Thèses : « MOLECULAR PRINCIPLE »

1

Kirchhoff, Florian. « Simulation of liquid chalcogenides by first-principle molecular dynamics ». Thesis, Keele University, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.339849.

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Sutcliffe, Julia H. « Quantum studies of molecular dynamics ». Thesis, University of Nottingham, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282566.

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Yasuda, Koji, et Daisuke Yamaki. « Simple minimum principle to derive a quantum-mechanical/molecular-mechanical method ». American Institute of Physics, 2004. http://hdl.handle.net/2237/8738.

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Zhang, Lei, et 張磊. « First principle calculation : current density in AC electric field ». Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B43278437.

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Zhang, Lei. « First principle calculation : current density in AC electric field / ». Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43278437.

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Jou, Wen Chi. « The theoretical studies of time-correlation functions with the first principle molecular dynamics simulations on surfaces / ». Tamsui : Tamkang University, Department of Chemistry, 2007. http://etds.lib.tku.edu.tw/etdservice/view_metadata?etdun=U0002-0207200714531200.

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Wild, Michael de. « Novel principle for 2D molecular self-assembly : self-intermixed monolayer phases of sub-phthalocyanine and C₆₀ on Ag(111) / ». Basel : Universität Basel, 2002. http://edoc.unibas.ch/diss/DissB_6271.

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Afaneh, Akef. « Computational investigations of the electronic structure of molecular mercury compounds : ion-selective sensors ». Springer International Publishing AG, 2012. http://hdl.handle.net/1993/30661.

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This thesis presents the basic concepts of electronic structure theory and the chemical properties of mercury. The theoretical foundation of DFT and the consequences of relativity are also introduced. The electronic structure of Hg(II) ions, [Hg(L)n(H2O)m]q (L = HO-, Cl-, HS-, S2-) has been studied. We show, in this thesis, that the charge transfer (that is calculated from the hard-soft-acid-base principle (Pearson’s principle)), the total NBO charge and the interaction energies are strongly correlated. Our studies indicate the effect of the solvent on the global electrophilicity, the charge transfer and consequently the interaction strength between Hg(II) and ligand L. The formation constants, logK, of Hg2+−complexes are calculated. The procedure that we follow in this thesis to calculate the formation constants, logK’s, are in good agreement with the extrapolated experimental values. We introduce and explain why it is important adding water molecules explicitly during the calculations of the logK. The recommended logK value of HgS is 27.2. We examined two different types of organic compounds as sensors for heavy metal ions: lumazine (Lm) and 6-thienyllumazine (TLm). We found that the simple calculation of pKa values using DFT methods and implicit solvent models failed to reproduce the experimental values. However, calculated orbital energies and gas phase acidities both indicate that the compound TLm is inherently more acidic than the parent species Lm. We demonstrate that: (1) we need to take in our consideration the population of each tautomer and conformer during the calculations of the pKa values, and (2) thienyl group has indirect effect on the acidity of the proton on N1 in the uracil ring. Last but not least, the fluorescence spectrum of the sensors (L) and their [(L)nM(H2O)m]2+ complexes (L = Lumazine (Lm) and 6-thienyllumazine (TLm) and M = Cd2+and Hg2+) are calculated using time dependent DFT (TDDFT). The results show that TDDFT is in good agreement with experimental results. This chapter provides a new concept in the design of fluorescence turn-on/off sensors that has wider applicability for other systems. Finally, we provide a summary of the works compiled in this thesis and an outlook on potential future work.
October 2015

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Yang, Qiufeng. « Separation and Properties of La₂O₃ in Molten LiF-NaF-KF Salt ». Thesis, Virginia Tech, 2018. http://hdl.handle.net/10919/87058.

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Studies on nuclear technology have been ongoing since nuclear power became uniquely important to meet climate change goals while phasing out fossil fuels. Research on the fluoride salt cooled high temperature reactor (FHR), which is funded by the United States Department of Energy (DOE), has developed smoothly with the ultimate goal of a 2030 deployment. One challenge presented by FHR is that the primary coolant salt can acquire contamination from fuel failure and moisture leaking into the system. If contamination happens, it will result in a low concentration of fission products, fuel, transuranic materials and oxide impurities in the coolant. These impurities will then affect the properties of the molten salt in the long term and need to be removed without introducing new impurities. Most of the research conducted recently has focused on impurity separation in chloride molten salts. More research urgently needs to be conducted to study the impurity separation method for the fluoride molten salts. In this study, the La₂O₃-LiF-NaF-KF (La₂O₃-FLiNaK) system is used to demonstrate impurity separation in molten fluoride salt. Since lanthanum oxide needs to be dissolved in the fluoride molten salt and studies in this field are still not complete, the solubility of lanthanum oxide in FLiNaK have been measured at different temperatures to obtain the temperature-dependent solubility and understand the corresponding dissolution mechanisms first. In the solubility related experiments, Inductively Coupled Plasma Mass Spectrometry (ICP-MS) is utilized to analyze the concentration of lanthanum ions in the molten FLiNaK salt, while X-ray powder diffraction (XRD) was applied to determine the phase patterns of molten salt. Second, electrochemical experiments with tungsten and graphite as working electrodes were conducted individually to demonstrate the separation of the dissolved oxide from the salt. When the tungsten working electrode was applied, the lanthanum ions were reduced to lanthanum metal at the tungsten cathode, while the fluorine ions reacted with the tungsten anode to form tungsten fluoride. In the experiments, the production of tungsten fluoride could lead to increasing current in the cell, even overload. Moreover, theoretically, tungsten fluoride WF4 is soluble in the fluoride salt thus introducing new impurities. All these issues make tungsten not the best choice when applied to the separation of oxygen ions. Therefore, another common working electrode graphite is used. It not only has all the advantages of tungsten, but also has good performance on separation of oxygen ions. When the graphite electrode was applied, the lanthanum ions were separated in the form of lanthanum carbide (LaC₂), while the oxygen ions can be removed in the form of carbon dioxide (CO₂) or carbon monoxide (CO). In addition, only graphite was consumed during the whole separation process, which is why the graphite anode electrode is called the “sacrificial electrode”. Third, First Principle Molecular Dynamics (FPMD) simulations with Vienne Ab initio Simulation Package (VASP) was conducted to study the properties of the fluoride molten salt. In this study, the structure information and enthalpy of formation were obtained. Generally, the simulation process can be divided into four steps: (1) the simulation systems are prepared by packing ions randomly via Packmol package in the simulation cell; (2) an equilibrium calculation is performed to pre-equilibrate the systems; (3) FPMD simulations in an NVT ensemble are implemented in VASP; (4) based on the FPMD simulations results, the first peak radius and the first-shell coordination number were evaluated with partial radial distribution function (PRDF) analysis to determine the statistics of molten salt structure information, while the transport properties, e.g., the self-diffusion coefficient was calculated according to the function of mean square displacement (MSD) of time generated by the Einstein-Smoluchowshi equation. The viscosity and ionic conductivity were obtained by combining the self-distribution coefficient with the Einstein-Stokes formula and Nernst-Einstein equation.
Master of Science
With the fast development of modern society and economy, more and more energy is urgently needed to meet the growth of industry. Since the traditional energy, such as nature gas, coal, has limited storage and not sustainable, nuclear energy has attracted much attention in the past few decades. Although lots of study has been conducted by thousands of researchers which has attributed to application of nuclear power, there are still some concerns in this field, among which, impurities removal is the most difficult part. Fluoride salt cooled high temperature reactor (FHR) is one of the most promising Gen IV reactor types. As the name indicates, molten salt is the coolant to serve as the heat exchanger intermedium. In addition, it’s inevitable that fission products, i.e. lanthanum, moisture, would leak into the coolant pipe, thus affect the molten salt properties, even degrade reactor performance, therefore, those impurities must be removed without introducing new impurities. In this study, the La₂O₃-LiF-NaF-KF (La₂O₃-FLiNaK) system is used to demonstrate impurity separation into molten fluoride salt. First, solubility of lanthanum oxide in FLiNaK has been measured at different temperatures to understand its dissolution mechanisms. Then, electrochemical experiments with tungsten and graphite as working electrodes were conducted individually to demonstrate the separation of the dissolved oxide from the salt. It has been concluded that tungsten performed well to separate La3+, while failed in the separation of O2-. However, graphite working electrode has succeeded in the removal of La³⁺ and O²⁻. Finally, molecular dynamic simulation with first principle was also conducted to further understand the local structure and heat of formation in the molten FLiNaK and La₂O₃-FLiNaK salt.

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Batisteti, Caroline Belotto [UNESP]. « Os estudos de Avery, Macleod e Mccarty e a idéia do DNA como responsável pela hereditariedade : interpretações historiográficas e apontamentos para o ensino de biologia ». Universidade Estadual Paulista (UNESP), 2010. http://hdl.handle.net/11449/90888.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Um dos momentos históricos interessantes no estabelecimento da Biologia Molecular diz respeito às pesquisas realizadas por Avery, MacLeod e McCarty, que indicaram que a natureza química do princípio transformante bacteriano era o DNA. A nosso ver, esse episódio pode ser explorado do ponto de vista histórico, e assim fornecer elementos relevantes para o Ensino de Ciências. Em relação à perspectiva histórica, embora os estudos de Avery e colaboradores sejam atualmente considerados referência no estabelecimento de relações entre DNA e hereditariedade, há na literatura apontamentos sobre a provável não aceitação imediata desses pela comunidade científica da época (1944). Assim, o objetivo da presente pesquisa foi investigar, por meio da análise de fontes primárias, como artigos, documentos e correspondências que envolvem Avery e colaboradores, os motivos para a resistência inicial aos resultados de seus trabalhos. Dentre as razões levantadas, podemos mencionar dúvidas de cunho técnico, que indicavam a presença de proteínas nos preparados utilizados por Avery e colaboradores, a suposta timidez de Avery e a idéia de sua proposta ter sido cientificamente prematura. Outra razão, que aparentemente, abrange um maior número de aspectos envolvidos no processo de construção do conhecimento em questão, refere-se à hipótese de que a idéia do DNA como responsável pela hereditariedade encontrou dificuldades em ser aceita, pois, foi produzida e apresentada inicialmente fora da área de domínio da temática de interesse, no caso, a Genética. Acerca da utilização do episódio histórico em questão no Ensino, essa se justifica, pois possibilita a observação de diversos elementos que caracterizam e estão envolvidos na produção científica, como por exemplo: implicações metodológicas, subjetividade dos indivíduos, coletividade...
One of the interesting historical moment on the establishment of Molecular Biology is related to Avery, MacLeod and McCarty’s research, which indicated that the chemical nature of the transforming principle in bacteria was DNA. In our view, this episode can be explored from a historical perspective, and thus provide relevant information to the Teaching of Science. Regarding the historical perspective, although Avery and his colleague’s studies are now considered landmark in the establishment of relations between DNA and heredity, in literature there are notes on the probable immediate rejection of this by the scientific community of that time (1944). The objective of this research was to investigate, through analysis of primary sources such as articles, documents and correspondence involving Avery and his colleagues, the reasons for the initial resistance to the results of their work. Among the reasons raised, we can mention technical-doubt, which indicated the presence of protein in the preparations used by Avery and his colleagues, the alleged Avery’s timidity and the idea of his proposal was scientifically premature. Another reason, which apparently includes a greater number of issues involved in building the knowledge in discussion, refers to the hypothesis that the idea of DNA as responsible for heredity found difficulties to be accepted, because it was produced and presented initially outside of Genetics field. As far as use of the referred historical episode in Education or in Teaching of Biology, this is justified because it enables the observation of several elements that characterize and are involved in scientific research, such as: methodological implications, the subjectivity of individuals, collective production of knowledge, social influences (hostility), the impact of the journal in which they release a specific publication, ... (Complete abstract, click electronic access below)

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Weiß, Richard Gregor. « The role of water in the kinetics of hydrophobic molecular recognition investigated by stochastic modeling and molecular simulations ». Doctoral thesis, Humboldt-Universität zu Berlin, 2018. http://dx.doi.org/10.18452/18814.

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Die Assoziation kleiner Moleküle (Liganden) in hydrophobe Bindungstaschen spielt eine fundamentale Rolle in der Biomolekularerkennung und den Selbstassemblierungsprozessen der physikalischen Chemie wässriger Lösungen. Während der Einfluss des Wassers auf die freie Energie der Bindung (die Bindungsaffinität) im thermischen Gleichgewicht in den letzten Jahren auf immer stärkere Aufmerksamkeit stößt, ist die Rolle des Wassers in der Kinetik und der Bestimmung der Bindungsraten noch weitestgehend unverstanden. Welche nanoskaligen Effekte des Wassers beeinflussen die Dynamik des Liganden in der Nähe der Bindungstasche, und wie lassen sie sich durch die chemischen Eigenschaften der Tasche steuern? Neuste Forschungen haben mithilfe von molekularen Computersimulationen eines einfachen Modells gezeigt, dass Hydrationsfluktuationen in der hydrophoben Bindungstasche an die Dynamik des Liganden koppeln und damit seine Bindungsrate beeinflussen. Da die Wasserfluktuationen wiederum durch die Geometrie und Hydrophobizität der Bindungstasche beeinflusst werden, entsteht die Möglichkeit, kontrollierte Fluktuation zu kreieren, um die Bindungsraten des Liganden zu steuern. In dieser Arbeit wird diese Perspektive mithilfe eines theoretischen Multiskalenansatzes für prototypische Schlüssel-Schloss-Systeme aufgegriffen. Wir untersuchen den Einfluss der physikochemischen Eigenschaften der Bindungstasche auf die Diffusivität und die Bindungsraten des Liganden, und wie die Orientierung eines anisotropen Liganden an die Hydrationsfluktuationen der Tasche koppelt. Damit stellen wir fest, dass kleine Änderungen der Taschentiefe eine extreme Beschleunigung der Bindungsraten bewirken kann und, dass gleichzeitig die Bindung in konkave Taschen vorteilhaft für die Reorientierungsdynamik des Liganden ist. Die Resultate dieses Projekts sollen somit helfen, maßgeschneiderte Lösungen für funktionale „Host-Guest“-Systeme sowie pharmazeutische Moleküle in biomedizinischen Anwendungen zu entwickeln.
The association of small molecules (ligands) to hydrophobic binding pockets plays an integral role in biochemical molecular recognition and function, as well as in various self-assembly processes in the physical chemistry of aqueous solutions. While the investigation of water contributions to the binding free energy (affinity) in equilibrium has attracted a great deal of attention in the last decade, little is known about the role of water in determining the rates of binding and kinetic mechanisms. For instance, what are the nanoscale water effects on ligand diffusion close to the hydrophobic docking site, and how can they be steered by the chemical composition of the pocket? Recent studies used molecular simulations of a simple prototypical pocket-ligand model to show that hydration fluctuations within the binding pocket can couple to the ligand dynamics and influence its binding rates. Since the hydration fluctuations, in turn, can be modified by the pocket’s geometry and hydrophobicity, the possibility exists to create well-controlled solvent fluctuations to steer the ligand’s binding rates. In this work, we pick up this appealing notion employing a theoretical multi-scale approach of a generic key-lock system in aqueous solution. We explore the influence of the physicochemical properties of the pocket on local ligand diffusivities and binding rates and demonstrate how the orientation of a (non-spherical) ligand couples to a pocket’s hydration fluctuations. We find that minor modulation in pocket depth can drastically speed up the binding rate and that, concurrently, binding to molded binding sites is advantageous for the rotational dynamics of the ligand. The results and discussion of this work shall, therefore, imply generic design principles for tailored solutions of functional host-guest systems as well as optimized drugs in biomedical applications.

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Batisteti, Caroline Belotto. « Os estudos de Avery, Macleod e Mccarty e a idéia do DNA como responsável pela hereditariedade : interpretações historiográficas e apontamentos para o ensino de biologia / ». Bauru : [s.n.], 2010. http://hdl.handle.net/11449/90888.

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Resumo: Um dos momentos históricos interessantes no estabelecimento da Biologia Molecular diz respeito às pesquisas realizadas por Avery, MacLeod e McCarty, que indicaram que a natureza química do princípio transformante bacteriano era o DNA. A nosso ver, esse episódio pode ser explorado do ponto de vista histórico, e assim fornecer elementos relevantes para o Ensino de Ciências. Em relação à perspectiva histórica, embora os estudos de Avery e colaboradores sejam atualmente considerados referência no estabelecimento de relações entre DNA e hereditariedade, há na literatura apontamentos sobre a provável não aceitação imediata desses pela comunidade científica da época (1944). Assim, o objetivo da presente pesquisa foi investigar, por meio da análise de fontes primárias, como artigos, documentos e correspondências que envolvem Avery e colaboradores, os motivos para a resistência inicial aos resultados de seus trabalhos. Dentre as razões levantadas, podemos mencionar dúvidas de cunho técnico, que indicavam a presença de proteínas nos preparados utilizados por Avery e colaboradores, a suposta timidez de Avery e a idéia de sua proposta ter sido cientificamente prematura. Outra razão, que aparentemente, abrange um maior número de aspectos envolvidos no processo de construção do conhecimento em questão, refere-se à hipótese de que a idéia do DNA como responsável pela hereditariedade encontrou dificuldades em ser aceita, pois, foi produzida e apresentada inicialmente fora da área de domínio da temática de interesse, no caso, a Genética. Acerca da utilização do episódio histórico em questão no Ensino, essa se justifica, pois possibilita a observação de diversos elementos que caracterizam e estão envolvidos na produção científica, como por exemplo: implicações metodológicas, subjetividade dos indivíduos, coletividade... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: One of the interesting historical moment on the establishment of Molecular Biology is related to Avery, MacLeod and McCarty's research, which indicated that the chemical nature of the transforming principle in bacteria was DNA. In our view, this episode can be explored from a historical perspective, and thus provide relevant information to the Teaching of Science. Regarding the historical perspective, although Avery and his colleague's studies are now considered landmark in the establishment of relations between DNA and heredity, in literature there are notes on the probable immediate rejection of this by the scientific community of that time (1944). The objective of this research was to investigate, through analysis of primary sources such as articles, documents and correspondence involving Avery and his colleagues, the reasons for the initial resistance to the results of their work. Among the reasons raised, we can mention technical-doubt, which indicated the presence of protein in the preparations used by Avery and his colleagues, the alleged Avery's timidity and the idea of his proposal was scientifically premature. Another reason, which apparently includes a greater number of issues involved in building the knowledge in discussion, refers to the hypothesis that the idea of DNA as responsible for heredity found difficulties to be accepted, because it was produced and presented initially outside of Genetics field. As far as use of the referred historical episode in Education or in Teaching of Biology, this is justified because it enables the observation of several elements that characterize and are involved in scientific research, such as: methodological implications, the subjectivity of individuals, collective production of knowledge, social influences (hostility), the impact of the journal in which they release a specific publication, ... (Complete abstract, click electronic access below)
Orientador: João José Caluzi
Coorientador: Elaine Sandra Nicolini Nabuco de Araujo
Banca: Maria Elice Brzezinski Prestes
Banca: Ana Maria de Andrade Caldeira
Mestre

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Adam, Colin John. « Molecular properties of mesogenic fragments and molecules from first principles ». Thesis, University of Edinburgh, 1999. http://hdl.handle.net/1842/10776.

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In order to gain a deeper understanding of the relationship between molecular structure and liquid crystal properties, accurate data is required on single molecule properties of mesogenic fragments and molecules. This thesis applies a pseudopotential plane wave total energy method to calculate molecular properties of prototypical mesogenic fragments and the molecule 4-n-pentyl-4'-cyanobiphenyl (5CB) from first principles. Optimised molecular structures, vibrational properties and torsional potentials are determined and found to compare well with experimental observations and other ab initio investigations. A study is made of the transferability of torsional potentials between mesogenic fragments and 5CB. Also investigated is the conformation-dependence of dipole and quadrupole moments. The strength of the coupling is found to depend sensitively on the molecular structure and the conformation-dependence of quadrupole moments is found to significantly influence inter-molecular interactions. Finally, by combing first principles calculations with an empirical mean field approximation, conformational distributions of the alkyl tail in 5CB are examined.

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Khandaker, Md Shahriar K. « Investigation on the Mechanisms of Elastomechanical Behavior of Resilin ». Diss., Virginia Tech, 2015. http://hdl.handle.net/10919/64362.

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Resilin is a disordered elastomeric protein and can be found in specialized regions of insect cuticles. Its protein sequence, functions and dynamic mechanical properties vary substantially across the species. Resilin can operate across the frequency range from 5 Hz for locomotion to 13 kHz for sound production. To understand the functions of different exons of resilin, we synthesize recombinant resilin-like hydrogels from different exons, and investigate the water content and dynamic mechanical properties, along with estimating surface energies relevant for adhesion. The recombinant resilin-like hydrogel has 80wt% water and does not show any sign of tack even though it satisfies the Dahlquist criterion. Finally, doubly shifted dynamic moduli master curves are developed by applying the time-temperature concentration superposition principle (TTCSP), and compared to results obtained with natural resilin from locusts, dragonflies and cockroaches. The resulting master curves show that the synthetic resilin undergoes a prominent transition, though the responsible mechanism is unclear. Possible explanations for the significant increase in modulus include the formation of intramolecular hydrogen bonds, altered structural organization, or passing through a glass transition, all of which have been reported in the literature for polymeric materials. Results show that in nature, resilin operates at a much lower frequency than this glass transition frequency at room temperature. Moreover, recombinant resilins from different clones have comparable resilience with natural resilin, though the modulus is around 1.5 decades lower. Results from the clones with and without chitin binding domains (ChBD) indicate that the transition for the clone without ChBD occurs at lower frequencies than for those with the ChBD, perhaps due to the disordered nature of the clone without ChBD. Atomistic molecular modeling is applied on the repetitive motifs of resilin and different elastomeric proteins to better understand the relationship between elastomeric behavior and amino acid sequences. Results show that the motifs form a favorable bent conformation, likely enabled by glycine's lack of steric hindrance and held in place through intramolecular hydrogen bonds. During Steered Molecular Dynamic (SMD) pulling of these motifs, the hydrogen bonds break and they reform again when the peptides are released to move freely, returning to similar bent conformations. The transition seen in the master curves of recombinant resilins might be due to either these intramolecular hydrogen bonds or to glass transition behavior, though evidence indicates that the transition probably due to the glass transition. What we learned from the synthesized recombinant resilin and simulating the repetitive motifs of resilin may be applicable to the biology and mechanics of other elastomeric biomaterials, and may provide deeper understanding of their unique properties.
Ph. D.

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Singh-Miller, Nicholas E. (Nicholas Edward). « Molecular-scale devices from first principles ». Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/52792.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2009.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (p. 155-167).
Electronic structure calculations are becoming more widely applied to complex and realistic materials systems and devices, reaching well into the domain of nanotechnology, with applications that include metal-molecule junctions, carbon-nanotube field effect transistors, and nanostructured metals or semiconductors. For such complex systems, characterizing the properties of the elementary building blocks becomes of fundamental importance. In this thesis we employ first-principles calculations based on density-functional theory (DFT) to investigate fundamental properties of molecular-scale devices. We focus initially on the constituent components of these devices (polymers, metal surfaces, carbon nanotubes), following with studies of entire device geometries (nanotube/metal interfaces). We first study a proposed molecular actuating system in which the interaction between oligothiophenes is the driving force behind an electromechanical response. The oligothiophenes are attracted to each other through p-stacking interactions driven by redox reactions. We show that counterions strengthen this interaction further through enhanced screening of the electrostatic repulsion. Many molecular scale devices require contact with a metallic conductor, we also study the fundamental properties of metal surfaces in the slab-supercell approximation; in particular layer relaxation, surface energy, work function, and the effect that slab thickness has on these properties. The surfaces of interest are the low index, (111), (100), and (110) surfaces of Al, Au, Pd, and Pt and the close packed (0001) surface of Ti.
(cont.) We show that these properties are well converged for slabs that have between 5 and 10 layers, depending on the property considered and the surface orientation. We then focus on understanding and characterizing devices. Since it is widely proposed that carbon nanotubes (CNTs) could replace Si in future transistor devices, we examine the work function of single-wall CNTs and the effects that covalent functionalization could have in engineering performance. Electrostatic dipoles form due to the charge asymmetries in the functionalized CNT unit cell, and the use of periodic boundary conditions affects our calculations. We correct for these spurious dipole-dipole interactions with a real-space potential derived directly from the solution to Poisson's equation in real-space with open boundary conditions. We find that the functionalizations can be clearly labeled as electropositive and electronegative, and that they decrease or increase the work function of the CNT accordingly. Finally, we join metal surfaces and CNTs to study Schottky barrier heights (SBHs) that form at the interface. We take Al(111) and Pd(111) as examples of low- and high-work function metal surfaces and contact them with the semiconducting (8,0) CNT. We find that in all cases a surface dipole forms that shifts the band structure of the CNT locally. In these systems, we investigate the effects of surface roughness and functionalization on SBHs, and find that controlling the electrostatics at the interface (with functionalization, adsorbates, and device geometry) can lead to further engineering of the SBHs.
by Nicholas E. Singh-Miller.
Ph.D.

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Su, Wenyong. « First Principles Study of Molecular Electronic Devices ». Licentiate thesis, Stockholm : Bioteknologi, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3882.

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Ning, Zhanyu. « First principles quantitative modeling of molecular devices ». Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=97011.

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In this thesis, we report theoretical investigations ofnonlinear and nonequilibrium quantum electronic transport propertiesof molecular transport junctions from atomistic first principles.The aim is to seek not only qualitative but alsoquantitative understanding of the correspondingexperimental data. At present, the challenges to quantitativetheoretical work in molecular electronics include two most importantquestions: (i) what is the proper atomic model for the experimentaldevices? (ii) how to accurately determine quantum transportproperties without any phenomenological parameters? Our research iscentered on these questions. We have systematically calculatedatomic structures of the molecular transport junctions by performingtotal energy structural relaxation using density functional theory(DFT). Our quantum transport calculations were carried out byimplementing DFT within the framework of Keldysh non-equilibriumGreen's functions (NEGF). The calculated data are directly comparedwith the corresponding experimental measurements. Our generalconclusion is that quantitative comparison with experimental datacan be made if the device contacts are correctly determined.We calculated properties of nonequilibrium spin injection from Nicontacts to octane-thiolate films which form a molecular spintronicsystem. The first principles results allow us to establish a clearphysical picture of how spins are injected from the Ni contactsthrough the Ni-molecule linkage to the molecule, why tunnelmagnetoresistance is rapidly reduced by the applied bias in anasymmetric manner, and to what extent ab initio transporttheory can make quantitative comparisons to the correspondingexperimental data. We found that extremely careful sampling of thetwo-dimensional Brillouin zone of the Ni surface is crucial foraccurate results in such a spintronic system.We investigated the role of contact formation and its resultingstructures to quantum transport in several molecular wires and showthat interface contacts critically control charge conduction. It wasfound, for Au/BDT/Au junctions, the H atom in -SH groupsenergetically prefers to be non-dissociative after the contactformation, which was supported by comparison between computed andmeasured break-down forces and bonding energies. TheH-non-dissociated (HND) junctions give equilibrium conductances from0.054G0 (equilibrium structure) to 0.020G0 (stretchedstructure) which is within a factor of 2-5 of the measureddata. On the other hand, for all H-dissociated contact structures - whichwere the assumed structures in the literature, the conductance is atleast more than an order of magnitude larger that the experimentalvalue. The HND-model significantly narrows down thetheory/experiment discrepancy. Finally, a by-product of this work isa comprehensive pseudopotential and atomic orbital basis setdatabase that has been carefully calibrated and can be used by theDFT community at large.
Cette thèse présentera nos recherches théoriquessur les propriétés quantiques de transport électroniquedes jonctions de transport moléculaire. Cette analyse a été effectuéeà l'aide de méthodes ab initio atomiques qui sont validesdans les régimes non-linéaire et hors-équilibre.L'objectif est de rechercher non seulement une compréhensionqualitative des données expérimentales mais aussi quantitative. Les deux questions les plus importantesquant au travail théorique en électronique moléculaire sont:(i) quel est le bon modèle atomique pour simuler les dispositifsexpérimentaux? (ii) comment déterminer avec précisionles propriétés de transport quantique sans l'utilisation deparamètres phénoménologiques?Nos recherches sont centrées sur ces questions. Nous avonssystématiquement calculéles structures atomiques de jonctions moléculaires en effectuantla relaxation structurelle dans le cadre de la théorie de la fonctionnelle de la densité (DFT).Les calculs de transport quantique ont été reàlises encombinant la DFT avec les fonctions de Green hors-équilibre deKeldysh (NEGF).Les calculs sont directement comparésaux données expérimentales correspondantes. Notre conclusiongénérale est qu'un accord quantitatif entre les valeurs théoriqueset empiriques est possible si la structure atomique du contact estcorrectement déterminée.Nous avons calculé les propriétés hors-équilibred'injection de spin à travers un film d'octane-thiole en contactavec des électrodes en Ni, formant ainsi un systèmespintronique moléculaire.Les résultats obtenus par premiers principes nous fournissentune compréhension claire sur la façon dont les spins sontinjectés à partir des électrodes en Ni à la molécule par la liaisonNi-molécule. De plus, nous expliquonspourquoi la magnéto-résistance à effet tunnel décroîtrapidement avecune augmentation du potentiel électrique, et ce, de manière asymétrique.Finalement, nous démontrons que la théorie ab initiodu transport électronique est en mesure d'effectuer des comparaisonsquantitatives avec les données expérimentales.Nous avons constaté qu'un échantillonnage minutieux de la zonede Brillouin 2D de la surface du Ni est crucial afin d'obtenir desrésultats précis dans un tel système spintronique.Nous avons étudié le rôle de la formation du contact,ainsi que la structure atomique associée sur l'influence dutransport quantique dans le cas de plusieurs jonctions moléculaires.Nous démontrons que l'interface reliant les électrodes aux moléculescontrôle très sensiblement la conduction de charge.Il a été trouvé, pour les jonctions Au/BDT/Au, quel'atome d'hydrogène dans les groupes -SHpréfère énergétiquement la non-dissociation après la formationdu contact. En effet, ceci a été corroboré par la comparaison entreles donnéees calculées et mesurées des forces de rupture et desénergies de liaison.Les jonctions avec l'hydrogène non-dissocié (HND) donnentdes valeurs de conductances à l'équilibre de 0.054G$_0$ (structure d'équilibre) à0.020G$_0$ (structure étirée). Ces valeurs sontà l'intérieur d'un facteur de 2-5 aux données expérimentales actuelles.D'autre part, toutes les structures de contact H-dissociées --- quiont été les structures supposées dans la littérature --- résultenten des valeurs de conductancescalculées au moins un ordre de grandeur plus élevé que lesvaleurs empiriques.Le modèle HND réduit de manière significative l'écart entrela théorie et les expériences. Pour terminer, une conséquence de ce travail estle regroupement d'une base de données complète incluant des pseudo-potentielset des orbitales atomiques. Celle-ci a été soigneusement calibrée et est disponibleà toute la communauté DFT.

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Zhang, Lei, et 张磊. « First principles transport study of molecular device ». Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B50899557.

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This thesis discusses DC and AC transport properties of molecular devices from first principles. For dc bias, based on the non-equilibrium Green’s function (NEGF) technique coupled with the density functional theory (DFT), the dc current density distribution of a molecular device Al-C60-Al is numerically investigated from first principles. Due to the presence of non-local pseudo-potential, the conventional definition of current density is not suitable to describe the correct current density profile inside the molecular device. By using the new definition of current density which includes the contribution due to the nonlocal potential, our numerical results show that the new definition of current density J(r) conserves the current. In addition, the current obtained from the current density calculated inside the molecular device equals to that calculated from the Landauer-Büttiker formula. When the external bias is time dependent, a theoretical formalism to study the time dependent transport behavior of molecular device from first principles is proposed based on the non-equilibrium Green’s function (NEGF) and time dependent density functional theory (TDDFT). For the purpose of numerical implementation on molecular devices, a computational tractable numerical scheme is discussed in detail. The transient current of two molecular devices Al-1,4-dimethylbenzene-Al and Al-Benenze-Al are numerically studied from first principles. To overcome the computational complexity due to the memory term, a fast algorithm has been employed to speed up the calculation and CPU time has been reduced from the scaling N^3to N^2 log(_2^2)(N) for the step like pulse, where N is the number of time step in the time evolution of Green’s function.
published_or_final_version
Physics
Doctoral
Doctor of Philosophy

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Gao, Bin. « First Principles Studies of Carbon Based Molecular Materials ». Doctoral thesis, Stockholm : Bioteknologi, Biotechnology, Kungliga Tekniska högskolan, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4724.

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Kim, Sejoong Ph D. Massachusetts Institute of Technology. « Inelastic transport In molecular junctions from first principles ». Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/77496.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Physics, February 2012.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 159-166).
This work is dedicated to development of a first-principle approach to study electron-vibration interactions on quantum transport properties. In the first part we discuss a general implementation for inelastic transport calculations based on maximally localized Wannier functions and non-equilibrium Green's functions. Our approach is designed to determine inelastic transport properties such as differential conductances, inelastic tunneling spectroscopies and nonequilibrium vibrational populations. Our approach is first applied to benzene molecular junctions connected to cumulene and carbon nanotube electrodes. In these examples, we discuss the role of the multichannel effect and of parity selection rules on the polarity of conductance steps, and the appearance of a non-monotonic behavior in the vibrational population. In the second part, we extend our formalism to study the effect of the electron-vibration interactions on the local current distribution. Using non-equilibrium Green's functions, we derive an expression for the local distribution of the inelastic current. Applying this to the benzene-cumulene junction, we show that the electron-vibration interaction can lead to a locally inverted current direction and the formation of loop currents. In the third part, we present a comprehensive study of the elastic and inelastic transport properties of carbon nanotube-zigzag graphene nanoribbon junctions, as realized in recent experiments, focusing on the local current distribution over the junctions. We calculate the local distribution of the elastic current to visualize the current injection pattern from the CNT electrodes to the ZGNRs and the current path inside the ZGNRs. For inelastic transport properties, we find a similarity in the IETS peaks and the corresponding vibrational configurations for the CNT/ZGNR/CNT junctions with different widths. As observed in the benzene-cumulene junction, we find that the inelastic current emerges from a complex network that includes loop currents. Our method and implementation can be generalized to other types of interactions, and is not limited to the electron-vibration interactions. Thus our work will be a starting point to understand the role of different and diverse interaction effects on quantum transport, using realistic predictive first-principle calculations.
by Sejoong Kim.
Ph.D.

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Hagelberg, Frank. « Electron Dynamics in Molecular Interactions : Principles and Applications ». Digital Commons @ East Tennessee State University, 2014. http://amzn.com/1848164874.

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This volume provides a comprehensive introduction to the theory of electronic motion in molecular processes an increasingly relevant and rapidly expanding segment of molecular quantum dynamics. Emphasis is placed on describing and interpreting transitions between electronic states in molecules as they occur typically in cases of reactive scattering between molecules, photoexcitation or nonadiabatic coupling between electronic and nuclear degrees of freedom. Electron Dynamics in Molecular Interactions aims at a synoptic presentation of some very recent theoretical efforts to solve the electronic problem in quantum molecular dynamics, contrasting them with more traditional schemes. The presented models are derived from their roots in basic quantum theory, their interrelations are discussed, and their characteristic applications to concrete chemical systems are outlined. This volume also includes an assessment of the present status of electron dynamics and a report on novel developments to meet the current challenges in the field. Further, this monograph responds to a need for a systematic comparative treatise on nonadiabatic theories of quantum molecular dynamics, which are of considerably higher complexity than the more traditional adiabatic approaches and are steadily gaining in importance. This volume addresses a broad readership ranging from physics or chemistry graduate students to specialists in the field of theoretical quantum dynamics.
https://dc.etsu.edu/etsu_books/1055/thumbnail.jpg

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Akin-Ojo, Omololu. « First-principles studies of solvated molecules ». Access to citation, abstract and download form provided by ProQuest Information and Learning Company ; downloadable PDF file 3.25 Mb., 248 p, 2006. http://proquest.umi.com/pqdlink?did=1251856821&Fmt=7&clientId=79356&RQT=309&VName=PQD.

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Lendel, Christofer. « Molecular principles of protein stability and protein-protein interactions ». Doctoral thesis, Stockholm, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-480.

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Pugh, Steven. « First-principles simulation of molecular adsorption at oxide surfaces ». Thesis, Keele University, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.321407.

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Salvadó, López Baldiri. « Design principles in two component systems and his-asp phosphorelays ». Doctoral thesis, Universitat de Lleida, 2016. http://hdl.handle.net/10803/393740.

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L’objectiu d’aquesta tesi és trobar principis generals que permetin relacionar l’estructura i les propietats funcionals dels circuits moleculars de transducció de senyals two-component systems (TCS) i his-asp phosphorelays (PR). La tesi s’inicia revisant els mètodes usats per a l’estudi de principis de disseny en sistemes moleculars i alguns dels resultats obtinguts fins ara, i discutint la importància de l’estudi dels principis de disseny. A continuació, explorem els proteomes seqüenciats de més de 7000 organismes i fem un inventari dels diferents tipus d’organització en operons i proteïnes multidomini dels dominis proteics que intervenen en TCS i PR. A partir d’aquesta informació deduirem alternatives existents en la natura pel que fa al disseny d’aquests circuits moleculars. Per acabar, comparem mitjançant modelització matemàtica el comportament dinàmic de 3 circuits diferents de TCS, i trobem que un tercer component que modula l’activitat de la histidina quinasa o bé el response regulator pot modificar l’espai paramètric on el sistema es comporta de forma biestable.
El objectivo principal de esta tesis es la búsqueda de principios de diseño que relacionen la estructura y la función de redes bioquímicas de transducción de señales, concretamente en two-component systems (TCS) y phosphorelays (PR). La tesis se inicia con una revisión de los métodos usados para el estudio de principios de diseño en sistemas moleculares y algunos de los resultados obtenidos hasta ahora, seguida de una discusión sobre la importancia del estudio de dichos principios de diseño. A continuación, exploramos los proteomas secuenciados de más de 7000 organismos y hacemos un inventario de los distintos tipos de organización en operones o proteínas de los dominios proteicos implicados en TCS y PR, con el objetivo de deducir el repertorio de estructuras existentes en la naturaleza para estos circuitos moleculares. Para terminar, comparamos mediante modelización matemática las propiedades dinámicas de tres circuitos distintos de TCS, y observamos que una proteína adicional que interacciona con la histidina quinasa o con el response regulator modifica el espacio de valores de los parámetros del sistema en el cual existe biestabilidad.
The ultimate goal of this thesis is to set the stage for finding general design principles underlying the relationship between network design and network function in two-component (TCS) and His-Asp phosphorelay (PR) signal transduction systems. This thesis starts with a review of the methods for and results from the study of design principles in molecular systems, and a discussion about the importance of studying those design principles. Next, a survey of the fully sequenced and annotated genomes and proteomes of more than 7000 different organisms is performed in order to identify different types of organizations of the TCS/PR protein domains in operons and multidomain proteins. From this data, the existing diversity of TCS/PR circuit designs will be inferred. Finally, we compare through mathematical modeling the dynamic properties associated with three types of TCS circuit designs, and find that a third component that binds to and modulates the activity of either the sensor kinase or the response regulator can modify the parameter space in which bistability in the system’s response is possible.

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Siddick, Muhammad Murshed. « Some new applications in first-principles simulation of molecular crystals ». Thesis, University of Edinburgh, 2005. http://hdl.handle.net/1842/14422.

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Work presented in this thesis details the development of new applications for molecular crystalline systems using first-principles simulation. In particular work has focused on the most important type of intermediate interactions-the hydrogen bond. A new computational procedure to more accurately mimic the crystalline environment has been developed and applied to two systems: the test system ammonia and the more unusual dihydrogen bonded system BH₃NH₃. Both generated surprising results, which challenged the conventional view of bonding in the solid state. Work has also focused on the dynamics of the hydrogen bond, resulting in the implementation of a constraint molecular dynamics (MD) algorithm for the popular simulation package, CASTEP. This code development allows molecular systems to be treated as rigid or semi-rigid bodies, thus allowing appreciable increase in the first-principles MD time step. It also allows interesting chemistry to be explored at the ab-initio level, which would be inaccessible by any other route. The method has been applied to the phase I structure of ammonia and a full vibrational analysis is reported.

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MOTTA, CARLO. « First-principles study of electronic transport in organic molecular junctions ». Doctoral thesis, Università degli Studi di Milano-Bicocca, 2013. http://hdl.handle.net/10281/40094.

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This thesis focuses on the theoretical description of coherent electronic transport in organic molecular junctions. The ab-initio theoretical methods and the theory of quantum transport in nanoscale systems are presented. The Landauer theory of transport formulated in terms of Green's function is analyzed by means of the embedding theory for a simplified model in which electrons are considered as moving in a one-dimensional modulated potential introduced to simulate resonant tunneling junctions. Following the introductory section, relevant systems of interest from both basic and technology points of view are investigated. The transport properties of two-dimensional graphene/graphene-nanoribbon (GNR) heterojunctions are shown to critically depend upon the geometrical features of the GNR. Diarylethene junctions with graphene electrodes are comprehensively analyzed, with emphasis on the photoswitching properties of the system. The use of graphene electrodes can improve the performance of such switching junctions as compared with the use of other substrates. A full characterization of a platinum/pyrazine bistable junction studied in a recent experiment is then established. The switching mechanism has been determined as a result of a molecule-lead configurational rearrangement. A final section is devoted to the description of a new methodology to calculate the elastic lifetimes of electronic states of adsorbates on surfaces. The method has been applied to dye molecules on TiO2 substrates, which are relevant for photovoltaics applications. The effects of modification of the spacers between the acceptor and donor part of the dyes are analyzed.

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Ji, Yongfei. « Theoretical Studies on the Molecular Mechanisms of Photo-Catalytic Reactions on TiO2 Surfaces ». Doctoral thesis, KTH, Teoretisk kemi och biologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-145146.

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Photocatalysis is a promising technology that can effectively convert the solar energyinto sustainable green energy. However, theoretical studies on the molecular mechanisms of photocatalytic reactions are rare. This thesis is devoted to investigate several typical photocatalytic reactions on the surfaces of the most popular photocatalysis TiO2 with density functional theory. We start our study with the characterization of both the free and trapped hole on the surface generated by the light. The oxidation of physisorbed H2O molecule by the hole trapped at bridge oxygen on rutile TiO2(110) surface has been studied. The hole is found to transferto the molecule via the anti-bonding orbital as a result of the hybridization between the hole orbital and the HOMO of the molecule. The energy and symmetry mismatching between the trapped hole orbital and the HOMO of the molecule explains why the trapped hole cannot directly transfer to the chemisorbed H2O molecule. On the other hand, we have found that the chemisorbed H2O moleculecan be more efficiently oxidized by the free hole with a lower barrier and higher reaction energy compared to the oxidation by the trapped hole. In this reaction, the free hole is transferred to the chemisorbed H2O after the dissociation. This is different from the oxidation of chemisorbed H2O on anatase TiO2(101) surface by free hole, in which the hole is transferred concertedly with the dissociation of themolecule. In order to understand the hole scavenger ability of organic molecules, the oxidation of three small organic molecules (CH3OH, HCOOH and HCOH) onanatase TiO2(101) surface has been systematically investigated. The concerted hole and proton transfer is found for all these molecules. The calculations suggestthat both kinetic and thermodynamic effects need to be considered to correctly describe the hole transfer process. The order of hole scavenging power is found tofollow: HCOH > HCOOH > CH3OH > H2O, which agrees well with experiments. Photo-selective catalytic reduction of the NO by NH3 and the photooxidationof CO by O2 are closely related to the environment application. Both reactionsinvolve the formation and/or breaking of non R–H bonds. The mechanism for the photoreduction of NO proposed by experiment has been verified by our calculations.The role of the hole is to oxidize the adsorbed NH3 into ·NH2 radical, which canform a NH2NO complex with a gaseous NO molecule easily. The photooxidation of CO by O2 is the first multi-step photoreaction we ever studied. By combining thepotential energy surfaces at the ground and excited state we have found that thehole and electron both take part in the reaction. A molecular mechanism which is in consistent with various experiments is proposed. These studies show that density functional theory is a powerful tool for studying the photocatalytic reaction. Apparently, more work needs to be done in orderto improve the performance of the existing materials and to design new ones thatcan take advantage of the solar light more efficiently

QC 20140522

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McNellis, Erik R. [Verfasser]. « First-principles modeling of molecular switches at surfaces / Erik R. McNellis ». Berlin : Freie Universität Berlin, 2010. http://d-nb.info/1024784681/34.

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Ji, Tao. « Inelastic electron tunneling spectroscopy in molecular electronic devices from first-principles ». Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=96883.

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In this thesis, we present the first-principle calculations of inelastic electron tunneling spectroscopy(IETS) in single molecular break junctions. In a two-probe electrode-molecule-electrode setup, density functional theory(DFT) is used for the construction of the Hamiltonian and the Keldysh non-equilibrium Green's function(NEGF) technique will be employed for determining the electron density in non-equilibrium system conditions. Total energy functional, atomic forces and Hessian matrix can be obtained in the DFT-NEGF formalism and self-consistent Born approximation(SCBA) is used to integrate the molecular vibrations (phonons) into the framework once the phonon spectra and eigenvectors are calculated from the dynamic matrix. Geometry optimization schemes will also be discussed as an indispensable part of the formalism as the equilibrium condition is crucial to correctly calculate the phonon properties of the system.To overcome the numerical difficulties, especially the large computational time demand of the electron-phonon coupling problem, we develop a numerical approximation for the electron self-energy due to phonons and the error is controlled within numerical precision. Besides, a direct IETS second order I-V derivative expression is derived to reduce the error of numerical differentiation under reasonable assumptions. These two approximations greatly reduce the computation requirement and make the calculation feasible within current numerical capability.As the application of the DFT-NEGF-SCBA formalism, we calculate the IETS of the gold-octanedithiol(ODT) molecular junction. The I-V curve, conductance and IETS from ab-inito calculations are compared directly to experiments. A microscopic understanding of the electron-phonon coupling mechanism in the molecular tunneling junctions is explained in this example. In addition, comparisons of the hydrogen-dissociative and hydrogen-non-dissociative ODT junctions as well as the different charge transfer behaviors are presented to show the effects of thiol formation in the ODT molecular junction.
Dans cette thèse, nous présentons des calculs ab initio de la spectroscopie à effet tunnel par électron inélastique (IETS)appliqués à des jonctions moléculaires. Dans le cadre d'une configuration électrode-molécule-électrode,la théorie de la fonctionnelle de la densité (DFT) est utilisée pour construire l'hamiltonien et les fonctions de Green hors-équilibres(NEGF) sont employées pour déterminer la densité électroniquedans des conditions hors-équilibre. Le cadrede la DFT-NEGF nous permet de calculer des quantités telles que la fonctionnelle d'énergie totale,les forces atomiques ainsi que la matrice de Hessian. L'approximationauto-consistante de Born (SCBA) est employée afin d'intégrer les vibrations moléculaires (phonons) dans le formalisme DFT-NEGF,une fois que le spectre des phonons et les vecteurs propres ont été calculés à partir de la matrice dynamique. Des méthodes d'optimisations géométriques sont aussi discutées en tant que part indispensable du formalisme,étant donné que la condition d'équilibre mécanique est essentielle afin de calculer correctement les propriétés des phonons du système.Afin de surmonter les difficultés numériques, particulièrement concernant la grande demandecomputationnelle requise pour le calcul du couplage électron-phonon, nous développons une approximation numérique pour la self-énergie associée aux phonons. De plus, en employant quelques hypothèses raisonables, nous dérivons une expression pour l'IETS calculée à partir de laseconde dérivée de la courbe I-V dans le butde réduire l'erreur associée à la différentiation numérique. L'utilisation de ces deux approximations diminuent grandement les exigences computationnelles et rendent les calculs possibles avec les capacités numériques actuelles.Comme application du formalisme DFT-NEGF-SCBA, nous calculons l'IETS de la jonction moléculaire or-octanedithiol(ODT)-or. La courbe I-V, la conductance et l'IETS obtenues par calculs ab initio sontdirectement comparées aux données expérimentales. Une compréhension microscopique du couplage électron-phonon pour une jonction moléculaire à effet tunnel est élaborée dans cet exemple. De plus, des comparaisons entre les jonctions ODT à hydrogène dissociatif et à hydrogène non-dissociatif ainsi queles différents comportements de transfert de charges sont présentés afin de montrer les effets de la formation du thiol dans la jonction moléculaire ODT.

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Brena, Barbara. « First principles modeling of soft X-ray spectroscopy of complex systems ». Doctoral thesis, Stockholm, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-403.

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Plaisance, Brandon P. « First principles approach to identification of potential ferroelectric and multiferroic molecular materials ». Thesis, Georgia Institute of Technology, 2016. http://hdl.handle.net/1853/55039.

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Flexible electronics have garnered much interest over the past several decades. Hybrid organic-inorganic materials, such as metal-organic frameworks, offer a unique opportunity to encompass the effective electronic properties of the inorganic material and the flexible nature of the organic with the potential of enhancing other desirable properties, such as the contributing multiferroicity. Using a first principles approach, the goal of this thesis is to serve as a guide for identifying potential ferroelectric and multiferroic metal-organic frameworks. This is done through a screening method of metal-organic frameworks based on their geometry; certain symmetry operators cannot be present in a ferroelectric material. We report the theoretical spontaneous polarization for several dozens of MOFs in which ferroelectricity has not previously been tested, and further we discuss the likelihood that these materials could be engineered to have either increased polarization or added ferromagnetism, the latter of which would lead to multiferroicity.

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Погребняк, Олександр Дмитрович, Александр Дмитриевич Погребняк, Oleksandr Dmytrovych Pohrebniak, V. Ivashchenko et S. Veprek. « First-Principles Quantum Molecular Dynamics Study of TixZr1-xN(111)/SiNy Heterosrtructures ». Thesis, Sumy State University, 2012. http://essuir.sumdu.edu.ua/handle/123456789/35184.

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Heterostructures with 1 monolayer of Si3N4-like Si2N3 interfacial layer between five monolayers thick B1-TixZr1-xN(111), x 1.0, 0.6, 0.4 and 0.0, slabs were investigated by means of first-principles quantum molecular dynamics and structure optimization procedure using the Quantum ESPRESSO code. Slabs consisting of stoichiometric TiN and ZrN and random, as well as segregated B1-TixZr1-xN(111) solutions were considered. The calculations of the B1-TixZr1-xN solid solutions as well as of the heterostructures showed that the pseudo-binary TiN-ZrN system exhibits a miscibility gap. The segregated heterostructures in which the Zr atoms surround the SiyNz interface were found to be most stable. For the Zr-rich heterostructures, the total energy of the random solid solution was lower compared to that of the segregated one, whereas for the Ti-rich heterostructures the opposite tendency was observed. When you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/35184

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Song, Xiuneng. « Theoretical Characterization of Functional Molecular Materials ». Doctoral thesis, KTH, Teoretisk kemi och biologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-94540.

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Nowadays, material, energy and information technologies are three pillar industries. The materials that have close relation with our life have also been the foundation for the development of energy and information technologies. As the new member of the material family, functional molecular materials have become increasingly important for many applications, for which the design and characterization by the theoretical modeling have played the vital role. In this thesis, three different categories of functional molecular materials, the endohedral fullerenes, the fullerene derivatives and the self-assembled monolayers (SAMs), have been studied by means of first principles methods. The non-metal endohedral fullerene N@C60 is a special endohedral fullerene that is believed to be relevant to the construction of future quantum computer. The energy landscape inside the N@C60 has been carefully explored by density functional theory (DFT) calculations. The most energy favorable potential energysurfaces (PESs) for the N atom to move within the cavity have been identified. The effect of the charging on the PESs has also been examined. It is found that the inclusion of dispersion force is essential in determining the equilibriumstructure of N@C60. Furthermore, the performance of several commonly useddensity functionals with or without dispersion correction has been verified for ten different endohedral fullerenes A@C60 with the atom A being either reactive nonmetal or nobel gases elements. It shows that the inclusion of the dispersion forcedoes provide better description for the binding energy (BE), however, none ofthem could correctly describe the energy landscape inside all the ten endohedral fullerenes exclusively. It thus calls for the further improvement of current density functionals for weak interacting systems. Soft X-ray spectroscopy is a powerful tool for studying the chemical and electronic structures of functional molecular materials. Theoretical calculations have been proven to be extremely useful for providing correct assignments for spectraof large systems. In this thesis, we have performed first principles simulations forthe near-edge X-ray absorption fine structure (NEXAFS) and X-ray photoelectron spectra (XPS) of fullerene derivatives and aminothiolates SAMs. Our calculatedspectra can accurately reproduce experimental results available for all the systemsunder investigations, and identify the species or structures that are responsible for those unexpected spectral features observed in experiments. We have suggested a modified building block (MBB) approach that allows to calculate NEXAFS spectraof a large number of fullerene derivatives with very small computational cost, and resolved the long standing puzzle around the experimental XPS and NEXAFS spectra of SAMs with aminothiolates.

QC 20120523

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Patrick, Christopher Edward. « Photoemission spectra of nanostructured solar cell interfaces from first principles ». Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:fa2333ea-7016-4d6f-8d55-aee4178482a6.

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Photovoltaic (PV) technologies could provide abundant, clean and secure energy through the conversion of sunlight into electricity, but currently are too expensive to compete with conventional sources of power. Novel PV devices incorporating nanostructured materials, such as the dye-sensitized solar cell (DSC), have been identified as viable, low-cost alternatives to traditional solar cell designs. In spite of technological progress in the field over the last twenty years, the underlying physics governing DSC operation is still not well understood. In this thesis, first-principles (i.e. parameter-free) calculations are performed with the aim of connecting experimentally-measured photoemission data to the underlying atomistic and electronic structure of interfaces found in DSCs. The principal system under study is the interface between anatase titanium dioxide (TiO₂) and the "N3" dye molecule, one of the most widely-investigated device designs in DSC research. Atomistic models of the interface are determined within density-functional theory. Core-level spectra of these interface models are then calculated using a ∆SCF approach. Comparison of the calculations to published experimental data finds that intermolecular interactions have a significant effect on the spectra. Next, the electronic structure of bulk TiO₂ and of isolated N3 molecules is calculated using the GW approximation and ∆SCF method respectively. For the former, it is shown that including Hubbard U corrections in the initial Hamiltonian reduces the GW gap by 0.4 eV. These calculations are then used to determine the valence photoemission spectrum of the full interface. By including image-charge effects, thermal broadening and configurational disorder, quantitative agreement with experimentally-measured spectra is demonstrated. In addition to the N3/TiO₂ system, calculations of the core-level spectra of the interfaces between TiO₂ and H₂O and bi-isonicotinic acid are also presented. The thesis concludes with a study of the X₂Y₃/TiO₂ interfaces (X=Sb, Bi; Y=S, Se) found in recently-developed semiconductor-sensitized solar cells.

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Ledyastuti, Mia. « First Principles and Classical Molecular Dynamics of Oil-Quartz Interfacial Phenomena in Nanogeoscience ». 京都大学 (Kyoto University), 2012. http://hdl.handle.net/2433/157547.

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Kaun, Chao-Cheng 1969. « First-principles study of charge transport in molecular wires and field effect devices ». Thesis, McGill University, 2003. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=84269.

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In this work, we present theoretical analysis of charge transport at the molecular scale. We use a state-of-the-art theoretical tool to investigate a number of key issues of molecular electronics, paying particular attention to quantitative comparison with experimental data which have been confirmed by different labs. Our analysis allows us not only to understand the data, but also to make quantitative predictions.
We have calculated the length dependence of resistance for molecular wires, including oligophenylene thiol and alkanethiol molecules. Our results are in excellent agreement with the corresponding measured data. Our analysis provides a good understanding of charge conduction mechanism in these molecular wires. This is the first time in molecular conduction research that a parameter-free modeling agrees so well with real data. We have also studied the conformational dependence of current of a biphenyldithiol molecule in terms of the dihedral angle variations. The charge current can be tuned by this parameter, and the ratio of tuning can be as large as several hundred fold. A physical picture emerges from our analysis.
We have investigated the momentum filtering effect due to molecule orbitals. This study allows us to understand why some incoming Bloch states can conduct through the molecule, while others cannot. By adding different end-groups to the molecule, we found that conduction channels can be varied. We have also studied the gate potential control of electric current. The gate voltage shifts the resonance state of the molecule thereby inducing a current modulation. We found that the gating efficiency strongly depends on the geometry of the gate electrode. The current through a biphenyl dimethanethiol molecule is found to be switchable by applying gate voltages, and the on/off current ratio can be substantial.
Finally, using carbon nanotubes with substitutional nitrogen, we clearly demonstrate that conventional equilibrium conductance analysis was not enough to describe the whole transport features in molecular devices. A nitrogen doped zigzag nanotube showed that even a single atom substitution has increased the current flow and, for small radii tubes, narrowed the current gap. Periodical substitution makes zigzag semiconducting tubes metallic, a prediction which has been confirmed by a subsequent experiment. For an armchair metallic nanotube, doping with a single impurity reduces current. The physics of these behaviours has been addressed.

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Kröncke, Susanne [Verfasser]. « Toward a First-Principles Evaluation of Transport Mechanisms in Molecular Wires / Susanne Kröncke ». Hamburg : Staats- und Universitätsbibliothek Hamburg Carl von Ossietzky, 2021. http://d-nb.info/1233429582/34.

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Vitale, Valerio. « Computational methods for first-principles molecular dynamics with linear-scaling density functional theory ». Thesis, University of Southampton, 2017. https://eprints.soton.ac.uk/415668/.

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Nowadays, Kohm-Sham density functional theory (KS-DFT) calculations are routinely employed in several research fields, due to the ability of KS-DFT to provide great accuracy for a wide class of molecular systems and materials. Unfortunately, conventional KS-DFT calculations, although very powerful, require a computational cost that goes with the cube of the system size, also known as ON³ scaling, undermining in practice the study of large systems. The advent of linear-scaling, or O (N ), DFT (LS-DFT) methods, relying on the locality of the electronic matter, has enabled calculations on increasingly large systems, up to tens of thousands of atoms. The central tenet of linear-scaling methods is the exponential decay in real space of the single-particle reduced density matrix. This property allows to enforce localisation constraints on the electronic structure, significantly reducing the size of the matrices, such as the Hamiltonian matrix, and increasing their sparsity. The single-particle density matrix in the LS-DFT formalism is expanded in terms of a set of atom-centred, strictly localised functions. Employing periodic boundary conditions (PBCs), the energy is minimised with respect to all the degrees of freedom in the density matrix, which allows to attain chemical accuracy using a high-resolution minimal basis set. The combination of localisation constraints and sparse algebra form the substrate for O (N ) calculations. In this thesis, we used Onetep, a linear-scaling DFT program, to carry out our calculations. The aim of our research is to combine molecular dynamics simulations, within the Born-Oppenheimer approximation (BOMD), with linear-scaling DFT methods. In particular, our main goal is to advance current methodology by developing new algorithms to better exploit locality in BOMD and to reduce the computational load while maintaining DFT accuracy. Dipole moment autocorrelation functions can directly be employed to obtain the IR spectrum of a given molecular system. DFT-MD simulations offer the perfect tool to generate accurate autocorrelation functions which automatically take into account the anharmonicity of the potential energy surface and temperature effects. Computational IR spectroscopy plays a pivotal role in the understanding of conformational changes of biomolecules, which tend to show several almost-degenerate conformers at room temperatures (floppy molecules). It is particularly valuable when interpreting their fingerprint in solution in combination with experimental spectra. We have implemented two algorithms for the computation of the local electronic dipole moments of molecules in solution. Both methods demand a strategy to partition the density. These methods enable the computation of IR spectra of large molecules, such as polypeptide, in explicit solvent. In the resulting IR spectrum the effect of the solvent on the target molecule is automatically captured, whereas its IR signature is removed. We expect these new functionalities to be very helpful in the understanding of how bio-molecules interact with the solvent at room temperature and the effect of these interactions on conformational changes. Computationally, the most demanding step in molecular dynamics simulations is the evaluation of energies and forces. This has particular severe consequences on BOMD-based approaches. In fact, a self-consistent field (SCF) step is required at each MD step, which in turn requires multiple energy evaluations. As a consequence, the SCF loop has a major effect on the computational load and overall wall-time. MD Schemes that are capable to by-pass the SCF loop altogether, e.g. Car-Parrinello MD or fixed charge force fields in classical MD, are inherently faster in terms of wall-time per MD step, although they usually demand a much smaller time-step. Moreover, the quality of the converged density matrix is crucial for energy conservation and forces in the LS-DFT BOMD approaches. In theory, the self-consistent solution does not depend on the initial guess. In practice, the SCF optimisation is always incomplete, leading to memory effects and the breaking of time-reversal symmetry, which gives rise to systematic errors in energy gradients that manifest as a drift in microcanonical energy. To ameliorate this problem, we present two integration schemes based on an extended-Lagrangian (XL) approach which introduces extended or auxiliary electronic degrees of freedom to generate good quality time-reversible initial guesses in the SCF loop. Both schemes are improvements over the original XL formulation, which suffered from numerical noise accumulation. The first approach, known as dissipative XL (dXL), introduces a dissipative-like term in the Verlet integration (modified Verlet) of the auxiliary degrees of freedom; the second approach, known as inertial XL (iXL), introduces a thermostat, hence requiring a velocity Verlet integrator. We have implemented both schemes in Onetep and studied their performance using liquid water as test case. In collaboration with the authors of the schemes, we have analysed the energy driftt in both classical polarisable force field MD calculations and LS-DFT BOMD. We have found that both schemes are very efficient in reducing the number of SCF iterations while maintaining good energy driftss and have similar performance. We believe that our implementation and analysis will be very beneficial for future applications both with LS-DFT BOMD and classical polarisable force field MD since both schemes constitute important algorithmic improvements that markedly extend the timescales accessible to classical and LS-DFT MD simulations alike.

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Borck, Øyvind. « Adsorption of organic molecules at sufaces : A first principles investigation ». Doctoral thesis, Norwegian University of Science and Technology, Department of Physics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-1764.

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The adsorption of a molecule at a surface is a fundamental step in a wide variety of industrially relevant phenomena, including adhesion, corrosion, and catalysis. The work presented in this thesis is motivated by the desire to contribute to a better understanding of the factors affecting the adhesion between an organic coating/adhesive and an aluminium alloy surface. A key factor is the nature and strength of the interfacial bonds between the binder polymers of the organic coating/adhesive and the substrate. The size of the polymers and complexity of the polymer-substrate interactions preclude a detailed, atomic-level description. The strategy followed in this thesis is to study the adsorption of small organic molecules, representing fragments of the industrially relevant amine-cured epoxides, with various surfaces, of metal oxides (α-Al₂O₃(0001) and α-Cr₂O₃(0001)), bimetallic alloys (NiAl(110)), and graphite(0001).

This thesis consists of two parts, an introductory text and a collection of five papers. In the included papers we present results from density functional theory (DFT) calculations on the adsorption of methanol and methylamine on α-Al₂O₃(0001) and α-Cr₂O₃(0001), phenol on α-Al₂O₃(0001) and graphite(0001), and methoxy on α-Cr₂O₃(0001) and NiAl(110). We describe in detail the adsorption sites and geometry, and the nature and strength of the bonding at these surfaces.

The majority of adsorption systems considered in this thesis are well described by traditional implementations of DFT. However, the adsorption of phenol on graphite is predominantly governed by van der Waals interactions. These interactions requires approximations beyond traditional DFT. In this thesis a recently presented functional (vdW-DF) is employed, and is found to be of decisive importance for describing the phenol-graphite interactions. We calculate the contribution from vdW interactions to the adsorption of phenol on α-Al₂O₃(0001), and compare their contribution to the adsorption bond to other forces.

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Lin, Lili. « Theoretical Modeling of Intra- and Inter-molecular Charge Transport ». Doctoral thesis, KTH, Teoretisk kemi och biologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-94103.

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This thesis focuses on theoretical study of charge transportproperties in molecular systems. The understanding of the transportprocess and mechanism in molecular systems is essential forthe design of new functional molecular materials and molecularelectronic devices. The molecular junctions and organic molecularcrystals have been used as the model systems to highlight the usefulnessof theoretical modelling. A molecular junction is a system that consists ofone or several molecules sandwiched between two electrodes.The charge transport in molecular junctions is a very complex processthat is affected by the interaction between molecules and electrodes,the surroundings, as well as electron-electron (e-e) andelectron-phonon (e-p) couplings. When the molecule-electrode couplingis strong, the transport process can be very quick. If the e-p couplingis weak, the inelastic tunneling has only negligible contributions to thetotal current and the elastic electron tunneling plays the dominant role.Furthermore, the hopping process becomes dominant in the case of strong e-pcoupling, for which the geometric relaxation of the molecule needsto be considered. In this thesis, we have examined these three kinds oftransport processes separately. The first studied system is a molecular junction consisting of aromaticallycoupled bimolecules. Its elastic electron tunneling property is simulatedusing Green's functional theory at density functional theory level.The dependence of the conductance of bimolecular junctions on the vertical distances,horizontal distances and the tilt angles has been systematically studied. Theinelastic electron tunneling spectra (IETS) of molecular junctions have beencalculated for several systems that were experimentally measured with conflictingresults and controversial assignments. Our calculations provide the reliableassignments for the experimental spectra and revealed unprecedented detailsabout the molecular conformations within the junctions under different conditions.It demonstrates that a combined theoretical and experimental IETS study is capableof accurately determining the structure of a single molecule inside the junction.The hopping process is a dominant charge transfer process in organic molecularcrystals. We have studied the charge transport ability of four kinds of n-typeorganic semiconductor materials to find out the related structure-to-propertyrelationship. It is done by adopting the quantum charge transfer rate equationcombined with the random walk approach.
QC 20120515

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Durek, Pawel. « Comparative analysis of molecular interaction networks : the interplay between spatial and functional organizing principles ». Phd thesis, Universität Potsdam, 2008. http://opus.kobv.de/ubp/volltexte/2009/3143/.

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The study of biological interaction networks is a central theme in systems biology. Here, we investigate common as well as differentiating principles of molecular interaction networks associated with different levels of molecular organization. They include metabolic pathway maps, protein-protein interaction networks as well as kinase interaction networks. First, we present an integrated analysis of metabolic pathway maps and protein-protein interaction networks (PIN). It has long been established that successive enzymatic steps are often catalyzed by physically interacting proteins forming permanent or transient multi-enzyme complexes. Inspecting high-throughput PIN data, it has been shown recently that, indeed, enzymes involved in successive reactions are generally more likely to interact than other protein pairs. In this study, we expanded this line of research to include comparisons of the respective underlying network topologies as well as to investigate whether the spatial organization of enzyme interactions correlates with metabolic efficiency. Analyzing yeast data, we detected long-range correlations between shortest paths between proteins in both network types suggesting a mutual correspondence of both network architectures. We discovered that the organizing principles of physical interactions between metabolic enzymes differ from the general PIN of all proteins. While physical interactions between proteins are generally dissortative, enzyme interactions were observed to be assortative. Thus, enzymes frequently interact with other enzymes of similar rather than different degree. Enzymes carrying high flux loads are more likely to physically interact than enzymes with lower metabolic throughput. In particular, enzymes associated with catabolic pathways as well as enzymes involved in the biosynthesis of complex molecules were found to exhibit high degrees of physical clustering. Single proteins were identified that connect major components of the cellular metabolism and hence might be essential for the structural integrity of several biosynthetic systems. Besides metabolic aspects of PINs, we investigated the characteristic topological properties of protein interactions involved in signaling and regulatory functions mediated by kinase interactions. Characteristic topological differences between PINs associated with metabolism, and those describing phosphorylation networks were revealed and shown to reflect the different modes of biological operation of both network types. The construction of phosphorylation networks is based on the identification of specific kinase-target relations including the determination of the actual phosphorylation sites (P-sites). The computational prediction of P-sites as well as the identification of involved kinases still suffers from insufficient accuracies and specificities of the underlying prediction algorithms, and the experimental identification in a genome-scale manner is not (yet) doable. Computational prediction methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding P-sites. However the recognition of such motifs by the respective kinases is a spatial event. Therefore, we characterized the spatial distributions of amino acid residue types around P-sites and extracted signature 3D-profiles. We then tested the added value of spatial information on the prediction performance. When compared to sequence-only based predictors, a consistent performance gain was obtained. The availability of reliable training data of experimentally determined P-sites is critical for the development of computational prediction methods. As part of this thesis, we provide an assessment of false-positive rates of phosphoproteomic data.
Ein zentrales Thema der Systembiologie ist die Untersuchung biologischer Interaktionsnetzwerke. In der vorliegenden Arbeit wurden gemeinsame sowie differenzierende Prinzipien molekularer Interaktionsnetzwerke untersucht, die sich durch unterschiedliche Ebenen der molekulareren Organisation auszeichnen. Zu den untersuchten Interaktionsnetzwerken gehörten Netzwerke, die auf metabolischen Wechselwirkungen, physikalischen Wechselwirkungen zwischen Proteinen und Kinase-Interaktionen aufbauen. Zunächst wird eine integrativen Analyse der metabolischen Pfade und Protein Interaktionsnetzwerke vorgestellt. Es wird seit schon seit langem angenommen, dass aufeinander folgende enzymatische Schritte oft durch permanente oder transiente Multienzymkomplexe, die auf physikalischen Wechselwirkungen der involvierten Proteine basieren, katalysiert werden. Diese Annahme konnte durch die Auswertung von Ergebnissen aus Hochdurchsatz-Experimenten bestätigt werden. Demnach treten aufeinander folgende Enzyme häufiger in physikalische Wechselwirkung als zufällige Enzympaare. Die vorliegende Arbeit geht in ihrer Analyse weiter, in dem die Topologien der zugrundeliegenden Netzwerke, die auf metabolischen und physikalischen Wechselwirkungen basieren verglichen werden und der Zusammenhang zwischen der räumlichen Organisation der Enzyme und der metabolischen Effizienz gesucht wird. Ausgehend von Interaktionsdaten aus Hefe hat die Analyse der auf metabolischen und physikalischen Wechselwirkungen aufbauenden Interaktionswege eine weitgehende Korrelation der Distanzen aufgezeigt und somit eine wechselseitige Übereinstimmung der Architekturen nahegelegt. Allerdings folgen physikalische Wechselwirkungen zwischen metabolischen Enzymen anderen organisatorischen Regeln als Proteininteraktionen im allgemeinem PIN, das alle Proteininteraktionen enthält. Während Proteininteraktionen im allgemeinen PIN sich dissortativ verhalten, sind physikalische Enzyminteraktionen assortativ, d.h. dass die Anzahl der Interaktionen benachbarter Proteine im allgemeinem Netzwerk negativ und im metabolischen Netzwerk positiv korreliert. Ferner scheinen Enzyme von höherem metabolischen Durchsatz häufiger in Wechselwirkungen involviert zu sein. Enzyme der zentralen katabolischen Prozesse sowie der Biosynthese komplexer Membranlipide zeigen dabei einen besonders hohen Verknüpfungsgrad und eine dichte Clusterbildung. Einzelne Proteine wurden identifiziert, die die Hauptkomponenten des zellulären Metabolismus verbinden und so die Integrität verschiedener biosynthetischer Systeme essenziell beeinflussen könnten. Neben dem metabolischen Aspekt der PIN wurde auch der Aspekt der Regulation sowie der Signaltransduktion, der Kinase-Interaktionen, näher analysiert. Dabei wurden charakteristische topologische Unterschiede der mit dem Metabolismus und der Phosphorylierung assoziierten PIN gefunden, die die unterschiedlichen Aufgaben beider Netzwerke widerspiegeln. Die Rekonstruktion von Phosphorylierungs-Netzwerken basiert im Wesentlichen auf der Vorhersage von Kinase-Zielprotein Relationen und kann deshalb immer noch an der nicht genügenden Vorhersagegüte der angewandten Vorhersage-Algorithmen während der Bestimmung von Phosphorylierungsstellen (P-Stellen) und der dazugehörigen Kinasen leiden. Auch die experimentelle, genomweite Bestimmung der P-Stellen ist (noch) nicht durchführbar. Bisherige computergestützte Vorhersagemethoden beruhten für gewöhnlich auf der Auswertung charakteristischer Merkmale der lokalen, die P-Stelle umgebenden Proteinsequenz. Dieser Ansatz wird durch die Verwendung räumlicher 3D-Information in der vorliegenden Arbeit erweitert. Hierbei wird die Verteilung der Aminosäuren um die P-Stelle berechnet und spezifische 3D-Signaturen zur Vorhersage extrahiert. Beim Vergleich mit sequenz-basierten Vorhersagemethoden konnte eine konsistente Verbesserung der Vorhersage durch die Einbeziehung räumlicher Information gezeigt werden. Weiterhin wird in der vorliegenden Arbeit auch der Frage nach der Fehlerrate der experimentellen Phosphoprotein-Daten nachgegangen und ihre Verlässlichkeit bewertet. Die Verfügbarkeit eines verlässlichen Datensatzes ist bei der Entwicklung einer Vorhersagemethode ein entscheidendes Kriterium.

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Liu, Yi 1971. « First-principles study of transport properties of molecular devices : fullerene and carbon nanotube systems ». Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=85571.

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The discovery of fullerenes and carbon nanotubes has been very significant to the field of nanotechnology by providing an abundance of stable, highly symmetric, non-reactive, and relatively large molecules that can, in principle, be manipulated one at a time. At the present stage, a theoretical effort should be carried out in order to find and understand novel phenomena in molecule-based nanostructures which could serve as a basis for fabricating useful molecular devices. In this thesis we investigate from first-principles the transport properties of molecular devices: fullerene and carbon nanotube systems.
We begin with charge transport in carbon nanotubes with oxygen, and find that the interaction between oxygen molecules and carbon nanotubes significantly modifies the electronic structure near the Fermi level for both zigzag and armchair tubes. The subtle difference of the adsorption sites of oxygen and the distance between oxygen and nanotubes can cause totally different results of their transport properties.
Then we investigate current flow from the point of view of current density distribution in molecular devices, for current density gives local information of nonequilibrium transport, thereby providing useful and vivid insight to transport properties of molecular electronics. It has been found when an intrinsic carbon nanotube is doped with either a boron or a nitrogen atoms through a replacement of a carbon atom, the local physical properties around the impurity atoms (boron or nitrogen) undergo a significant change, resulting in a dramatic change of the local current distribution. It is suggested that there appears a chiral current flow in the B- and N-doped armchair nanotubes near the impurity. As for a gated C 60 molecular device, the current distribution and the total current flow are both obviously affected by the gate voltage, which indicates the importance of the gate voltage in such a molecular device.
Finally, we discuss the contact effects on transport properties of the molecular devices. We study the effects of the contact geometry as well as the electrode material and find that different orientations of C 60 connected to Au(111) leads can cause significant changes in the current-voltage (I-V) characteristics of such C60 molecular devices. On the other hand, the electrode material is crucial to obtain low resistance ohmic contacts. Our first-principles calculations of transport suggest that Ti has higher affinity for carbide formation. So the choice of proper electrode materials will play an important role in the design of nanoscale devices.

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Klarbring, Johan. « A first-principles non-equilibrium molecular dynamicsstudy of oxygen diffusion in Sm-doped ceria ». Thesis, Linköpings universitet, Teoretisk Fysik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-118773.

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Solid oxide fuel cells are considered as one of the main alternatives for future sources of clean energy. To further improve their performance, theoretical methods able to describe the diffusion process in candidate electrolyte materials at finite temperatures are needed. The method of choice for simulating systems at finite temperature is molecular dynamics. However, if the forces are calculated directly from the Schrödinger equation (first-principles molecular dynamics) the computational expense is too high to allow long enough simulations to properly capture the diffusion process in most materials. This thesis introduces a method to deal with this problem using an external force field to speed up the diffusion process in the simulation. The method is applied to study the diffusion of oxygen ions in Sm-doped ceria, which has showed promise in its use as an electrolyte. Good agreement with experimental data is demonstrated, indicating high potential for future applications of the method.

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Lo, Cynthia. « First-principles molecular modeling of structure-property relationships and reactivity in the zeolite chabazite ». Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/28842.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2005.
Includes bibliographical references (p. 123-139).
Zeolites are crystalline, porous aluminosilicates; while a pure silicate structure is charge-neutral, the substitution of A1³⁺ for Si⁴⁺ creates in the framework a negative charge, which can be compensated by a proton that acts as a strong, acid-donating Bronsted site. Zeolites are widely used in industry, most commonly for catalysis and separations. Unfortunately, they have not yet been able to replace all homogeneous catalysts in industrial processes due to the difficulties in reactant and product diffusion to and from the zeolite surface in the absence of a solvent. However, it is believed that if we had a thorough understanding of how solid acids, especially zeolites, catalyze reactions, then we would be able to design heterogeneous catalysts to overcome these difficulties. The nature of the acid sites in zeolites and the factors contributing to enhanced catalytic activity have been the subject of much study in the literature. In particular, the issue of whether all of the acid sites in a particular zeolite are homogeneous or heterogeneous in acid strength requires the development of a systematic way to quantify acidity. To address this, a detailed density functional theory (DFT) investigation of the reactivity of the acid sites in the zeolite chabazite was performed. Energies of adsorption of bases, deprotonation energies, and vibrational frequencies were calculated on a periodic chabazite (SSZ-13) model with various loadings of acid sites per unit cell, and with various structural framework defects. The four acidic oxygens at the aluminum T-site were found to all have roughly the same proton affinity, and the deprotonation energy is not correlated to the O-H bond length or vibrational stretch frequency. Furthermore, the adsorption energy of various bases at
(cont.) each acid site oxygen was found to be roughly the same and correlated only to the gas-phase proton affinity of the base; it does not vary significantly with acid site concentration or framework defects near the acid site. Given the range of local chemical structure that we investigated, these results suggest that the strength of the acid sites in chabazite is not influenced significantly by chemical or structural variations in the framework near the acid site. A comprehensive methodology was also developed and implemented for studying the mechanism for the coupling reaction of two methanol molecules to form ethanol and water in the zeolite chabazite. This test reaction models an initial carbon-carbon bond formation, which is thought to be the rate limiting step in the industrial methanol-to-gasoline and methanol-to-olefins processes. Transition path sampling and constrained molecular dynamics, within the Car-Parrinello approach, were used to study this reaction. A new mechanism was found for the carbon-carbon bond formation, which proceeds at 400⁰C via stable intermediates of water, methane, and protonated formaldehyde. The carbon-carbon bond forms directly and concurrently with a proton transfer from methane to water. This mechanism does not involve the formation of dimethyl ether or surface methoxy groups at the acid site, as previously postulated. Also, the free energy barriers for the reaction in chabazite were compared to the free energy barriers ...
by Cynthia S. Lo.
Ph.D.

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Kucukbenli, Emine. « Nuclear Magnetic Resonance Study of Complex Molecular Crystals From First Principles : Case of Cholesterol ». Doctoral thesis, SISSA, 2011. http://hdl.handle.net/20.500.11767/4295.

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The layout of this thesis is as follows: In Chapter 2 we present the theoretical background relevant to our study, namely NMR, Density Functional Theory (DFT), PAW and GIPAW. We also report the performed computational tests that validate our implementation. In Chapter 3 we first give the experimentally determined structural properties of cholesterol crystals for all known phases and compare our theoretical results with these reports. In this chapter we also examine the adequacy of classical force field calculations in structure determination through comparisons with both ab initio results and experiment. In Chapter 4 we report our results for NMR spectrum of all known phases and comment on the accuracy of our calculations. Factors affecting the ab initio NMR calculations are investigated in detail, such as the impact of structural optimization and exchange-correlation functionals. A systematic error observed in GIPAW calculations is also discussed and a possible correction is proposed. We further test the validity of the introduced correction using the results of spectral editing experiments. Finally using all the information gathered, we perform peak assignment for the observed NMR spectra. We also compare the NMR spectrum obtained from molecules and crystals to draw conclusions on the intermolecular interactions present in cholesterol crystals.

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Landerville, Aaron Christopher. « First-principles studies of shock-induced phenomena in energetic materials ». [Tampa, Fla] : University of South Florida, 2009. http://purl.fcla.edu/usf/dc/et/SFE0002902.

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Landerville, Aaron Christopher. « First-Principles Atomistic Simulations of Energetic Materials ». Scholar Commons, 2014. https://scholarcommons.usf.edu/etd/5056.

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This dissertation is concerned with the understanding of physico-chemical properties of energetic materials (EMs). Recently, a substantial amount of work has been directed towards calculations of equations of state and structural changes upon compression of existing EMs, as well as elucidating the underlying chemistry of initiation in detonating EMs. This work contributes to this effort by 1) predicting equations of state and thermo-physical properties of EMs, 2) predicting new phases of novel EMs, and 3) examining the initial stages of chemistry that result in detonation in EMs. The motivation for the first thrust, is to provide thermodynamic properties as input parameters for mesoscale modeling. Such properties are urgently sought for a wide range of temperatures and pressures, and are often difficult or even impossible to obtain from experiment. However, thermo-physical properties are obtained by calculating structural properties and vibration spectra using density function theory and employing the quasi-harmonic approximation. The second thrust is directed towards the prediction and investigation of novel polymorphs of known azide compounds to identify precursor materials for synthesis of polymeric nitrogen EMs. Structural searches are used to identify new polymorphs, while theoretical Raman spectra for these polymorphs are calculated to aid experimentalists in identifying the appearance of these azide compounds under high pressure. The final thrust is concerned with elucidating the initial chemical events that lead to detonation through hypervelocity collision simulations using first-principles molecular dynamics. The chemical mechanisms of initiation are determined from the atomic trajectory data, while heats of reaction are calculated to quantify energy trends of chemical transformations.

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Jofré, Escobar Javier Andrés. « Mejoramiento de la termoestabilidad de enzimas mediante dinámica molecular y análisis de componentes principales ». Tesis, Universidad de Chile, 2013. http://www.repositorio.uchile.cl/handle/2250/114024.

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Magíster en Ciencias de la Ingeniería - Mención Química
Ingeniero Civil con Mención en Biotecnología
La industria biotecnológica precisa del uso de enzimas optimizadas, en particular, de termoestabiliad elevada ya que procesos industriales como la elaboración de biocombustibles de segunda generación requieren temperaturas de operación por sobre las temperaturas óptimas para la mayoría de las enzimas. El diseño de nuevas enzimas modificando enzimas ya existentes puede ser un proceso extensivo en términos experimentales y analíticos y no asegura necesariamente un grado determinado de mejora. En el presente trabajo se desarrolló una nueva herramienta para el mejoramiento de la termoestabilidad de enzimas con énfasis en dinámica molecular. Se diseñó un procedimiento para simular el comportamiento de la estructura de la proteína estudiada a tres diferentes temperaturas, 300, 350 y 400K. Se elaboró un nuevo índice de flexibilidad usando análisis de componentes principales, el valor if, que a partir de la simulación, permite determinar las regiones más flexibles y candidatas a ser rigidizadas para mejorar la termoestabilidad. Las estructuras de las variantes diseñadas a partir de lo anterior se simularon para evaluar su grado de mejora en términos de la flexibilidad y compactación. El procedimiento se validó mediante su aplicación a las estructuras de las enzimas Cel7A de Talaromyces emersonii y Cel7B de Melanocarpus albomyces. Se recuperaron regiones identificadas en otro estudio como flexibles y se encontraron nuevas regiones para ser rigidizadas. De la aplicación del procedimiento a la enzima Cel72 se obtuvieron 3 nuevas enzimas de las cuales dos mostraron reducir la compactación respecto de la nativa y una mostró reducir la flexibilidad de la estructura. Se diseñó una estrategia para mejorar la termoestabiliad de enzimas, fue posible identificar regiones flexibles y se vieron cambios en la flexibilidad y compactación de variantes respecto de sus enzimas nativas. El procedimiento aquí descrito tiene el potencial de ser una herramienta rápida y de bajo costo, sin embargo, se requerirá de ensayos de termoestabilidad de las enzimas aquí propuestas para validar experimentalmente el procedimiento.

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Gebretnsae, Samson Yebio. « Synthetic studies toward pavettamine, the active principle from Pavetta harborii ». Diss., University of Pretoria, 2005. http://hdl.handle.net/2263/31186.

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Gousiekte (“quick” disease) is a plant-induced cardiomyopathy of livestock in South Africa, that is characterized by the sudden death of animals within a period of 3-6 weeks after the initial ingestion of toxic plant material. Six species of three genera of the Rubiaceae family viz. Pachystigma pygmaeum, P. thamnus, and P. latifolium; Pavetta harborii and P. schuman-niana, and Fadogia homblei have been identified as the causative agents of the disease. The toxin responsible for the poisoning, named pavettamine, has been isolated and the structure and absolute configuration established as (2S,4R,8R,10S)-1,11-diamino-6-aza-undecane-2,4,8,10-tetraol, or the enantiomer, by mass spectrometry and NMR spectroscopy. Retrosynthetic analysis of the pavettamine molecule as outlined in the dissertation showed that the secondary amine function could be obtained from the amide functional group in an intermediate such as (2R,4S)-N-[(2′R,4′S)-2,4,5-trihydroxypentan-1′-yl]-2,4,5-trihydroxy-pentanamide A. Disconnection of the amide bond then generated two C5 building blocks viz. an amine B and a carboxylic acid C which through a set of functional group transformations led to a common C5 building block, a pentane-1,2,4,5-tetraol D. The terminal primary hydroxy groups required different protecting groups at all times in order to safe-guard the integrity of the two stereogenic centres. In addition identical protecting groups but different to those used for the primary hydroxy groups, were necessary for the secondary hydroxy groups. Further analysis of the C5 building block D showed that it could be obtained from (2S)-malic acid by functional group transformations, chiral sulfoxide methodology and an appropriate protective group strategy. A suitable protective group strategy was developed and an 11 step synthetic route for the C5 building block established. The successful conversion of this moiety through functional group transformations provided the C5 amine B and C5 carboxylic acid C which were linked to give the target compound, the amide D but with the hydroxy groups protected. The synthetic study presented in the dissertation provides an efficient methodology toward the synthesis of any of the 10 possible stereoisomers of pavettamine.
Dissertation (MSc)--University of Pretoria, 2009.
Chemistry
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