or atomic wires sandwiched between leads. A few molecular electronic devices are characterized; namely, conducting molecular wires, molecular switches and molecular recognition sensors. The considered applications are interconnection of different nanoelectronic units with cumulene molecular wires; adding switching functionality to the molecular connectors by applying stress to the CNT-cumulene-CNT junction or by introducing phthalocyanine unit; sensing of individual nucleotides, e.g., for DNA sequencing applications. The obtained results provide useful insights into the electron transport properties of molecules. Several interesting and significant features are analyzed and explained in particular such as, level pinning, negative differential resistance, interfering of conducting channels etc.
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Chapman, Darren Mark. "Ab initio vibrational analyses of complex molecular species." Thesis, University of York, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.286053.
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Comeau, Donald Clifford. "Large-scale ab initio molecular electronic structure calculations /." The Ohio State University, 1990. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487684245466345.
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Silva, Rodrigo Azevedo Moreira da. "Eletrônica molecular: estudo ab initio da separabilidade eletrodo." Universidade Federal de Pernambuco, 2013. https://repositorio.ufpe.br/handle/123456789/12166.
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CNPq
Devido à crescente importância da nanotecnologia nos dias de hoje, muito se tem pesquisado sobre suas aplicações nas mais diversas áreas. A substituição dos componentes microeletrônicos comuns por outros ainda mais compactos é um exemplo prático de sua possível aplicação. Em escala nanométrica, os efeitos quânticos de interação entre os componentes aumenta a complexidade da obtenção de alternativas viáveis aos dispositivos microeletrônicos comumente utilizados. Tem-se estudado muito ao longo dos últimos anos as propriedades de transporte de cargas através de várias moléculas orgânicas individuais isoladas, ou acopladas a meios que não correspondem a situações reais aplicadas. O objetivo dessa dissertação é o estudo da estrutura eletrônica de componentes individuais a saber, um fio nanoscópico e uma molécula estendida, de forma a elucidar os possíveis efeitos de interação entre ambos, e de buscar alternativas na modelagem de sistemas mais próximos da realidade. Ao utilizar ferramentas de análise baseadas em projetores, e matematicamente mais consistentes e rigorosas, observamos que, apesar dos efeitos quânticos de interação entre um eletrodo e uma molécula orgânica não poderem ser desprezados, dentro de um limite razoável, é possível separar as características do fio nanoscópico de modo a melhor estudar seus efeitos na molécula orgânica a ele acoplada.
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Knowles, D. B. "Ab initio and empirical potentials for small molecules." Thesis, University of Sussex, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.373152.
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Au, Yat-yin. "Ab initio calculations : an extension of Sankey's method /." Hong Kong : University of Hong Kong, 1999. http://sunzi.lib.hku.hk/hkuto/record.jsp?B21482706.
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Sahli, Beat. "Ab initio molecular dynamics simulation of diffusion in silicon /." Zürich : ETH, 2006. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=16888.
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Temelso, Berhane. "Computation of Molecular Properties at the Ab Initio Limit." Diss., Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/14638.
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The accuracy of a quantum chemical calculation inherently depends on the ability to account for the completeness of the one- and n-particle spaces. The size of the basis set used can be systematically increased until it reaches the complete one-particle basis set limit (CBS) while the n-particle space approaches its exact full configuration interaction (FCI) limit by following a hierarchy of electron correlation methods developed over the last seventy years. If extremely high accuracy is desired, properly correcting for very small effects such as those resulting the Born-Oppenheimer approximation and the neglect of relativistic effects becomes indispensable. For a series of chemically interesting and challenging systems, we identify the limits of conventional approaches and use state-of-the-art quantum chemical methods along with large basis sets to get the “right answer for the right reasons.” First, we quantify the importance of small effects that are ignored in conventional quantum chemical calculations and manage to achieve spectroscopic accuracy (agreement of 1 cm−1 or less with experimental harmonic vibrational frequencies) for BH, CH+ and NH. We then definitively resolve the global minimum structure for Li₆ , Li₆⁺ , and Li₆- using high accuracy calculations of the binding energies, ionization potentials, electron affinities and vertical excitation spectra for the competing isomers. The same rigorous approach is used to study a series of hydrogen transfer reactions and validate the necessary parameters for the hydrogen abstraction and donation steps in the mechanosynthesis of diamondoids. Finally, in an effort to overcome the steep computational scaling of most high-level methods, a new hybrid methodology which scales as O(N⁵) but performs comparably to O(N⁶) methods is benchmarked for its performance in the equilibrium and dissociation regimes.
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Wang, Michael Wei-Lueng. "An ab-initio analysis of bimetallic oligoaniline molecular junctions." Texas A&M University, 2003. http://hdl.handle.net/1969.1/5914.
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The electron transport characteristics of Oligoaniline molecular junctions
terminated with thiol-ends are analyzed with the density functional theory and the
Green's function approach. The molecular junction consists of an Oligoaniline molecule
attached to metal electrodes at each end. By applying an electric field, the molecule
conducts a current that depends on either the molecular conformation or the ionization
state. Ab initio optimization methods are performed on various Oligoaniline systems to
analyze how different conformational changes are associated with different
conductivities. The density functional theory and Green's function are used to calculate
the density of states, transmission probability functions, and current-voltage calculations
for each Oligoaniline system to complement the results from the molecular analysis. An
inelastic tunneling spectrum analysis is also performed through frequency calculations to
examine the different characteristics of each conducting state. Molecular orbits of each
conformation was used to investigate further the relation between structure and electrical
properties of the molecular junction. The combined results from the different
calculations provided insight into the possible mechanisms for electron transfer
throughout the junction.
16
Chang, Jianlin. "Ab initio calculations of semiconductor surfaces and molecular clusters." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/nq22449.pdf.
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Sahli, Beat. "Ab initio molecular dynamics simulation of diffusion in silicon /." Konstanz : Hartung-Gorre, 2007. http://www.loc.gov/catdir/toc/fy0804/2007481782.html.
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Watson, Stuart. "Structural relaxation at defects by Ab initio molecular dynamics." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.320648.
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Hyde, G. "Ab initio studies of weak force mediated molecular enantioselectivity." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.604912.
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This thesis project investigates two of the mechanisms that have been postulated to explain the origin of the molecular homochirality found in living systems. These mechanisms are i. the Yamagata-Rein Hypothesis, which predicts that the weak neutral currents between electrons and nucleons result in a Parity-Violating Energy Difference (PVED) between a pair of molecular enantiomers; and ii. the Vester-Ulbricht Hypothesis, which predicts that the β-particles produced during weak force mediated nuclear β-decay interact differently with each of a pair of molecular enantiomers. Both hypotheses predict a small enantiomeric excess and theorise that such an excess might have been the prebiotic chiral influence that led to homochirality, which is generally accepted to be a prerequisite for biology. It is found that those PVED computations carried out the coupled-perturbed level of theory are approximately one order of magnitude larger than those previously computed at the entry-level uncoupled-perturbed level of theory. The results computed as part of this thesis project include the first to apply Density-Functional theory to the computation of the PVED. The coupled-perturbed Hartree-Fock and Kohn-Sham computations of the PVED are found to be in good agreement with recent related computational studies. The hypersensitivity of the PVED to small conformational changes, coupled to the difficulties in knowing the aqueous phase structure of even small chiral biomolecules such as α-alanine, means that it is difficult to make any unambiguous conclusions regarding which of a pair of biomolecular enantiomers might have been favoured by the PVED in a probiotic regime. These results do indicate that the largest β-asymmetries are generated in the forward scattering regimes and that the sign of the asymmetries may change suddenly as the energy of the incoming β-particle increases so as to allow the removal of electrons from successive molecular orbitals during the impact ionisation of the molecule.
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Walker, Brent Graham. "Ab initio molecular dynamics studies of liquid metal surfaces." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615985.
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Kochman, Michal. "Ab initio simulations of reactions occurring in molecular crystals." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/8906.
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Although the solid state may not usually be thought of as an environment suitable for chemical reactions under mild conditions, a growing number of organic compounds are known to undergo interesting and, in many cases, practically useful chemistry in the molecular crystal phase. Of particular interest are photochemical reactions occurring in molecular crystals, which possess a number of characteristic features that make them attractive to study using the methods of theoretical chemistry. Firstly, molecular packing and steric effects strongly influence the mechanistic course of reactions in the crystal phase, which in some cases enables clean and controllable chemistry, including synthetic reactions as well as reversibly switchable isomerisations accompanied by a change of the macroscopic properties of the crystal, such as shape and colour. Secondly, in part due to their fast (subpicosecond) timescales and relatively low conversion rates (of the order of a few per cent), many of these reactions present challenges to experimental techniques, which computer simulation methods are uniquely positioned to overcome. Finally, these systems lend themselves well to simulation using a hybrid combination of two ab initio electronic structure methods, one of which is used to describe the electronic excitation of a reactive molecule while the other is applied to the surrounding bulk lattice. This thesis describes the computational modelling of two such reactions: the syn-anti photoisomerisation of 7-(2-pyridyl)indole and the reversible cis-enol⇄trans-keto photoisomerisation of N-salicylidene-2-chloroaniline. The solid-state mechanisms and rates of both reactions are computed using the TD-DFT/DFT hybrid method, in the latter case validating a previously postulated reaction mechanism. Furthermore, the thermal (ground-state) tautomerisation reaction in the photochromic and non-photochromic polymorphs of N-salicylidene-2-chloroaniline is investigated through calculations at the DFT level of theory. The results of these calculations indicate that both polymorphs are thermochromic, but tautomeric equilibrium in the non-photochromic polymorph is more sensitive to temperature than in the photochromic polymorph. Additionally, a critical assessment is presented of the accuracy of the various emphab initio methods employed throughout this work.
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Watts, J. D. "Some applications of ab initio molecular electronic structure theory." Thesis, University of Sussex, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.370442.
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Laino, Teodoro. "Multigrid QM/MM approaches in ab initio molecular dynamics." Doctoral thesis, Scuola Normale Superiore, 2006. http://hdl.handle.net/11384/85799.
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Costa, Cleidinéia Cavalcante da. "Dinâmica ab initio de líquidos polares : acetonitrila e metanol." reponame:Repositório Institucional da UFOP, 2014. http://www.repositorio.ufop.br/handle/123456789/6461.
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Programa de Pós-Graduação em Ciências – Física de Materiais. Departamento de Física, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro PretoSubmitted by Marise Leite (marise_mg@yahoo.com.br) on 2016-05-05T13:52:05Z No. of bitstreams: 2 license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) DISSERTAÇÃO_DinâmicaInitioLíquidos.pdf: 1363157 bytes, checksum: 58029137c10736e2e0907ffbe43da905 (MD5)
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區逸賢 and Yat-yin Au. "Ab initio calculations: an extension of Sankey's method." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1999. http://hub.hku.hk/bib/B31222195.
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Puglisi, Alessandra. "Ab-initio study of x-ray spectroscopy of molecular ions." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066257/document.
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La signature spectroscopique des ions moléculaires est fondamentale pour l'étude et la caractérisation de plasma en astrophysique et en laboratoire. Différentes techniques peuvent être utilisées pour caractériser ces plasmas parmi lesquelles la spectroscopie de photoélectrons induits par rayons X et la photo-absorption X. L'objectif de cette thèse est la simulation des spectres de photo-absorption au seuil L (2p) des ions moléculaires de silicium SiHn+ (n= 1, 2, 3) et au seuil K (1s) des ions moléculaires de l'oxygène OHn+ (n=1, 2) et du carbone CHn+ (n= 1, 2) produits lors d'une décharge plasma. Nous avons développé différents protocoles numériques permettant de calculer les spectres d'absorption aux seuils K et L en combinant des méthodes de structures électroniques et de propagation de paquet d'ondes. Les optimisations de géométrie et le calcul des seuils d'ionisation (IP) sont obtenus en utilisant la théorie de la fonctionnelle de la densité (DFT). Les effets de relaxation électronique due à la formation d'un trou en couche interne sont pris en compte au niveau SCF (convergence de la fonction d'onde électronique à N-1 électrons). Les surfaces d'énergie potentielle (PES) et les moments de transition dipolaires sont calculés à un niveau Post-HF (Interaction de configurations, CI). L'introduction explicite du couplage spin-orbite à l'aide de l'opérateur Breit-Pauli est utilisée pour l'étude du processus d'excitation au seuil L du silicium. Les spectres théoriques calculés pour les différentes molécules étudiées présentent un accord raisonnable avec les mesures expérimentales. La présence d'états électroniques métastables produits lors de la décharge plasma est discutéeMolecular ions cover important roles in study and characterization of astrophysical and laboratory plasma. To this purposes, different spectroscopic techniques are used among which we found the X-ray photoelectron spectroscopy and the X-ray photoabsorption spectroscopy. This PhD work is focused on the calculation of X-ray photoabsorption spectra of molecular ions of silicon, carbon and oxygen XHn+ (X= Si, C, O; n= 1, 2, 3). The former is excited on the L (2p) shell while the others on the K (1s) shell produced in plasma discharged. We developed numerical protocols which permits to compute with reasonable precision the K and L-shell photoabsorption spectra combining electronic structure and nuclear wavepacket propagation methods. The optimization of the geometries and the calculation of the ionization potentials (IP) are carried out using the density functional theory (DFT). The relaxation effects due to the core hole creation are taken into account at the self-consistent field (SCF) level. The potential energy surfaces (PES) and the dipole moment transitions are computed at the post Hartree-Fock (configuration interaction, CI) level. The spin-orbit coupling effect are explicitly taken into account through the Breit-Pauli operator. The theoretical results have been compared with the experimental data and they allow the interpretation of the experimental bands
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Neto, JoÃo Rufino Bezerra. "Ab initio approach of alendronate molecular and three its crystals." Universidade Federal do CearÃ, 2014. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=14303.
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Well know therapies for the treatment of osteoporosis, syndrome characterized by increased bone fragility and fracture consist primarily of drugs which prevent bone losses, such as bisphosphonates. Among them, alendronate (PO3)-(OH)-C-((CH2)3 NH3)-(PO3) is one of the chosen treatments in the clinic, IC50 = 50 nM. In this work a study of the molecular alendronate and three of its crystals (sodium alendronate trihydrate and anhydrous
and calcium alendronate ) is performed in the scope of Density Functional Theory (DFT). In the first case, the focus is the lowest energy conformations of the molecular
alendronate in vacuum, in an aqueous medium in accordance with the model of polarization continuum (PCM), and interacting with three molecules of water of a sodium atom based on the characteristics structural relevadas diffraction X-ray crystal alendrontao sodium trihydrate; their vibrational infrared and Raman spectra are calculated to explain in detail the abundant signatures of the phosphate group in the frequency range 400-1400 cm
−1 with the assignments of the most important vibrational modes. In the case of crystals, their structural, electronic and optical properties are obtained in the generalized gradient approximation taking into account the description of the term correlation and exchange
Tchatschenko (GGA+TS ); Hirshfeld population analysis in which verified is presented alendronate is that the three crystals is in zwitterionic state. From the calculation of the band structure was obtained GAPs with very close values for the three crystals, however, with the density of states and characteristic for each crystal. The effective masses, dielectric function and theoretical optical absorptions for all crystals are presented.Terapias estabelecidas para o tratamento da osteosporose, sÃndrome caracterizada por aumento na fragilidade Ãssea e fraturas, consistem primariamente de drogas que previnem a perda Ãssea, como os bisfosfonatos. Entre eles, o alendronato (PO3)-(OH)-C-((CH2)3 NH3)-(PO3) à um dos tratamentos escolhidos na clÃnica, pois possui o IC50=50 nM. Neste trabalho à realizado um estudo do alendronato molecular e de trÃs de seus cristais (alendronato de sÃdio trihidratado e anidro, e alendronato de cÃlcio) utilizando da Teoria do Funcional da Densidade (DFT). No primeiro caso, o foco sÃo os confÃrmeros de menor energia do alendronato molecular no vÃcuo, em meio aquoso de acordo com o modelo contÃnuo polarizÃvel (PCM), e interagindo com trÃs molÃculas de Ãgua e um Ãtomo de sÃdio de acordo com as caracterÃsticas estruturais reveladas por difraÃÃo de raios-X do cristal do alendrontao de sÃdio trihidratado; seus espectros vibracionais no infravermelho e Raman sÃo calculados para explicar com detalhes as abundantes assinaturas do grupo fosfato no intervalo de frequÃncia 400-1400 cm−1, com as atribuiÃÃes dos modos vibracionais mais importantes. No caso dos cristais, sÃo obtidas suas propriedades estruturais, eletrÃnicas e Ãpticas na aproximaÃÃo da gradiente generalizado levando-se em conta a descriÃÃo do termo de correlaÃÃo e troca de Tchatschenko (GGA+TS); à apresentada a anÃlise populacional de Hirshfeld na qual verificou-se que o alendronato nos trÃs cristais encontra-se no estado zwitterionico. A partir do cÃlculo de estrutura de banda, foi obtido GAPs com valores muito prÃximos para os trÃs cristais, porÃm, com densidade de estados bem caracterÃstica para cada cristal. SÃo apresentadas as massas efetivas, funÃÃo dielÃtrica e absorÃÃes Ãpticas teÃricas para todos os cristais.
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COURA, D. V. B. "Estudo ab initio do sistema molecular HCO de interesse atmosférico." Universidade Federal do Espírito Santo, 2018. http://repositorio.ufes.br/handle/10/7371.
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Previous issue date: 2018-02-08Neste trabalho foram feitos cálculos ab initio de alto nível usando determinantes CASSCF para uma função MRCI e uma base ACV5Z-DK, juntamente com um ajuste preliminar de uma função de energia potencial a esses pontos. Até a data da defesa dessa dissertação foi possível realizar um estudo do mínimo global da superfície de energia potencial do HCO, mínimos locais e alguns estados de transição. O objetivo final do trabalho aqui iniciado é a construção de uma superfície de energia potencial global para o estado fundamental da molécula HCO.
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Luo, Ye. "Ab initio molecular dynamics of water by quantum Monte Carlo." Doctoral thesis, SISSA, 2014. http://hdl.handle.net/20.500.11767/3896.
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The chapter 2, we deal with the challenge b). It focuses on the variational
Monte Carlo (VMC) and the wavefunction optimization methods based on
VMC. The performance of different methods are displayed through the op-
timization of the Jastrow factor in our test case Beryllium dimer and the
efficiency is improving surprisingly during the evolution of these methods.
In chapter 3, we focus on the challenge a). It describes the wavefunc-
tion ansatz used by our simulation. In this thesis, we introduce the atomic
hybrid orbitals which significantly increase the compactness of our wavefunc-
tion without hurting accuracy. This chapter also explain how to optimize
the determinant in a way that the number of variational parameters scales
only linearly with the system size. This further helps the efficiency of the
wavefunction optimization.
In chapters 4 and 5, the issue c) is explained in detail. In chapter 4,
a second order Langevin dynamics (SLD) scheme is devised particularly for
QMC and this thesis improves this scheme by developing a better integration
method. Here, we also highlight the remarkable power of the force covari-
ance matrix which can be defined only in QMC and is capable of accelerating
the slow modes of a dynamics. In chapter 5, this SLD for QMC is validated
through intensive benchmarking on the calculation of the vibrational frequen-
cies of water and other small molecules. It is shown that many systematic
biases in our MD scheme and QMC evaluation can be controlled so that we
are confident to push forward this ab initio molecular dynamics for applica-
tions on large systems.
Finally in chapter 6, we perform the simulation of liquid water with all the
preparation done in the previous chapters. The results are encouraging since
we’ve closed the discrepancy of the peak positions of RDFs between experi-
ments and ab initio simulations. The power of QMC is also demonstrated by
the fact that the shapes of our RDFs are much less structured than previous
DFT-based ab initio simulations even if the two water molecule interaction is
dealt with the same level of accuracy as the DFT/BLYP calculation. In this
chapter, we have also studied the features of hydrogen bonds in our simulation
of liquid water. All our results indicate that it is important to consider the
quantum nature of the ions for a faithful description of liquid water. This will
be left for future studies, possible in principle even within the QMC approach.
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Li, Ming, and 李銘. "Some AB initio studies of positron annihilation in semiconductors." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1998. http://hub.hku.hk/bib/B31238919.
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Li, Ming. "Some AB initio studies of positron annihilation in semiconductors /." Hong Kong : University of Hong Kong, 1998. http://sunzi.lib.hku.hk/hkuto/record.jsp?B20128496.
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Custódio, Fábio Lima. "Algoritmos genéticos para predição ab initio de estrutura de proteínas." Laboratório Nacional de Computação Científica, 2008. http://www.lncc.br/tdmc/tde_busca/arquivo.php?codArquivo=159.
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Métodos de predição ab initio de estrutura de proteínas (PSP) buscam prever, baseando-se em primeiros princípios, a estrutura tridimensional que uma dada seqüência de aminoácidos irá adotar no espaço. Os métodos de predição ab initio atualmente possuem aplicações biotecnológicas que envolvem desde a criação de novas proteínas, o auxílio no desenho racional de fármacos (estrutura do receptor), o refinamento de modelos teóricos e a obtenção de estruturas a partir de dados experimentais incompletos. Entretanto, a predição envolve um problema de otimização que lida com milhares de graus de liberdade e está associado à hipersuperfícies de energia extremamente complexas o que torna o problema difícil de ser tratado computacionalmente.
Neste trabalho utilizamos um modelo tridimensional de proteínas simplificado (modelo hidrofóbico-polar, HP) para reduzir os custos computacionais associados ao problema de PSP de modo que uma metodologia de otimização, robusta e eficiente, baseada em algoritmos genéticos, fosse desenvolvida mais rapidamente. Em seguida a metodologia foi adaptada para um modelo com descrição atômica que utiliza um campo de forças clássico como função de energia. Durante o desenvolvimento foram implementadas e analisadas várias estratégias para o problema. Foi descrita uma nova abordagem, baseada em crowding, para a manutenção da diversidade na população que resulta na obtenção simultânea de múltiplas soluções.
A metodologia para o modelo HP foi aplicada a 35 seqüências disponíveis na literatura e os resultados comparativos mostraram que o algoritmo genético desenvolvido é superior a outros algoritmos evolutivos publicados, e comparável a métodos especializados. A metodologia para o modelo atômico foi inicialmente testada em poli-alaninas e em seguida em cinco outras proteínas de maior complexidade. Foram encontradas estruturas apresentando RMSDs entre 2,0 e 6,7 Å, em relação à estrutura determinada experimentalmente. O algoritmo genético se mostrou superior a outros métodos semelhantes, em termos de custo computacional.
Os resultados obtidos mostram que as estratégias de otimização envolvendo a busca por múltiplos mínimos possuem duas grandes vantagens. A primeira delas está em uma investigação mais efetiva de uma hipersuperfície complexa aumentando a probabilidade de se encontrar soluções ótimas (de mais baixa energia); a segunda delas está no aumento da probabilidade de se obter estruturas próximas daquelas determinadas experimentalmente mesmo quando estas não são o mínimo global da hipersuperfície de energia investigada.
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Alfonso, Prieto Mercedes. "Estudi de la reactivitat de catalases mitjançant dinàmica molecular ab initio." Doctoral thesis, Universitat Autònoma de Barcelona, 2009. http://hdl.handle.net/10803/3607.
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El peròxid d'hidrogen és una espècie reactiva de l'oxigen que està involucrada en el dany oxidatiu i en la transducció intracelular de senyals. Per tant, és molt important regular la concentració de H2O2 per tal de mantenir la senyalització sense danyar les biomolècules. Les catalases són el principal sistema regulador dels nivells de peròxid d'hidrogen i per això participen en processos imflamatoris, mutagènesi, prevenció de l'apoptosi i estimulació d'un ampli espectre de tumors. Les hemo catalases són enzims que dismuten el peròxid d'hidrogen en aigua i oxigen (2 H2O2 →2 H2O + O2). Estan presents en pràcticament tots els organismes aeròbics i són uns dels enzims més eficients coneguts, amb 106 molècules de H2O2 degradades per segond. Degut a aquest augment excepcional de la velocitat de dismutació del H2O2 respecte als catalitzadors que no són proteïnes, la catalasa va ser un factor clau per reconèixer que els enzims són proteïnes i que tenen especificitat de substrat.
S'ha observat que algunes catalases contenen un hemo modificat (hemo d), en comptes del més abundant hemo b (protoporfirina IX de ferro). Malgrat que el cicle catalític d'aquests dos tipus de catalases és el mateix, no es coneix l'efecte de la modificació de l'hemo en l'estructura i configuració electrònica dels intermedis de reacció o en les seves propietats redox i àcid-base.
El principal intermedi del cicle catalític és una espècie de ferro de valència alta (Por·+-FeIV=O) anomenada Compost I (Cpd I). El Cpd I reacciona amb una mol·lècula de peròxid d'hidrogen produint aigua i oxigen molecular. Aquesta reacció també és duta a terme per altres hemoproteïnes, però a una velocitat molt méss baixa. La causa d'aquesta disparitat s'ha estudiat durant molts anys, i, tot i que aquesta reacció es coneix des del 1940, el seu mecanisme molecular detallat encara no s'ha clarificat.
Aquesta tesi té com a objectiu respondre aquestes preguntes, considerant dues catalases com a prototip: la catalasa de Helicobacter pylori (HPC, que conté hemo b) i la catalasa de Penicillium vitale (PVC, basada en hemo d). Aquest estudi s'ha realitzat utilitzant dinàmica molecular (clàssica i ab initio).
La tesi s'ha organitzat de la següent manera. El Capítol I introdueix els enzims a estudiar, les hemo catalases, i presenta els objectius generals d'aquest treball. Els fonaments metodològics s'expliquen al Capítol II. Els Capítols III-VII contenen una breu introducció al problema investigat, seguida d'una descripció i discussió de les simulacions realitzades. En primer lloc (Capítol III), s'ha estudiat l'efecte de la modificació de l'hemo en els intermedis de la catalasa utilitzant models en fase gas. Al Capítol IV, s'ha analitzat l'estructura dels intermedis formats per HPC and PVC i s'ha confirmat l'estat de protonació del Compost II (Cpd II) de catalasa. Al Capítol V s'han investigat els factors que determinen que HPC and PVC formin diferents intermedis (Compost I i Compost I, respectivament). Al Capítol VI, s'ha avaluat la validesa dels arguments utilitzats normalment per predir l'estat de espín de l'oxigen molecular produït per la catalasa. El mecanisme molecular de la reacció de la catalasa s'ha estudiat al Capítol VII. Finalment, el Capítol VIII llista les principals conclusions d'aquesta tesi. Informació addicional sobre les simulations realitzades als Capítols IV-VII es pot trobar als Apèndixs A-D.
Hydrogen peroxide is a reactive oxygen species that is involved in oxidative damage as well as in intracellular redox-sensitive signal transduction. Therefore, a fine balance of the H2O2 concentration is essential for mantaining signaling without damaging biomolecules. Catalases are the primary enzymes regulating these hydrogen peroxide levels and thus they have been implicated as an important factor in inflammation, mutagenesis, prevention of apoptosis and stimulation of a wide spectrum of tumors.
Heme catalases are enzymes that decompose hydrogen peroxide into water and oxygen (2 H2O2 →2 H2O + O2). They are present in almost all aerobic organisms and are one of the most efficient enzymes known, with 106 molecules of H2O2 degraded per second. Indeed, because of the exceptional rate enhancement of H2O2 dismutation compared to catalysts that are not proteins, catalase was a key factor in the early recognition that enzymes are proteins and have substrate specificity.
It has been shown that some catalases contain a modified heme (heme d) instead of the most abundant heme b (i.e. iron-protoporphyrin IX). Although the reaction cycle performed by the two types of catalases is the same, the effect of the heme modification on the structure and electronic configuration of the reaction intermediates, as well as on their redox and acid-base properties is not known.
The principal active species of the catalase reaction cycle is a high valent iron species (Por·+-FeIV=O) named Compound I (Cpd I). Cpd I reacts with a molecule of hydrogen peroxide releasing water and molecular oxygen. This reaction is also performed by other hemeproteins, although at much slower pace. The origin of this disparity has long been sought, and even though the catalase reaction has been known since 1940s, its detailed molecular mechanism has yet to be clarified.
The present thesis is aimed at answering these questions, considering two catalases as a test case: Helicobacter pylori catalase (HPC, a heme b-containing catalase) and Penicillium vitale catalase (PVC, based on heme d). This investigation will be performed by means of molecular dynamics (classical and ab initio).
The thesis is organized as follows. Chapter I introduces the enzymes under study, heme catalases, and presents the general objectives of this work. The basics of the methodologies used are given in Chapter II. Chapters III-VII contain a brief introduction to the problem investigated, followed by a description and discussion of the simulations performed. First, the effect of the heme modification on catalase intermediates is investigated in Chapter III by using gas phase models. In Chapter IV, we analyze the structure of the intermediates formed by HPC and PVC and ascertain the protonation state of catalase Compound II (Cpd II). The factors determining that HPC and PVC show different oxidized intermediates (i.e. Compound I* and Compound I, respectively) are investigated in Chapter V. In Chapter VI, we assess the validity of the arguments commonly used to predict the spin state of the molecular oxygen released by catalase. The molecular mechanism of the catalase reaction is studied in Chapter VII. Finally, Chapter VIII lists the main conclusions of this work. Additional information on the simulations performed in Chapters IV-VII can be found in Appendixes A-D.
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Spura, Thomas [Verfasser]. "Ab initio path integral molecular dynamics : theory and applications / Thomas Spura." Paderborn : Universitätsbibliothek, 2015. http://d-nb.info/1078666504/34.
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Blumberger, Jochen. "Ab-initio molecular dynamics simulation of redox reactions in aqueous solution." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.616223.
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Tocci, G. "Realistic modelling of water/solid interfaces from ab initio molecular dynamics." Thesis, University College London (University of London), 2014. http://discovery.ucl.ac.uk/1457448/.
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Water/solid interfaces are of utmost importance to a number of technological processes. Theoretical studies, based on ab initio approaches are suitable to unveil processes occurring at water/solid interfaces and can therefore be instrumental to delineate guidelines to improve the efficiency of these processes. In this thesis we study several systems of current interest using ab initio methods based on density functional theory (DFT). By going often beyond the use of standard DFT methods and approximations we have provided insights into processes occurring at water/solid interfaces under ambient conditions and in non stoichiometric conditions. Specifically, we will investigate the interactions between water and ZnO, an important metal-oxide especially used in industry to produce methanol. One of the most mportant results of this study is that proton hopping is dramatically enhanced under wet conditions compared to ideal ultra-high vacuum conditions. Also, we will compute the friction between liquid water in contact with 2-D layered materials, and delineate the guidelines on how to alter the friction coe cient in membranes used for desalination or osmotic power harvesting. Finally, in collaboration with Geoff Thornton's group we have investigated the role of defects on the surface chemistry of the rutile TiO2(110), which is the model oxide surface used in photocatalysis applications. On the whole, in this work we have used ab initio methods to reduce the gap between the ultra-high vacuum-style studies of adsorption on perfect defect-free surfaces and the complex behaviour of liquid/solid interfaces under technologically relevant conditions.
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McCarthy, William James 1964. "An ab initio study of low-frequency, large-amplitude molecular vibrations." Diss., The University of Arizona, 1996. http://hdl.handle.net/10150/290692.
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The ab initio treatments of molecular vibrational motion often invoke only the harmonic oscillator approximation. For vibrational modes whose amplitudes access anharmonic regions of the potential energy surface, the harmonic oscillator approximation fails. Low-frequency large-amplitude vibrations, in particular, can access anharmonic regions in addition to other minima of the potential energy surface. Ab initio harmonic frequencies are often scaled to lower values by empirical factors which presumably account for anharmonicity effects as well as an incomplete basis set and account of electron correlation. However, the scaling of those ab initio harmonic frequencies corresponding to low-frequency large-amplitude vibrations results in theoretical values that are still typically several times larger than the experimental values. It is demonstrated in this dissertation that transforming the nuclear motion Hamiltonian to internal coordinates facilitates construction of ab initio potential energy curves, or surfaces, pertaining to low-frequency large-amplitude molecular vibrational modes. The use of internal coordinates complicates the expression of the kinetic energy in the Hamiltonian, and makes it difficult to obtain. Six different methods for determining the kinetic energy expression in internal coordinates are presented and reviewed. The computational implementation of these six methods was performed to allow their critique. Several example calculations of the presented methodology are given. The solution for the vibrational expectation values of the modes expressed by the developed Hamiltonian was also computationally implemented. The resultant theoretical transition frequencies of the molecular systems of 2-sulpholene and 2-aminopyrimidine are combined with experimental studies, and demonstrate the practical usefulness of the presented methodology.
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Ardèvol, Grau Albert. "Study of molecular mechanisms in glycoside hydrocases and transferases by ab initio molecular dinyamics." Doctoral thesis, Universitat Autònoma de Barcelona, 2012. http://hdl.handle.net/10803/83945.
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Carbohydrates had historically been associated to two biological functions: energy storage and structural support. However, in the last decades, new complex structures of oligosaccharides have been found to play vital roles in many biological processes, such as signal transduction, immune response, cell differentiation and cancer development, among others.
Advances in the functional understanding of carbohydrate-protein interactions represented a breakthrough in the field of glycobiology and glycochemistry, opening a new branch of potential therapeutic targets (carbohydrate acting enzymes), glycomimetic drugs and biomarkers. The bottleneck in the field of glycochemistry is the synthesis of complex saccharides; hence many efforts have been devoted to the development of novel enzymatic strategies for carbohydrate synthesis.
Glycoside transferases (GT) and glycoside hydrolases (GH) are the enzymes that catalyze the formation and the cleavage of the glycosidic linkage respectively. They are used in complex oligosaccharides synthesis, and recently they have been engineered to produce enzymes with particular substrate specificities or even activities.
In spite of these advances, the understanding of the molecular mechanisms of enzymatic carbohydrate synthesis and degradation is far from complete. Structural studies have shown that the puckering of the sugar ring at the cleavage point must change during catalysis. Knowing the conformational catalytic itinerary has an impact in the design of GHs inhibitors. However, these itineraries are not known for all families of GHs. On the other hand, the saccharide puckering is not an issue in GTs, but the reaction mechanism is not known. In fact, the glycosidic bond formation in GTs remains one of the most intriguing and unanswered questions in the field of glycobiology.
The coming of age of powerful theoretical methods such as quantum mechanics / molecular mechanics (QM/MM) and ab initio molecular dynamics (AIMD) has enabled the elucidation of complex reactive processes in proteins and enzymes. In particular, the modeling of the Michaelis complex and the reaction mechanisms of GHs highlighted the interplay between electronic and structural changes that preactivate the substrate for catalysis. Some of these changes can already be anticipated by analyzing the conformational energy landscape of the substrate.
Part of the research of this Thesis complements previous studies of our group by analyzing the factors that govern substrate distortion in GHs. In this respect, it extends the use of conformational free energy landscapes of simple sugars to predict the conformation of the substrate in Michalis complexes. Additionally, the molecular mechanism of retaining glycoside transferases is elucidated.
This Thesis is organized as follows:
Chapter I contains an introduction of the enzymes studied (GHs and GTs) and presents the main objectives of this work. The theoretical methods used are detailed in Chapter II.
Chapters III to V are focused on enzyme-substrate interactions affecting the conformation of the substrate in GHs. Concretely; in Chapter III we test how mutation of the acid/base catalytic residue, the use of a substrate-like thio-analogue inhibitor or fluorometric aglycons affects the distortion of the substrate. In Chapter IV we study the influence of the enzyme-substrate interactions through the 2-OH, in particular the effect of the commonly used 2-deoxy-2-fluoro substitution. The conformational itinerary of this inhibitor during catalysis is modeled in Chapter V.
In Chapter VI, the conformational flexibility of β-D-mannopyranose and α-L-fucopyranose molecules is investigated. The topologies of their corresponding conformational free energy landscapes are related with the observed crystallographic structures of β-mannosidases and α-fucosidases, and the predictive potential of such calculations is discussed.
Chapter VII focuses on trehalose 6-phosphate synthase (a family 20 retaining GT that belongs to fold type B). The mechanism of glycosidic bond formation in this enzyme is elucidated. Finally, in Chapter VI, the main conclusions of this work are summarized.
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Altschäffel, Jan [Verfasser]. "Ab initio molecular dynamics simulations of molecular scattering from metal(111) surfaces / Jan Altschäffel." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2021. http://nbn-resolving.de/urn:nbn:de:gbv:7-21.11130/00-1735-0000-0008-58F1-5-3.
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Sulpizi, Marialore. "Ab initio studies of targets for pharmaceutical intervention." Doctoral thesis, SISSA, 2001. http://hdl.handle.net/20.500.11767/4280.
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In this thesis we further explore the capability of first principle methods to provide
insights on drug/target interactions in different contexts.
In the first part of this work, we address the issue whether OFT methods can be used as
a potential tool for drug-screening. First principle calculations are particularly interesting
for screening the energetics of drug/target interactions, as they do not involve the
painstaking procedure of developing each set of new parameters for each novel drug. In
this context, we use ab initio_ methods as a novel tool to determine a scoring function in a series of prodrug I target (herpes simplex type 1 thyimidine kinase) complexes for
gene-therapy based anticancer approaches. This work, accompanied by experimental
data provided by Prof. Folkers' Lab (ETH, Zurich) provides a new, very simple, ab initiobased
approach to the construction of scoring functions for drug-screening.
In the second part of the thesis we investigate the capability of OFT to describe non
trivial interactions which are encountered in several inhibitor/enzyme complexes of
pharmaceutical interest. Clearly, the description of these non-trivial phenomena might
require the use of electronic structure methods. Here we present an example of cation-n
interaction found in the human immunodeficiency virus reverse transcriptase (HIV-1
RT), one of the major targets for anti-AIDS therapy(Furman et al., 2000)). Furthermore,
we provide a description of the hydroxyl-n interactions in the active site of μ-glutathione
S-transferase(Xiao et al., 1996) (μ-GST), whose differential expression has been
implicated in the development of cancers as well as their resistance to
chemotherapeutic drugs ((Mccallum et al., 2000) and reference therein).
Finally we present a classic problem treated by quantum-chemical methods: the
simulation of an enzymatic reaction. We focus on a class of cysteine proteases, the
caspases. These enzymes are extremely important targets for pharmaceutical
intervention in therapies against Alzheimer's and other neurodegenerative processes,
yet very few inhibitors have been so far designed. Since an important class of inhibitors
is the given by the transition state analogs, it is of importance to fully understand the ·
enzymatic reaction, that is the hydrolysis of peptides. Because of the crucial importance
of temperature and environment(Karplus, 2000; Glennon and Warshel, 1998; Varnai
and Warshel, 2000; Villa et al., 2000) effects for enzymatic catalysis, we use here a
hybrid Car-Parrinello Molecular dynamics I Molecular mechanics approach recently
developed in the Lab of Prof. U. Roethlisberger (Laio et al., 2001 ). This technique
allows to evaluate the intermolecular interactions at the active site from electronic
structure calculations as the simulation proceeds(Car and Parrinello, 1985). Steric and
electrostatic effects of the protein scaffold on the quantum region are included using
classical MD approach on the rest of the system. The free energy of the process is
calculated using a thermodynamic integration approach(Ciccotti et al., 1989; Carloni et
al., 2000; Piana et al., 2001). This thesis is organized as follows. The first chapter provides a description of the used
computational techniques. The following chapter describes the systems investigated
here and summarizes our findings. The subsequent three chapters are devoted to a -
detailed description of my thesis work. In a final chapter we draw some conclusions and
provide a perspective for possible future applications, which could follow this work.
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Leggott, Richard James. "On AB initio solutions to the phase problem for macromolecular crystallography." Thesis, University of York, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.336841.
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Kim, Gapsue. "Ab initio calculation of the excited states of some diatomic molecular ions." Thesis, University of Warwick, 1997. http://wrap.warwick.ac.uk/3958/.
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This thesis aims to provide theoretical information by using ab initio calculations as a bridge between theory and experiment. This thesis presents calculations of potential energy curves for the diatomic molecular ions NF+, PCl+, AsCl+ and BBr+ and preliminary potential energy surfaces for HC + NO. For the diatomic molecular ions, this work presents the low-lying electronic states of NF+, PCl+, AsCl+ and BBr+ correlating with the lowest dissociation asymptotes, namely N+(3p) + F(2p), P+(3P) + Cl(2p), As+(3p) + Cl(2p), B+(1S) + Br(2P) and B(2p) + Br+(3p). In this work CASSCF and CI calculations have been performed with the correlation-consistent valence quadruple-zeta (VQZ) basis sets for NF+ and PCl+, averaged atomic natural orbital (ANO) basis sets for AsCl+ and BBr+, and the correlation-consistent valence double-zeta (VDZ) basis sets for HC + NO. From the calculations of potential energy curves four bound states, namely X2Π, A2Π, 14Σ and 14Π, are found for NF+, PCl+ and AsCl+, and there are many more bound states, namely 12Σ+, 12Π, 22Π, 22Σ+, 12Δ, 12Σ-, 4Σ+, 4Δ, and 14Σ-, for BBr+. For all the bound states spectroscopic constants have been calculated. For NF+, PCl+ and AsCl+ our results are in good agreement with the available spectroscopic data. However, for BBr+ the theoretical values are in disagreement with experimental data. It is suggested that a reinvestigation of the experimental spectrum of this species would be worthwhile. Calculations of transition moments for bound-bound transitions have been carried out. For HC + NO the linear structures for 1Σ+, 1Σ-, 3Σ+ and 3Σ- states and the bent structure for 1A' state have been calculated. These calculations were intended to obtain potential energy surfaces for the reaction of HC with NO. However, due to the lack of time left, only preliminary calculations are completed. Reaction without an activation barrier may occur for a non-collinear approach of HC to NO.
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Gambino, Davide. "Titanium vacancy diffusion in TiN via non-equilibrium ab initio molecular dynamics." Thesis, Linköpings universitet, Teoretisk Fysik, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-129555.
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Transition metal nitrides (TMNs) refractory ceramic materials are widely employed as wear-resistant protective coatings in industrial machining as well as diffusion barriers inhibiting migration of metal impurities from the interconnects to the semiconducting region of electronic devices. TiN is the prototype of this class of materials and the most studied among TMNs. However, also for this system, a complete picture of the migration processes occurring at the atomic scale is still lacking. In this work I investigate the stability of Ti vacancy configurations and corresponding migration rates in TiN by means of density functional theory (DFT) calculations and ab-initio molecular dynamics simulations (AIMD). DFT calculations show that Ti vacancies tend to stay isolated because of repulsive interaction which decreases as the inverse of the distance between the vacancies.The equilibrium jump rate of single Ti vacancies in TiN is extrapolated temperature as a function of temperature from the results of non-equilibrium AIMD simulations accelerated by a bias force field according to the color diffusion algorithm. For each force field and, the jump occurrence times are fitted with the two parameters Gamma distribution in order to obtain the non equilibrium jump rate with the corresponding uncertainty. Extrapolated equilibrium values show an Arrhenius-like behavior, with activation energy Ea= (3.78 ± 0.28)eV and attempt frequency A = 4.45 (x3.6±1) x 1014 s-1.
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Hamada, Tomoyuki. "Ab Initio Molecular Orbital Study of Nonlinear Optical Materials for Optoelectronics Applications." Kyoto University, 1998. http://hdl.handle.net/2433/182321.
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Bruque, Nicolas Alexander. "High throughput ab initio modeling of charge transport for bio-molecular-electronics." Diss., [Riverside, Calif.] : University of California, Riverside, 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3359891.
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Thesis (Ph. D.)--University of California, Riverside, 2009.Includes abstract. Title from first page of PDF file (viewed March 12, 2010). Available via ProQuest Digital Dissertations. Includes bibliographical references (p. 117-136). Also issued in print.
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More, Joshua N. "Algorithms and computer code for ab initio path integral molecular dynamics simulations." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:b8ca7471-21e3-4240-95b1-8775e5d6c08f.
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This thesis presents i-PI, a new path integral molecular dynamics code designed to capture nuclear quantum effects in ab initio electronic structure calculations of condensed phase systems. This software has an implementation of estimators used to calculate a wide range of static and dynamical properties and of state-of-the-art techniques used to increase the computational efficiency of path integral simulations. i-PI has been designed in a highly modular fashion, to ensure that it is as simple as possible to develop and implement new algorithms to keep up with the research frontier, and so that users can take maximum advantage of the numerous electronic structure programs which are freely available without needing to rewrite large amounts of code. Among the functionality of the i-PI code is a novel integrator for constant pressure dynamics, which is used to investigate the properties of liquid water at 750 K and 10 GPa, and efficient estimators for the calculation of single particle momentum distri- butions, which are used to study the properties of solid and liquid ammonia. These show respectively that i-PI can be used to make predictions about systems which are both difficult to study experimentally and highly non-classical in nature, and that it can illustrate the relative advantages and disadvantages of different theoretical methods and their ability to reproduce experimental data.
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Silva, Frederico Teixeira. "Análise de algoritmos eficientes para uso em dinâmica molecular ab initio direta." Universidade Federal de Minas Gerais, 2014. http://hdl.handle.net/1843/SFSA-9P8QUS.
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A software that integrates classical equations of motion was developed. The program named DRKAI (Dinâmica Runge Kutta ab initio) was first tested in a simple differential equation, which has analytical solution, showing great accuracy in this case. Verified its efficiency, DRKAI was applied in a molecular system, known as molecular dynamics approach. Dynamic results showed good energy conservation and preservation of major feateres of the system. The second part of this paper came when high computational cost was perceived at desired approach. This made imperative the use of efficient algorithms. Many different algorithms are used in current works, making complex the choice of what
should be implemented. In this thesis a study was made for five integrators. Among these, the symmetric Runge Kutta integrators and Beeman-Verlet were the most efficient, the algorithm of Gauss Radau proved inadequate for long simulations and the algorithm of Runge Kutta Gill proved to be the slowest.Um software que integra as equações de movimento clássicas foi desenvolvido. O programa, de nome DRKAI (Dinâmica Runge Kutta ab initio) foi inicialmente testado em uma equação diferencial simples, a qual possui solução analítica, demonstrando grande precisão nesse caso. Verificada sua eficiência, foi aplicado em sistemas moleculares, abordagem conhecida como dinâmica molecular. Os testes da dinâmica resultaram em boa conservação de energia e preservação das características do sistema. A segunda parte deste trabalho surgiu ao perceber que a dinâmica, na abordagem desejada, possui alto custo computacional, tornando imperativo o uso de algoritmos eficientes. Muitos algoritmos diferentes são usados em trabalhos atuais, tornando complexa a escolha do que deveria ser implementado. Nesta dissertação foi feito um estudo de cinco integradores. Dentre esses, os integradores Runge Kutta simétrico e Beeman-Verlet foram os mais eficientes, o algoritmo de Gauss Radau se mostrou inadequado para simulações longas e o algoritmo de Runge Kutta Gill revelou-se como o mais lento.
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Ullrich, Susanne. "Conformers and non-covalent interactions studied by laser spectroscopies and Ab initio calculations." Thesis, University of York, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.247030.
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Cassone, Giuseppe. "Ab initio molecular dynamics simulations of H-bonded systems under an electric field." Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066061/document.
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Malgré le mécanisme de base du transport protonique (PT) dans l'eau ait été proposé en 1806, à ce jour il n'existe pas de théorie complète qui décrive la protolyse. Ce phénomène est à la base du fonctionnement des batteries à hydrogène et de nombreux processus biologiques. Grâce à la technique de dynamique moléculaire Car-Parrinello (CPMD) et à l'aide de l'application d'un champ electrique (EF), une partie de cette thèse a été consacrée à l'étude du PT dans deux phase de la glace: la phase Ih et sa contrepartie ferroélectrique, la glace XI. Certains mécanismes ont été révélés: le rôle joué par les oxygènes lorsque se produit le PT et la contribution du (dés)ordre afin d'assister ce processus [1,2]. Le phénomène du PT est aussi à la base de nombreaux convertisseurs d'énergie constitués par le méthanol tels que le Direct Methanol Fuel Cells et les membranes Nafion. Afin de révéler la nature intime du PT dans le méthanol liquide, une série de simulations CPMD ont été menées sous l'effet d'un EF extérieur. De cette façon il a été possible de comparer le rôle joué par les liasons hydrogène afin d'assister le PT [3]. De plus, quand les intensités du champ sont plus élevées que celles qui donnent lieu au PT, certaines réactions chimiques ont été observées dans le même échantillon "numérique" du méthanol. En exploitant des paramètres typique de la "Théorie de la fonctionnelle de la densité conceptuelle", il a été possible de clarifier les conditions qui donnent lieu à ces réactions chimiques. Enfin, afin de quantifier la contribution du EF à la formation de méthane et de formaldéhyde dans le système, des simulations de métadynamique en conjonction à ceux ab initio ont été menéesAlthough the basic mechanism of the proton transfer (PT) phenomenon in water has been envisaged in 1806, nowadays does not exist a detailed theoretical framework that envelop the protolysis process. This phenomenon is at the base of the operation of hydrogen batteries, as well as of many biological processes. Via the Car-Parrinello Molecular Dynamics (CPMD) technique and by means of the application of an electric field (EF), part of this thesis has been devoted to the detailed study of PT in two ice phases: ice Ih and its ferroelectric counterpart, ice XI. Several previously unknown mechanisms have been shown. As an example, the role played by the oxygens when a PT occurs and the contribution due to (dis)order in assisting this process [1,2]. The PT phenomenon is also at the base of the functioning of some methanol-based energy converters such as Nafion membranes. To the aim of disclosing the intimate nature of PT in liquid methanol, a series of CPMD simulations have been carried out by applying an external EF; the role played by the H-bond network have been also compared with the similar PT mechanism in water [3]. At field strengths higher than those leading to PT, several chemical reactions have been observed in this sample. By exploiting the conceptual Density Functional Theory framework, it has been possible to clarify the circumstances under which a given chemical reaction occurs. Moreover, in order to disclose the role played by the EF in assisting chemical reactions, the mechanism leading to the formation of formaldehyde and methane in the sample has been studied with metadynamics approaches in conjuction with the ab initio ones
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Koči, Love. "Studies of Material Properties using Ab Initio and Classical Molecular Dynamics." Doctoral thesis, Uppsala universitet, Kondenserade materiens teori (Fysik IV), 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8626.
Full textAbstract:
In this thesis, material properties have been examined under extreme conditions in computer-based calculations. The research on iron (Fe), nickel (Ni), and ferropericlase (Mg1-xFexO) are not only important for our understanding of the Earth, but also for an improved knowledge of these materials per se. An embedded-atom model for Fe demonstrated to reproduce properties such as structure factors, densities and diffusion constants, and was employed to evaluate temperature gradients at Earth core conditions. A similar interaction together with a two-temperature method was applied for the analysis of shock-induced melting of Ni. For Mg1-xFexO, the magnetic transition pressure was shown to increase with iron content. Furthermore, the C44 softening with pressure and iron composition supports the experimentally observed phase transition for Mg0.8Fe0.2O at 35 GPa. The properties of high density helium (He) is of great interest as the gas is one of the most abundant elements in the solar system. Furthermore, He and neon (Ne) are often used as pressure media in diamond anvil cells. The melting of He showed a possible fcc-bcc-liquid transition starting at T=340 K, P=22 GPa with a Buckingham potential, whereas the bcc phase was not seen with the Aziz form. For Ne, Monte Carlo calculations at ambient pressure showed very accurate results when extrapolating the melting temperatures to an infinite cluster limit. At high pressure, a one-phase ab initio melting curve showed a match with one-phase L-J potential results, which could imply a correspondence between ab initio/classical one-phase/two-phase calculations. In the search for hard materials, ab initio calculations for four TiO2 phases were compared. Just as imposed by experiment, the cotunnite phase was found to be very hard. The anomalous elastic behavior of the superconducting group-V metals V, Nb, Ta was found to be related to shrinking nesting vectors and the electronic topological transition (ETT).