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Souto, Salom Manuel. "Multifunctional Materials based on TTFPTM dyads: towards new Molecular Switches, Conductors and Rectifiers." Doctoral thesis, Universitat Autònoma de Barcelona, 2016. http://hdl.handle.net/10803/393986.
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Esta Tesis está centrada en el diseño, síntesis y caracterización de nuevos materiales moleculares multifuncionales basados en sistemas Dador-Aceptor (D-A) formados por la unidad dadora de electrones tetratiafulvaleno (TTF) enlazada a la unidad aceptora de electrones el radical policlorotrifenilmetilo (PTM) mediante diferentes puentes -conjugados. Estos compuestos pueden exhibir propiedades físicas muy interesantes como biestabilidad o propiedades ópticas no lineales en solución, conductividad en estado sólido o rectificación cuando son anclados en superficies. Por tanto, estos sistemas podrían encontrar aplicación en el campo de la electrónica molecular como interruptores, conductores o rectificadores.
En la primera parte de esta Tesis, se estudiará el fenómeno de biestabilidad en solución de un sistema D-A basado en un radical PTM conectado a un TTF mediante un puente vinileno. Este sistema puede exhibir un cambio inducido por la temperatura entre dímeros diamagnéticos a temperatura ambiente y monómeros paramagnéticos a alta temperatura. Los dos distintos estados presentan diferentes propiedades ópticas y magnéticas utilizando la temperatura como estímulo externo. Por otra parte, también se presentará el diradical A-D-A compuesto por dos subunidades PTM radicalarias conectadas mediante un puente TTF-vinileno que puede modificar reversiblemente sus propiedades ópticas, magnéticas y electrónicas al oxidarse o reducirse en solución. La modificación de la deslocalización electrónica y del acoplamiento magnético se observa cuando generamos las especies cargadas y los cambios han sido racionalizados mediante cálculos teóricos.
En la segunda parte de la Tesis, se presentará la síntesis y caracterización de distintos derivados TTF--PTM incrementando el número de vinilenos entre las unidades D y A. También se estudiará la transferencia de carga intramolecular y las propiedades ópticas no lineales (NLO) en solución y su dependencia con la estructura electrónica abierta así como con la longitud del puente de cada uno de los compuestos.
En la tercera parte de la Tesis, se estudiará las arquitecturas auto-ensambladas en estado sólido de un nuevo sistema TTF-PTM. La estructura cristalina muestra un ordenamiento supramolecular con una segregación de las unidades dadoras y aceptoras. Además, se estudiará la aparición de conductividad en los cristales del mismo sistema al aumentar la presión. El comportamiento de semiconductor a altas presiones se relacionará con el aumento de interacciones intermoleculares así como con el incremento de la deslocalización de carga.
Finalmente, en la última parte de la Tesis se presentará un nuevo compuesto TTF-PTM que ha sido funcionalizado con un grupo disulfuro para preparar monocapas auto-ensambladas (SAMs) en superficies de oro. Estas SAMs han sido caracterizadas mediante diversas técnicas espectroscópicas para estudiar la estructura electrónica del sistema. Además, se estudiará el transporte de carga a través de las SAMs para evaluar un posible comportamiento de rectificación.<br>This Thesis is focused on the design, synthesis and characterization of new multifunctional molecular materials based on donor-acceptor (D-A) dyads formed by the electron-donor tetrathiafulvalene (TTF) unit linked to the electron-acceptor polychlorotriphenylmethyl (PTM) radical moiety through different -conjugated bridges. These compounds can exhibit interesting physical properties such bistability and nonlinear optical properties in solution, conductivity in the solid state or electrical rectification when anchored on surfaces. Thus, these systems could find potential applications in the field of molecular electronics as switches, conductors or rectifiers.
In the first part of the Thesis, we have studied the bistability phenomenon in solution of a D-A dyad based on a PTM radical linked to a TTF moiety through a vinyelene bridge. This system exhibited a temperature-induced switching between diamagnetic dimers at room temperature and paramagnetic monomers at high temperature. The two different states showed different optical and magnetic properties when using the temperature as external input. On the other hand, we have also reported the A-D-A diradical triad based on two PTM radical subunits connected through a TTF-vinylene bridge that can reversibly modify the optical, electronic and magnetic properties by one-electron reduction and oxidation in CH2Cl2 solution. The modification of electron delocalization and magnetic coupling was observed when the charged species were generated and the changes were rationalized by theoretical calculations.
In the second part of the Thesis, we have reported the synthesis and characterization of different TTF--PTM dyad derivatives increasing the number of vinylene units between the D and A moieties. We have studied the intramolecular charge transfer and non-linear optical (NLO) properties in solution and their dependence on the open-shell structure as well as on the bridge length for this family of compounds.
In the third part of the Thesis, we have studied self-assembled architectures in the solid state of a new D-A dyad based on a PTM radical linked to a TTF moiety through a -phenyl-pyrrole bridge. The crystal structure showed an interesting supramolecular arrangement with segregated donor and acceptor units. Moreover, we reported the appearance of conductivity in single crystals of the same system when increasing the pressure. The semiconducting behavior at high pressures has been attributed to the enhanced intermolecular interactions and charge delocalization due to incorporation of TTF units which force the formation of close packed stacks of molecules.
Finally in the last part of the Thesis, we have reported a new TTF-PTM dyad that was functionalized with a disulfide group in order to prepare self-assembled monolayers (SAMs) on gold. These SAMs were fully characterized by different spectroscopic techniques in order to study the electronic structure of the system. Moreover, charge transport measurements through the SAMs were performed in order to evaluate the possible rectification behavior.
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Vichetti, Rafael Mário [UNESP]. "Síntese dos isótopos do monóxido de carbono no meio interestelar." Universidade Estadual Paulista (UNESP), 2009. http://hdl.handle.net/11449/91889.
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vichietti_rm_me_rcla.pdf: 842604 bytes, checksum: 731ca276a75c1b92840e57bd7497b5e1 (MD5)<br>Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)<br>De acordo com os resultados observacionais de condensações de nuvens moleculares escuras, grandes variações na razão 13CO/C18O são observadas quando se comparam os resultados obtidos nas condensações situadas dentro da mesma nuvem, bem como de nuvem para nuvem. O valor médio dessa razão na condensação principal de Ophiuchus é inferior a 5. Por outro lado, o valor encontrado nas condensações que estão situadas ao norte de Oph é maior que 10. Grandes diferenças também são encontradas quando se comparam os resultados observacionais de diferentes nuvens escuras, tais como Ophiuchus e Taurus, onde são observados também um decréscimo da razão C18O/C17O com o aumento da densidade. Os processos químicos e físicos que governam essas variações ainda não estão claros. Nesse sentido, o objetivo da presente proposta é analisar a influência do colapso gravitacional de condensações de nuvens moleculares escuras na síntese das moléculas CO, C17O, C18O, 13CO, 13C17O e 13C18O. Tal análise é feita com base em comparações entre modelos que consideram diferentes condições entre si, tais como, tamanho da cadeia química, velocidade de colapso, densidade inicial e processos de congelamento de espécies químicas na superfície de grãos de poeira. Os resultados obtidos mostram que o tamanho da cadeia química tem influência nas razões 13CO/C18O e C18O/C17O, mas não tanto quanto a densidade inicial e a velocidade do colapso. Além disso, o congelamento das espécies químicas nos grãos é mais significativo nos estágios mais avançados da evolução da condensação. Os modelos de condensações escuras que sofrem colapso gravitacional lento e em queda livre reproduzem satisfatoriamente as razões 13CO/C18O e C18O/C17O observadas, o que permite concluir que o colapso gravitacional pode ter um importante efeito nas referidas razões.<br>According to the observational results of dark molecular clouds condensations, large variations in the ratio 13CO/C18O are observed when comparing the results obtained in the condensations located within the same cloud and cloud to cloud. The average value of this ratio in the main condensation of Ophiuchus is below 5. On the other hand, the value found in the condensations that are located north of Oph is larger than 10. Large differences are also found when comparing the observational results of different dark clouds such as Ophiuchus and Taurus, in which are also found a decrease of the C18O/C17O ratio with increasing density. The chemical and physical processes that govern these variations are still unclear. In this sense, the objective of this proposal is to analyze the influence of the gravitational collapse of centrally condensed clumps of dense molecular gas in the synthesis of the CO, C17O, C18O, 13CO, 13C17O and 13C18O molecules. This analysis is based on comparisons among models that consider different condition, such as, chemical chain, initial density, speed of collapse and freezing processes of the chemical species on the surface of dust grains. The results show that the size of the chemical chain has influence on the 13CO/C18O and C18O/C17O ratios, but they are not as important as the initial density and the speed of the collapse. Furthermore, the freezing of chemical species on the grains occurs at later times of the collapse. The models of a gravitational free-fall collapsing core and of slowly contracting core with higher initial density are consistent with observations. These results indicate that the gravitational collapse of molecular cores can have an important effect in the 13CO/C18O and C18O/C17O ratios.
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Gatchell, Michael. "Molecular Hole Punching : Impulse Driven Reactions in Molecules and Molecular Clusters." Doctoral thesis, Stockholms universitet, Fysikum, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-129523.
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When molecules are excited by photons or energetic particles, they will cool through the emission of photons, electrons, or by fragmenting. Such processes are often thermal as they occur after the excitation energy has been redistributed across all degrees-of-freedom in the system. Collisions with atoms or ions may also lead to ultrafast fragmentation in Rutherford-like scattering processes, where one or several atoms can literally be knocked out of the molecule by the incoming projectile before the energy can be completely redistributed. The resulting fragmentation pathways can in such knockout processes be very different from those in thermal processes. This thesis covers extensive studies of collisions between ions/atoms and isolated Polycyclic Aromatic Hydrocarbon (PAH) molecules, isolated fullerene molecules, or clusters of these. The high stabilities and distinct fragmentation channels make these types of molecules excellent test cases for characterizing knockout-driven fragmentation and the reactions that these processes can lead to. I will present experimental measurements for a wide range of energies and compare them with my own molecular dynamics simulations and quantum chemical calculations. In this thesis, I present an in-depth study of the role of knockout in the energetic processing of molecules and clusters. The competition between knockout and thermally driven fragmentation is discussed in detail. Knockout-driven fragmentation is shown to result in exotic fragments that are far more reactive than the intact parent molecules or fragments from thermal processes. When such reactive species are formed within molecular clusters efficient molecular growth can take place on sub-picosecond timescales. The cluster environments are crucial here because they protect the newly formed molecules by absorbing excess energy. This is a possible pathway for the growth of large PAHs, fullerenes, and similar carbonaceous complexes found in, for instance, the interstellar medium.<br><p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 1: Submitted.</p>
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Sargant, Robert John. "Molecular dynamics simulations of elongated molecules." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/molecular-dynamics-simulations-of-elongated-molecules(35c31c02-aa1f-4c87-bab9-db81d813974b).html.
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The existence of a thermotropic biaxial nematic liquid crystal phase has been a topic of great interest for almost half a century. Of the various mesogenic shapes suggested as being able to form this phase, theory has suggested that the V-shaped or "bent-core" molecule is one of the most promising candidates. In this thesis we use a simple mesogenic model of a bent-core molecule, constructed from a number of repulsive Weeks-Chandler-Andersen potentials that are assembled into a rigid V shape. Using this model we explore the spontaneous phase behaviour that occurs in a wide array of different systems of mesogens, using molecular dynamics simulations and isotropic initial conditions. We study the relationship between molecular bend angle and phase behavior for molecules constructed from 11 potentials. We find that the phase behaviour splits into two regions, above and below a critical bend angle. Molecules wider than this angle exhibit isotropic, uniaxial nematic and smectic A phases. Narrower molecules show no uniaxially aligned phases, and instead have a clustered phase with short-range ordering and no global alignment director. Increasing system size improves the smectic layering in the wider molecules, but does not affect the global alignment of the narrower molecules. Our model is extended to include the effect of the arm length of the molecule by changing the number of potentials from which the mesogens are constructed. As the molecule is reduced in size, the critical bend angle is seen to move slowly towards more linear molecules, reducing the size of the parameter space in which uniaxial nematic alignment is possible. At 5 beads, all mesophases are seen to disappear and systems remain isotropic. We also study the behaviour of binary mixtures of bent-core molecules, both of differing arm lengths and of differing bend angles. For arm length mixtures, molecules are seen to remain mixed in the isotropic and nematic phases, and phase separate on transition to a smectic phase. In addition, uniaxial nematic phases are induced in systems that have no nematic phase of their own in isolation. For mixtures of different bend angles, systems remain fully mixed in the smectic phases for differences of up to 10 degrees, and beyond this the two components begin to separate at the nematic–smectic transition.
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Pietilä, Lars-Olof. "Molecular mechanics and force field studies of weakly coupled conjugated molecules and molecular crystals." Hki : Finnish Society of Sciences and Letters : Academic Bookstore [distr.], 1988. http://catalog.hathitrust.org/api/volumes/oclc/57854229.html.
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Palomar, Polo Ricardo. "Simulació per Dinàmica Molecular de Líquids Moleculars Sobrerefredats." Doctoral thesis, Universitat Politècnica de Catalunya, 2007. http://hdl.handle.net/10803/6589.
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L'objectiu fonamental d'aquesta tesi és l'estudi mitjançant dinàmica molecular del comportament de líquids sobrerefredats. S'ha escollit líquids amb pont d'hidrogen, concretament els alcohols de baix pes molecular etanol i metanol. En els dos sistemes s'ha trobat una temperatura crítica per a la qual apareix una divergència en els temps de relaxació i en diferents coeficients de transport. En totes les funcions de correlació analitzades, la relaxació presenta dues etapes. La dinàmica de translació del centre de massa molecular està d'acord amb les prediccions de la teoria mode coupling ideal. S'ha demostrat que la desviació respecte a un comportament gaussià és important en els dos sistemes a baixes temperatures i temps intermedis, i que aquesta desviació està relacionada amb la presència d' heterogeneïtats dinàmiques. <br/>S'ha analitzat també el paper dels ponts d'hidrogen en els resultats obtinguts. Hom ha estudiat un model idèntic al metanol excepte pel que fa a la capacitat d'establir ponts d'hidrogen. Per aquest s'ha trobat que, per temperatures decreixents, el ritme d'augment en el temps de relaxació de translació és superior al de reorientació. La supressió de l'enllaç d'hidrogen produeix una temperatura crítica més petita per la difusió i pels temps de relaxació. El comportament no gaussià de la dinàmica per a temps intermedis és menys important quan se suprimeix l'enllaç d'hidrogen, però la seva dependència temporal per a temps grans és independent de l'existència de l'enllaç.<br/>En el sistema format per molècules diatòmiques s'han investigat les heterogeneïtats dinàmiques. S'ha comprovat la correlació entre els desplaçaments consecutius d'una molècula per temps intermedis i a temperatures baixes, que tendeix a desaparèixer per a temps molt grans (relaxació ). La correlació és màxima quan la desviació del comportament gaussià de la dinàmica arriba també al seu màxim. La direccionalitat dels moviments de translació ha estat també estudiada, tot observant-se un comportament anisòtrop especialment a temps intermedis (relaxació ). Han estat també observades heterogeneïtats dinàmiques en la reorientació, de manera que són les molècules amb gran desplaçament les que presenten un gran moviment de reorientació. Aquest acoblament augmenta a mesura que la temperatura decreix. <br/>La relació entre heterogeneïtat dinàmica i espacial s'ha estudiat en el sistema de molècules diatòmiques. Al final d'un interval temporal s'han seleccionat les molècules que presenten el desplaçament més gran i més petit. S'ha demostrat que les molècules d'aquests dominis dinàmics s'agreguen formant agrupacions més grans que les resultants en un sistema estadísticament aleatori. En refredar el sistema, el nombre mitjà de molècules constituents d'una agrupació ràpida, així com la seva escala de longitud, creixen notòriament. Ambdues quantitats resulten ser màximes quan l'interval de monitorització és proper a l'instant per al qual la dinàmica del sistema més se separa de la dinàmica gaussiana. Les agrupacions de molècules ràpides tenen una geometria allargada. Les agrupacions de molècules lentes tenen una grandària més petita que les ràpides i tenen una geometria més compacta.<br>The aim of this thesis is the study of supercooled liquids by means of molecular dynamics simulations. We have investigated the behavior of hydrogen bonded liquids, specifically the low weight alcohols methanol and ethanol. In both systems, relaxation times and transport coefficients diverge at a critical temperature. For all correlators under study, a two-step relaxation behavior has been encountered. Translation dynamics of molecular centers-of-mass agrees reasonably well with Mode Coupling predictions. At low temperatures and intermediate time scales, a remarkable deviation from Gaussian dynamics is found. This deviation is related to the existence of dynamical heterogeneities. <br/>The role of hydrogen bonding in supercooled methanol has also been analyzed. The results obtained for methanol have been compared with those of an ideal methanol-like system whose diatomic molecules have the same dipole moment as the methanol ones but lack sites for hydrogen bonding. Upon cooling, it has been found that translational relaxation times increase more rapidly than reorientational ones, being this effect more important in the non-associated system. Suppression of hydrogen bonds also results in lower critical temperatures for diffusion and for several characteristic relaxation times. Deviations from Gaussian dynamics are more relevant in methanol, but the long time behavior does not depend on the existence of hydrogen bonds.<br/>Dynamic heterogeneities have been analyzed in the supercooled system of diatomic molecules. Correlations between molecular displacements performed during consecutive time intervals are apparent at low temperatures and intermediate times, whereas they tend to disappear at long times (-relaxation). These correlations maximize when the deviation from Gaussian dynamics takes a maximum. The molecular displacement has an important anisotropic component at intermediate time scales (-relaxation). Dynamic heterogeneities in reorientation have been observed at the beginning of the -relaxation regime, and it has been obtained that molecules that perform faster translational motions experience faster reorientational motions too. This coupling increases as temperature decreases.<br/>Finally, the connection between dynamic and spatial heterogeneities has been studied. It has been encountered that molecules belonging to the same dynamical domain are spatially correlated. They form clusters bigger than those resulting from random statistics. Clusters composed by mobile molecules are string-like shaped, and both their associated size and lenght scale grow notoriously upon cooling. Both quantities maximize when non-Gaussian dynamics maximizes too. Clusters made up by slow molecules have a smaller size and a more compact geometry than fast clusters.
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Barrett, Michael John Sheiko Sergei. "Molecular visualization of individual molecules during flow." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2009. http://dc.lib.unc.edu/u?/etd,2942.
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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2010.<br>Title from electronic title page (viewed Jun. 23, 2010). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Chemistry." Discipline: Chemistry; Department/School: Chemistry.
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Baker, Joseph Lee. "Steered Molecular Dynamics Simulations of Biological Molecules." Diss., The University of Arizona, 2011. http://hdl.handle.net/10150/205416.
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Molecular dynamics (MD) simulation, which employs an empirical potential energy function to describe the interactions between the atoms in a system, is used to investigate atomistic motions of proteins. However, the timescale of many biological processes exceeds the reach of standard MD due to computational limitations. To circumvent these limitations, steered molecular dynamics (SMD), which applies external forces to the simulated system, can be used.Dynamical properties of the gonococcal type IV pilus (GC-T4P) from the bacteria Neisseria gonorrhoeae are first considered. T4 pili are long, filamentous proteins constructed from a subunit (pilin) found to emanate from the surface of pathogenic bacteria. They can withstand large forces (~100 pN), and are implicated in infection. SMD simulations are performed to study the response of the filament to an applied force. Our simulations reveal that stability of the pilus likely results from hydrophobic contacts between pilin domains buried within the filament core. Along the filament surface, gaps are formed between pilin globular head domains. These gaps reveal an amino acid sequence that was also observed to become exposed in the experimentally stretched filament. We propose two other regions initially hidden in the native filament that might become exposed upon stretching.The multidrug resistance transporter EmrD, found in the inner membrane of Escherichia coli is also the target of our studies. EmrD removes harmful drugs from the bacterial cell. We use MD to explore equilibrium dynamics of the protein, and MD/SMD to study drug interactions and transport along its central cavity. Motions supporting a previously proposed lateral diffusion pathway for substrate from the cytoplasmic membrane leaflet into the central cavity were observed. Additionally, interactions of a few specific residues with CCCP have been identified.Finally, we describe network analysis as an approach for analyzing conformational sampling by MD simulations. We demonstrate for several model systems that networks can be used to visualize both the dominant conformational substates of a trajectory and the connectivity between them. Specifically, we compare the results of various clustering algorithms to the network layouts and show how information from both methods can be combined.
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Wildman, Jack. "Molecular dynamics simulations of conjugated semiconducting molecules." Thesis, Heriot-Watt University, 2017. http://hdl.handle.net/10399/3261.
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In this thesis, we present a study of conformational disorder in conjugated molecules focussed primarily on molecular dynamics (MD) simulation methods. Along with quantum chemical approaches, we develop and utilise MD simulation methods to study the conformational dynamics of polyfluorenes and polythiophenes and the role of conformational disorder on the optical absorption behaviour observed in these molecules. We first report a classical force-field parameterisation scheme for conjugated molecules which defines a density functional theory method of accuracy comparable to high-order ab-initio calculations. In doing so, we illustrate the role of increasing conjugated backbone and alkyl side-chain length on inter-monomer dihedral angle potentials and atomic partial charge distributions. The scheme we develop forms a minimal route to conjugated force-field parameterisation without substantial loss of accuracy. We then present a validation of our force-field parameterisation scheme based on self-consistent measures, such as dihedral angle distributions, and experimental measures, such as persistence lengths, obtained from MD simulations. We have subsequently utilised MD simulations to investigate the interplay of solvent and increasing side-chain lengths, the emergence of conjugation breaks, and the wormlike chain nature of conjugated oligomers. By utilising MD simulation geometries as input for quantum chemical calculations, we have investigated the role of conformational disorder on absorption spectral broadening and the formation of localised excitations. We conclude that conformational broadening is effectively independent of backbone length due to a reduction in the effect of individual dihedral angles with increasing length and also show that excitation localisation occurs as a result of large dihedral angles and molecular asymmetry.
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Healey, Eleanor G. "Molecular mechanisms of Repulsive Guidance Molecule signalling." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:3ba6699b-7919-47db-a58e-95970e5e8fcf.
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Repulsive Guidance Molecules (RGMs) control fundamental and diverse cellular processes including axon guidance, immune cell regulation and systemic iron metabolism. RGM dysfunction has been linked to diseases such as multiple sclerosis, cancer and the iron overload disorder juvenile hemochromatosis (JHH). RGMs signal by binding directly to the transmembrane receptor Neogenin (NEO1) to trigger cytoskeleton rearrangements and subsequent axon repulsion. Additionally, RGMs are important activators of the essential developmental Bone Morphogenetic Protein (BMP) signalling pathway. RGM-activated BMP signalling is crucial for the regulation of iron metabolism and mutations in RGMC cause JHH. This thesis outlines structural and functional studies of the molecular mechanisms of RGM signalling. In Chapter 3, an analysis of an RGMB-NEO1 crystal structure is presented. Combined with mutagenesis studies, analytical ultracentrifugation experiments and neurite outgrowth assays, this allowed a mechanism for RGM signalling through NEO1 to be proposed. RGM acts as a molecular staple, bringing together the juxtamembrane regions of two NEO1 receptors to activate downstream signalling. In Chapter 4, crystal structures of the N-terminal domains of all RGM family members in complex with the BMP2 ligand are presented. Together with biophysical and cellular assays these structures allowed an endocytosis-linked mechanism for RGM-activated BMP signalling to be proposed, which is dependent on the subcellular localisation of the BMP-receptors. The work outlined in both of these chapters also revealed a molecular rationale for the disease-causing mechanism of RGMC JHH-linked mutations. In Chapter 5, the crystal structure of the ternary BMP2-RGMBNEO1 complex is described along with super-resolution uorescence microscopy data demonstrating BMP-induced clustering of RGM-NEO1 complexes in the membrane. In summary, this work sheds light on the molecular mechanisms of RGM signalling through NEO1 and BMPs, and demonstrates for the first time that RGM forms a structural bridge between these two fundamental signalling pathways.
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Thomas, Philip Robert. "The molecular properties of zwitterionic, non-linear optical molecules and their evolution with molecular environment." Thesis, Durham University, 1998. http://etheses.dur.ac.uk/4998/.
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The concepts involved with the experimental techniques of Electric Field Induced Second Harmonic generation (EFISH), dipole moment measurement, and solvatochromism, are introduced with particular application to the properties of organic molecules. A number of organic chromophores are introduced, but emphasis is applied to the study of tetracyanoquinodimethane (TCNQ) derivatives which are expected to possess large dipole moments (µ) and large hyperpolarisabilities (β). Furthermore, the behaviour of and with respect to the local environment of the molecule is discussed where a novel evolution is predicted from theoretical calculations. The measurement of µ, is discussed with particular reference to the geometry of the local field factor and the size of the molecule. Consequently, the choice of local field is found to be critical when dipole moments are large, as is the case with the TCNQ derivatives. The EFISH experimental technique is introduced where the calibration of the experiment is discussed. The measurement of the molecular figure of merit, µβ at 1.064 µm and 1.907 µm in chloroform and dichloromethane is presented for the TCNQ derivatives, again paying attention to the geometry of the local field factor. µβ is found to be moderate for most of the compounds, but β is found to be unexpectedly small. This is partly due to the fact that µ is large. A novel evolution of the transition frequency with solvent polarity is found for three of the chromophores under study, where the solvatochromic shift reverses. Solvatochromism experiments are conducted with binary solvent mixtures to ascertain the position of the cyanine limit (β=0) with respect to reaction field. It is found that the materials reside close to the cyanine limit in chloroform and dichloromethane. This is attributed as a reason for the low β measurements. Comparisons of µ and β are also made with Sum-Over-State calculations. A better correlation is found for ellipsoidal local field factors.
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Myint, Mo Aung, and n/a. "Investigation of molecular interactions with molecularly imprinted polymers." University of Otago. Department of Chemistry, 2009. http://adt.otago.ac.nz./public/adt-NZDU20090617.131516.
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Currently, very little information is available for an in-depth understanding of the molecular binding interactions with molecularly imprinted polymers (MIPs). To address this issue MIPs that have high binding affinities for their template compounds were made so that the nature of these interactions could be elucidated using spectroscopic techniques.
12 functional MIPs were prepared using a series of azobenzene and anthracenyl derivatives as the templates. Affinities of these MIPs for the corresponding templates and analogues were determined by performing batch and competitive binding tests. It was found that extensively conjugated compounds that contain at least two OH groups, an electron-withdrawing substituent and have limited conformational freedom were effective templates.
The most efficient MIP, M34, was prepared with 4-[(4-nitrophenyl)azo]-1,2-benzenediol (12). M34 exhibited high affinities for azobenzene derivatives of catechol, and bound those that did not contain non electron-withdrawing substituents more specifically. M34 did not lose affinity for 12 in the presence of analogues, and vice versa, in competitive binding tests. These observations suggested a distribution of different binding sites on M34.
M34 bound substrates rapidly, which was attributed to its highly porous polymer matrix giving ready access to binding sites. Formation of the porous matrix was facilitated by the use of DMF as the porogen in the preparation of M34. DMF is not a conventional choice of porogen because use of such highly polar H-bonding solvents is thought to disrupt complexation between template and polymer precursors, which is required for the formation of binding sites.
Significant changes in the wavenumbers and the intensities of absorption bands assigned to the catechol substructure of 12 were observed in the FT-Raman spectra of 12 bound to M34. These findings suggested that the catechol substructure was responsible for interactions of 12 with M34 that are critical to rebinding and imprinting.
In-situ analyses of dithranol (8) being removed from and bound to its MIP, M23, were performed using ATR-IR spectroscopy. Only one band, assigned to the aromatic substructure of 8, was not obstructed by solvent bands in the spectra of unwashed M23 and washed M23 that was treated with the rebinding solution. The wavenumbers of the corresponding bands in the two spectra were significantly different. This observation suggested that there were differences in the vibrational characteristics of 8 bound to M23 under the two conditions.
Evidence was found for H-bonding between OH groups of 8 and C=O group of methacrylic acid using transmission FT-IR spectroscopy. However, no evidence was found that showed significant interactions between 12 and 2-vinylpyridine. Methacrylic acid and 2-vinylpyridine were used as the functional monomers in the preparations of M23 and M34. The FT-IR spectra of mixtures of 12 and 4-vinylpyridine showed three new bands assigned to H-bonded OH stretches. These observations indicated that 4-vinylpyridine H-bonds with 12, and would be a more effective functional monomer than 2-vinylpyridine in the preparation of the MIPs for 12.
Titration of 12 with 2-vinylpyridine was analysed by �H NMR spectroscopy. Only small changes to the signals of the corresponding compounds were observed. This lack of change was attributed to the use of d₇DMF, which would compete against 2-vinylpyridine for H-bonding interactions.
The findings made using ATR-IR spectroscopy and FT-Raman were novel because previously reported data on bound templates obtained using the corresponding techniques did not show changes in the vibrational characteristics of templates as they bind to MIPs. This investigation has shown that rebinding and spectroscopic studies can provide information about the nature of the binding interactions in MIPs.
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Schmid, Günter Maximilian. "Dynamical symmetry breaking in molecules and molecular aggregates." Thesis, Massachusetts Institute of Technology, 1994. http://hdl.handle.net/1721.1/17393.
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Dean, Delphine Marguerite Denise 1978. "Molecular electromechanics : modeling electrostatic forces between GAG molecules." Thesis, Massachusetts Institute of Technology, 2001. http://hdl.handle.net/1721.1/86649.
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Thesis (M.Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2001.<br>Includes bibliographical references (p. 81-83).<br>by Delphine Marguerite Denise Dean.<br>M.Eng.and S.B.
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Vichetti, Rafael Mário. "Síntese dos isótopos do monóxido de carbono no meio interestelar /." Rio Claro : [s.n.], 2009. http://hdl.handle.net/11449/91889.
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Orientador: Carmen Maria Andreazza<br>Banca: Edson Denis Leonel<br>Banca: José Williams dos Santos Vilas Boas<br>Resumo: De acordo com os resultados observacionais de condensações de nuvens moleculares escuras, grandes variações na razão 13CO/C18O são observadas quando se comparam os resultados obtidos nas condensações situadas dentro da mesma nuvem, bem como de nuvem para nuvem. O valor médio dessa razão na condensação principal de Ophiuchus é inferior a 5. Por outro lado, o valor encontrado nas condensações que estão situadas ao norte de Oph é maior que 10. Grandes diferenças também são encontradas quando se comparam os resultados observacionais de diferentes nuvens escuras, tais como Ophiuchus e Taurus, onde são observados também um decréscimo da razão C18O/C17O com o aumento da densidade. Os processos químicos e físicos que governam essas variações ainda não estão claros. Nesse sentido, o objetivo da presente proposta é analisar a influência do colapso gravitacional de condensações de nuvens moleculares escuras na síntese das moléculas CO, C17O, C18O, 13CO, 13C17O e 13C18O. Tal análise é feita com base em comparações entre modelos que consideram diferentes condições entre si, tais como, tamanho da cadeia química, velocidade de colapso, densidade inicial e processos de congelamento de espécies químicas na superfície de grãos de poeira. Os resultados obtidos mostram que o tamanho da cadeia química tem influência nas razões 13CO/C18O e C18O/C17O, mas não tanto quanto a densidade inicial e a velocidade do colapso. Além disso, o congelamento das espécies químicas nos grãos é mais significativo nos estágios mais avançados da evolução da condensação. Os modelos de condensações escuras que sofrem colapso gravitacional lento e em queda livre reproduzem satisfatoriamente as razões 13CO/C18O e C18O/C17O observadas, o que permite concluir que o colapso gravitacional pode ter um importante efeito nas referidas razões.<br>Abstract: According to the observational results of dark molecular clouds condensations, large variations in the ratio 13CO/C18O are observed when comparing the results obtained in the condensations located within the same cloud and cloud to cloud. The average value of this ratio in the main condensation of Ophiuchus is below 5. On the other hand, the value found in the condensations that are located north of Oph is larger than 10. Large differences are also found when comparing the observational results of different dark clouds such as Ophiuchus and Taurus, in which are also found a decrease of the C18O/C17O ratio with increasing density. The chemical and physical processes that govern these variations are still unclear. In this sense, the objective of this proposal is to analyze the influence of the gravitational collapse of centrally condensed clumps of dense molecular gas in the synthesis of the CO, C17O, C18O, 13CO, 13C17O and 13C18O molecules. This analysis is based on comparisons among models that consider different condition, such as, chemical chain, initial density, speed of collapse and freezing processes of the chemical species on the surface of dust grains. The results show that the size of the chemical chain has influence on the 13CO/C18O and C18O/C17O ratios, but they are not as important as the initial density and the speed of the collapse. Furthermore, the freezing of chemical species on the grains occurs at later times of the collapse. The models of a gravitational free-fall collapsing core and of slowly contracting core with higher initial density are consistent with observations. These results indicate that the gravitational collapse of molecular cores can have an important effect in the 13CO/C18O and C18O/C17O ratios.<br>Mestre
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Souza, Carolina Penhavel de. "Desenvolvimento de modelos para flavonoides e cumarinas utilizando o campo de força CGenFF /." São José do Rio Preto, 2014. http://hdl.handle.net/11449/128160.
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Orientador: Alexandre Suman de Araujo<br>Banca: Ernesto Raul Caffarena<br>Banca: Marinônio Lopes Cornélio<br>Resumo: A utilização de simulações computacionais como ferramenta no estudo dos mais variados sistemas biomoleculares nos traz a possibilidade de observar o comportamento, organização e interação de seus componentes em nível atômico/molecular. Dentre as inúmeras técnicas de simulação computacional existentes, a mais difundida atualmente é a Dinâmica Molecular (DM). A DM tem um papel importante no que diz respeito à determinação da estrutura, dinâmica e função de um sistema molecular graças à simplicidade de sua função potencial. Essa função potencial e sua respectiva parametrização são chamadas, genericamente, de campo de forças. Dentre os diversos campos de forças propostos na literatura, o CHARMM é um dos mais utilizados e aperfeiçoados atualmente. Com o objetivo de modelar moléculas de interesse farmacológico que interagem com biomoléculas, foi desenvolvida recentemente uma extensão desse campo de forças, o CHARMM General Force Field (CGenFF). A construção da versão inicial do CGenFF foi baseada em moléculas componentes do CHARMM como, por exemplo, o fenol, parametrizado como um precursor para a tirosina. Todos os parâmetros já disponíveis no CHARMM são convertidos e combinados de modo a produzir novos tipos de átomos. Mesmo assim, o CGenFF deve ser usado apenas para moléculas farmacológicas; as macromoléculas biológicas devem ser representadas pelo campo de forças CHARMM original. O estudo de moléculas de interesse farmacológico provenientes de fontes naturais (vegetais, animais ou minerais) sempre resultou no desenvolvimento de fármacos de grande eficiência para o combate de inúmeras doenças. Aproximadamente 50% dos fármacos introduzidos no mercado, durante os últimos 20 anos, são derivados de pequenas moléculas biogênicas. Dentre os compostos naturais com grande potencial para uso como fármacos podemos destacar os flavonoides: eles são...<br>Abstract: The use of computational simulations as a tool in the study of biomolecular systems creates the possibility to observe the behavior, organization and interaction of the components at atomic/molecular level. Among several computational simulation techniques, the most used is Molecular Dynamics (MD). MD plays an important role in structure determination, dynamics and function of molecular systems due to the simplicity of its potential function. This and their respective parameterization are generically known as force fields. Among the existing force fields, CHARMM is one of the most used and improved today. In order to model molecules of pharmaceutical interest that interact with biomolecules, an extension of this force field, the CHARMM General Force Field (CGenFF), was developed. The construction of the initial version of the CgenFF was based in molecules which compose CHARMM, such as phenol, parameterized as a precursor for tyrosine. All the parameters already available in the CHARMM are converted and combined to produce new types of atoms. Nevertheless, the CGenFF should be used only for pharmacological molecules; the biological molecules should be represented by the original CHARMM force field. The study of molecules of pharmacological interest from natural sources (vegetable, animal or mineral) always resulted in the development of drugs highly efficient to fight several diseases. Approximately 50% of the drugs introduced on the market, during the last 20 years, are derived from small biogenic molecules. Among the natural components with great potential for use as drugs we can highlight flavonoids, our study object: they are polyphenolic compounds naturally present in vegetables, fruit, seeds, nuts and drinks like tea and red wine. These molecules are derived from benzo-γ-pirone and present a wide range of biological activity (antiallergenic, anti-inflammatory, antioxidant, antiviral and...<br>Mestre
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Villabona, Pedemonte Marc. "Photofunctional processes and materials based on molecular switches." Doctoral thesis, Universitat Autònoma de Barcelona, 2021. http://hdl.handle.net/10803/673837.
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Els interruptors moleculars han estat un camp de recerca important en els últims anys degut a la seva capacitat per interconvertir-se entre múltiples estats al estar exposats a un estímul (escriptura) i al fet de modificar les seves propietats després del canvi (lectura). Els interruptors moleculars que interaccionen amb llum per canviar d’estat o bé que modifiquen les seves propietats òptiques són d’especial interès ja que la llum permet un alt control espai temporal de forma no invasiva i la seva detecció té una alta sensibilitat. Per aquest motiu, durant aquesta tesis s’han desenvolupat múltiples materials i processos fotofuncionals els quals poden resumir-se en dues parts:
Per una banda, el caràcter multiestat d’una família de interruptors molecular (fluoro)cròmics basats en compostos espirocíclics zwitteriònics de Meisenheimer (SZMC), es va ampliar mitjançant la identificació d’un nou estat catiònic amb propietats òptiques distintives, el qual és pot generar tant electroquímicament com a través de l’adició d’un àcid. A més, es va investigar el comportament termo(fluoro)cròmic dels SZMC i es va demostrar que podien respondre tant a canvis en el dissolvent com a la presència d’anions. Aquest comportament multiestat i de resposta a múltiples estímuls va ser emprat en la preparació de una sèrie de materials fotofuncionals basats en SZMC com: un detector de pH d’ampli espectre, dispositius electro(fluoro)cròmics i sensors iònics, termals i de dissolvents.
Per altra banda, es van controlar tres processos químics amb ditieniletens (DTE) mitjançant llum. Primer, la introducció d’un grup electroacceptor EWG va permetre la modulació del pKa de fenols funcionalitzats amb DTEs. Després, el control amb dues longituds d’ona d’una reacció d’amidació es va aconseguir amb un estratègia similar a l’anterior utilitzant un éster activat basat en DTE. Aquest va reaccionar fins a 24 vegades més ràpid en el estat tancat generat amb llum UV (ie. activació amb UV) que amb l’estat obert obtingut sota irradiació amb llum visible (ie. desactivació amb visible). Finalment, la estratègia de controlar reaccions amb dos colors també va ser aplicada en la fotoligació mitjançant una reacció de oxo-Diels Alder d’un dienòfil basat en DTE actiu en la forma tancada (ie. Activacióamb llum UV, desactivació amb llum visible) i un diè generat en llum UV basat en orto-metilbenzaldèhid.<br>Los interruptores moleculares han sido un campo de investigación importante en los últimos años debido a la capacidad de interconvertir-se entre múltiples estados al exponerse a un estímulo (escritura) y modificar sus propiedades (lectura). De especial interés han sido los interruptores moleculares que interaccionan con la luz ya sea para cambiar de estado o bien modificar sus propiedades ópticas en la transformación. Esto és debido a que la luz permite un alto control espaciotemporal al mismo tiempo que és no invasiva y altamente sensible a la detección. Por estos motivos, durante esta tesis se han desarrollados múltiples materiales y procesos fotofuncionales los cuales pueden resumirse en dos partes:
Por un lado, el carácter multiestado de una familia de interruptores moleculares (fluoro)crómicos basados en compuestos espirocíclicos zwitteriònicos de Meisenheimer (SZMC) se amplió mediante la identificación de un nuevo estado catiónico, con propiedades ópticas distintivas, que se puede generar tanto electroquímicamente, como a través de la adición de ácido. Además, se investigó el comportamiento termo(fluoro)crómico de los SZMC y se demostró que podían responder tanto a cambios en el disolvente como a la presencia de iones. Este comportamiento multiestado i de respuesta a múltiples estímulos fue utilizado en la preparación de varios materiales fotofuncionales basados en SZMC como: un detector de pH de amplio espectro, dispositivos electro(fluoro)crómicos i sensores iónicos, termales i de disolventes.
Por otro lado, se controlaron tres procesos químicos diferentes con interruptores moleculares fotoinducidos de tipo ditienileteno (DTE) mediante luz. Primero, la introducción de un grupo electroacceptor permitió la modulación del pKa de un fenol funcionalizado con un DTE. Segundo el control de una reacción de amidación con dos longitudes de onda fue conseguido con una estrategia similar a la anterior utilizando un ester activado basado en DTE. Este reacciona hasta 24 veces más rápido en el estado cerrado generado con luz ultravioleta (ie. activación con UV) que en el estado abierto que se obtiene al irradiar con luz visible (ie. desactivación con visible). Finalmente, el control de reacciones con dos colores de luz fue utilizado para controlar la reacción de oxo-Diels Alder entre un dienófilo basado en DTE activo en el estado cerrado (ie. activación con UV, desactivación con luz visible) i un dieno generado con luz UV basado en orto-metilbenzaldehido.<br>Molecular switches have been an important research field in the recent years due to its capacity to interconvert between multiple states through a stimulus (writing) and change their properties (reading). Of special interest are molecular switches that interact with light by either changing their optical properties or reacting as stimulus, due to its noninvasive high spatiotemporal control and sensitivity. As a result, several photofunctional materials and processes based on molecular switches were developed during this thesis which can be summarized in two topics.
On the one hand, the multistate character of a family of (fluoro)chromic molecular switches based on spirocyclic zwitterionic Meisenheimer compounds (SZMC) was broadened by identifying a novel cationic state with distinctive optical properties, which could be achieved electrochemically or via acid addition. Moreover, the thermo(fluoro)chromic behavior of SZMCs was investigated and successfully demonstrated that they can respond to certain ions and solvents. This multistimuli-responsive and multistate character was then exploited for the preparation of a variety of photofunctional materials based on SZMCs: wide-range pH detectors, electro(fluoro)chromic displays, and thermal, ionic and solvent sensors.
On the other hand, light controlled reactivity with dithienylethenes (DTE) was achieved for three chemical processes. First, the introduction of electrowithdrawing groups (EWG) allowed the modulation of the pKa in acetonitrile of a series of DTEs tethering phenol moieties. Second, a similar strategy allowed for the dual-color control of an amidation reaction employing DTE-based active esters which react up to 24 times faster in the UV-generated closed state (ie. activation with UV irradiation) than in the open state formed under visible illumination (ie depletion with visible light). Finally, two-wavelength control was also achieved for an oxo-Diels Alder reaction between a DTE-dienophile active in the closed state and a UV-generated diene based on orto-methylbenzaldehyde.<br>Universitat Autònoma de Barcelona. Programa de Doctorat en Química
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Vaitheeswaran, Subramanian. "Computer Simulations of Partially Confined Water." Fogler Library, University of Maine, 2004. http://www.library.umaine.edu/theses/pdf/VaitheeswaranS2004.pdf.
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Lindqvist, Lisa Margareta. "The molecular dissection of protein synthesis via small molecules." Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=96682.
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Protein synthesis is a highly regulated process and it is vital to life. If the rate of translation is too slow, proteins will not be replaced fast enough causing an imbalance in protein turnover and eventual cell death. On the other hand, if the rate of translation is too fast, it can lead to uncontrolled growth and potential tumorigenesis. The scientific community is now trying to exploit this concept to create novel anticancer therapies using inhibitors of translation. These inhibitors have also been invaluable to dissecting the mechanism of translation.Hippuistanol is an inhibitor of translation initiation which inhibits eIF4A:RNA interaction. Herein I characterize the binding site of hippuristanol on eIF4A and develop hippuristanol-resistant mutants to demonstrate that both helicase activity and eIF4G:eIF4A interaction are absolutely required for eIF4A to function in translation. As well, I utilize this compound to determine that eIF4B, eIF4H, and eIF3a cross-link to RNA in an eIF4A-dependent manner up to 52 nucleotides downstream from cap structure of the mRNA. We also demonstrate that eIF4E only cross-links to RNA within a few nucleotides of the cap structure and is not visible at 12 nucleotides downstream of the cap structure. These results shed light on the positioning of initiation factors within the 5'UTR.Herein I also present that cytotrienin A, an inducer of apoptosis in leukemia cell lines, as a novel inhibitor of translation elongation. The compound inhibits proper eEF1A function and inhibits translocation when aminoacyl-tRNA is loaded onto the ribosome in an eEF1A-dependent fashion. Cytotrienin A also hindered growth in several models of angiogenesis indicating that this compound has potential as an anticancer therapeutic. These results strengthen the idea that inhibitors of translation have great potential as anticancer agents as well as being great tools to dissect the mechanism of protein synthesis.<br>La synthèse protéique ou traduction est un processus hautement régulé et essentiel à la vie. Si le rythme de synthèse protéique est trop lent, les protéines ne sont pas remplacées assez rapidement créant un débalancement du taux de renouvellement protéique ce qui entraîne la mort cellulaire. À l'opposé, si le rythme de synthèse est trop rapide, ceci peut engendrer une croissance cellulaire anarchique et potentiellement initier la tumorigenèse. La communauté scientifique cherche à exploiter ce concept afin de créer de nouvelles thérapies anticancéreuses utilisant des inhibiteurs de la traduction. Ces inhibiteurs sont également des outils inestimables pour disséquer les mécanismes de la traduction.L'hippuristanol est un inhibiteur de la traduction qui bloque l'interaction entre eIF4A er l'ARN. Ici, j'ai caractérisé le site de liaison de l'hippuristanol sur eIF4A et j'ai développé des mutants résistant à l'hippuristanol qui ont servis à démontrer que la fonction d'hélicase et l'interaction eIF4G:eIF4A sont toutes deux requises pour que eIF4A soit fonctionnel dans la traduction. De plus, j'ai utilisé ce composé pour déterminer que eIF4B, eIF4H et eIF3a sont tous liés à l'ARN par chimio-pontage et ces interactions qui peuvent être détectées jusqu'à 52 nucléotides en aval de la coiffe requièrent eIF4A. Nous avons également démontré que l'association de eIF4E à l'ARNm n'est détectée par chimio-pontage qu'avec les quelques nucléotides immédiatement en aval de la coiffe et n'est pas détectable au niveau du douzième nucléotide. Ces résultats ont éclaircis le positionnement des facteurs d'initiation au niveau du 5'NTR.Ici, je démontre également que la cytotriénine A, un inducteur d'apoptose dans les cellules leucémiques, est un nouvel inhibiteur de l'élongation lors de a traduction. Ce composé inhibe le fonctionnement du facteur eEF1A et inhibe l'étape de translocation dépendante de eEF1A qui ensuit le chargement du complexe aminoacyl-tRNA sur le ribosome. Le cytotriène A empêche également la croissance dans plusieurs modèles d'angiogenèse, indiquant que ce composé possède un potentiel comme agent anticancéreux. Ces résultats renforcent l'idée que les inhibiteurs de la traduction possèdent un énorme potentiel en tant qu'agent anticancéreux, ainsi que comme outils afin de décortiquer les mécanismes gouvernant la synthèse protéique.
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Jagatia, Fiona Jennifer. "Excited state interactions between organic molecules and molecular oxygen." Thesis, Keele University, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.246864.
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Panesar, Kuldeep Singh. "Quantum molecular dynamics of guest molecules in supramolecular complexes." Thesis, University of Nottingham, 2009. http://eprints.nottingham.ac.uk/10741/.
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The quantum motion of guest molecules has been studied in a variety of calixarene host-guest complexes, and in a endohedral fullerene complex. The guest molecules of the calixarene complexes studied each comprise weakly hindered methyl groups, which undergo rotation via quantum tunnelling, even at cryogenic temperatures. The rotational motion of the guest methyl-groups has been studied by making temperature and frequency-dependent measurements of proton T1, using field-cycling NMR, thus revealing the spectral density functions of the magnetic dipole-dipole interaction. Crystallographically inequivalent methyl-group environments have been identified and characterised in p-tert-butylcalix[4]arene(1:1)toluene, p-tert-butylcalix[4]arene(1:1)gamma-picoline and p-isopropylcalix[4]arene(2:1)p-xylene. In many of the calixarene complexes the proton spin-lattice relaxation has been observed to be strongly dependent on the thermal history of the sample. Temperature-dependent measurements of proton T1 in samples of p-tert-butylcalix[4]arene(1:1)toluene with partially deuterated guest molecules reveal a systematic reduction in T1 at low temperatures with increased degree of deuteration. Calixarene and fullerene host-guest complexes have been identified as having a potential application in cryogenic MAS-NMR as cryorelaxor complexes, capable of being attached to a large biomolecule and encouraging proton spin-lattice relaxation. The suitability of the calixarene complexes for use in this capacity has been investigated by measuring the temperature-dependence of proton T1 at low temperatures. The quantised rotational and translational motion of dihydrogen confined within an open-cage fullerene—namely, aza-thio-open-cage-fullerene (ATOCF)—has been revealed by inelastic neutron scattering (INS) measurements. The splitting of excited rotational and translational states, due to the low symmetry of the ellipsoidal fullerene cavity, has been directly measured. Assignment of the peaks observed in the INS spectrum has been aided by analysis of the Q-dependence of excitation bands. The thermodynamics of ortho- and parahydryogen have been investigated via temperature dependence measurements. INS measurements have allowed the anistropic rotational potential experienced by the H2 rotor to be determined.
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Zotti, Linda Angela. "Molecular ordering and STM imaging of functionalized organic molecules." Thesis, University of Liverpool, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.479082.
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Kirsch, Nicole. "Molecular recognition of poorly functionalised molecules with imprinted polymers." Thesis, University of Reading, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325167.
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Roskilly, Stephen. "Molecular field theory of nematics composed of flexible molecules." Thesis, University of Southampton, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.259682.
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Wiles, Alan Andrew. "Redox active molecules with molecular electronics and synthetic applications." Thesis, University of Glasgow, 2013. http://theses.gla.ac.uk/4878/.
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Redox active molecules are ubiquitous to nature and have properties that make them coveted targets for applications in areas of synthesis as well as for the development of materials. This thesis describes the synthesis and characterisation of several flavin donor-acceptor dyads designed around an oligothiophene donor backbone and a flavin acceptor moiety. These show potential applications as optoelectronic materials. It also describes the synthesis of a ferrocene-flavin tetracyanobutadiene super-acceptor compound which showed preliminary evidence of non-linear-optic effects. Finally, a novel method was developed to investigate the redox umpolung activated reactions of vinylferrocene. The vinyl group of vinylferrocene was activated by polarity inversion of ferrocene to ferrocenium and was able to undergo Diels-Alder cycloadditions with cyclobutadiene and furan, as well as, Markovnikov addition of thiols. These reactions were then used to explore the use of vinylferrocene as a redox auxiliary and as a redox active tag in polymers and have the potential to be used in nanoparticles as well as biological systems.
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Warrell, Rachel Marie. "Synthetic and Conformational Studies in Molecular Encapsulation with a Twisted Molecular Basket Complexing Organophosphorus Molecules and Fentanyl Analogues." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1502899516087168.
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Hodgkin, E. E. "Molecular similarity in computer-aided molecular design." Thesis, University of Oxford, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.379971.
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Rajbanshi, Arbin. "Supramolecular interactions from small-molecule selectivity to molecular capsules." Diss., Manhattan, Kan. : Kansas State University, 2010. http://hdl.handle.net/2097/3879.
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Becker, Jan Martin. "A molecule-up approach to chiral molecular inorganic solids." Thesis, University of Warwick, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.495024.
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Chapter One gives an overview of molecular inorganic materials. The review focuses on areas such as metallo-organic frameworks (MOFs), organometallic Prussian Blue analogues and linear chain conductors in respect of their design. classification and potential applications. There is particular reference to the scope for the synthesis of chiral materials.
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Lowe, P. "Molecular de-wetting phenomena in adsorbed bio-molecule layers." Thesis, Cranfield University, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.269544.
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Rajagopal, Senthil Arun. "SINGLE MOLECULE ELECTRONICS AND NANOFABRICATION OF MOLECULAR ELECTRONIC DEVICES." Miami University / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=miami1155330219.
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Silva, Josimar Fernando da. "Energia eletrônica e polarizabilidade da mólecula de hidrogênio ionizada confinada /." São José do Rio Preto, 2014. http://hdl.handle.net/11449/127625.
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Orientador: Elso Drigo Filho<br>Banca: João Ruggiero Neto<br>Banca: Frederico Vasconcellos Prudente<br>Resumo: No presente trabalho estudamos a energia eletrônica e a polarizabilidade da molécula de hidrogênio ionizada confinada em cavidades de diferentes volumes. Usamos o Método Variacional para realizar os cálculos de energia. O objetivo principal deste trabalho é ampliar o tratamento matemático já existente na literatura. Introduzimos uma função de onda molecular alternativa, que faz uso de apenas um parâmetro variacional para resolver o problema da molécula de hidrogênio ionizada confinada numa cavidade elíptica<br>Abstract: In this work, we study the electronic energy and the polarizability of ion hydrogen molecule under confinement in different volumes of cavities. We use the Variational Method for estimate the energy. The aim of this work is to extend the mathematical treatment reported in the existing literature. We introduce an alternative molecular wave function, this wave function has only a variational parameter to solve the problem of ion hydrogen molecule under confinement in an elliptical cavity<br>Mestre
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Souza, Carolina Penhavel de [UNESP]. "Desenvolvimento de modelos para flavonoides e cumarinas utilizando o campo de força CGenFF." Universidade Estadual Paulista (UNESP), 2014. http://hdl.handle.net/11449/128160.
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000846523.pdf: 1336118 bytes, checksum: 2880c71486230bdcf69af197aa7c5284 (MD5)<br>Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)<br>A utilização de simulações computacionais como ferramenta no estudo dos mais variados sistemas biomoleculares nos traz a possibilidade de observar o comportamento, organização e interação de seus componentes em nível atômico/molecular. Dentre as inúmeras técnicas de simulação computacional existentes, a mais difundida atualmente é a Dinâmica Molecular (DM). A DM tem um papel importante no que diz respeito à determinação da estrutura, dinâmica e função de um sistema molecular graças à simplicidade de sua função potencial. Essa função potencial e sua respectiva parametrização são chamadas, genericamente, de campo de forças. Dentre os diversos campos de forças propostos na literatura, o CHARMM é um dos mais utilizados e aperfeiçoados atualmente. Com o objetivo de modelar moléculas de interesse farmacológico que interagem com biomoléculas, foi desenvolvida recentemente uma extensão desse campo de forças, o CHARMM General Force Field (CGenFF). A construção da versão inicial do CGenFF foi baseada em moléculas componentes do CHARMM como, por exemplo, o fenol, parametrizado como um precursor para a tirosina. Todos os parâmetros já disponíveis no CHARMM são convertidos e combinados de modo a produzir novos tipos de átomos. Mesmo assim, o CGenFF deve ser usado apenas para moléculas farmacológicas; as macromoléculas biológicas devem ser representadas pelo campo de forças CHARMM original. O estudo de moléculas de interesse farmacológico provenientes de fontes naturais (vegetais, animais ou minerais) sempre resultou no desenvolvimento de fármacos de grande eficiência para o combate de inúmeras doenças. Aproximadamente 50% dos fármacos introduzidos no mercado, durante os últimos 20 anos, são derivados de pequenas moléculas biogênicas. Dentre os compostos naturais com grande potencial para uso como fármacos podemos destacar os flavonoides: eles são...<br>The use of computational simulations as a tool in the study of biomolecular systems creates the possibility to observe the behavior, organization and interaction of the components at atomic/molecular level. Among several computational simulation techniques, the most used is Molecular Dynamics (MD). MD plays an important role in structure determination, dynamics and function of molecular systems due to the simplicity of its potential function. This and their respective parameterization are generically known as force fields. Among the existing force fields, CHARMM is one of the most used and improved today. In order to model molecules of pharmaceutical interest that interact with biomolecules, an extension of this force field, the CHARMM General Force Field (CGenFF), was developed. The construction of the initial version of the CgenFF was based in molecules which compose CHARMM, such as phenol, parameterized as a precursor for tyrosine. All the parameters already available in the CHARMM are converted and combined to produce new types of atoms. Nevertheless, the CGenFF should be used only for pharmacological molecules; the biological molecules should be represented by the original CHARMM force field. The study of molecules of pharmacological interest from natural sources (vegetable, animal or mineral) always resulted in the development of drugs highly efficient to fight several diseases. Approximately 50% of the drugs introduced on the market, during the last 20 years, are derived from small biogenic molecules. Among the natural components with great potential for use as drugs we can highlight flavonoids, our study object: they are polyphenolic compounds naturally present in vegetables, fruit, seeds, nuts and drinks like tea and red wine. These molecules are derived from benzo-γ-pirone and present a wide range of biological activity (antiallergenic, anti-inflammatory, antioxidant, antiviral and...
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Chen, Jen Hui. "Molecular Dynamics and Interactions in Liquids." Thesis, North Texas State University, 1985. https://digital.library.unt.edu/ark:/67531/metadc331452/.
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Various modern spectroscopies have been utilized with considerable success in recent years to probe the dynamics of vibrational and reorientational relaxation of molecules in condensed phases. We have studied the temperature dependence of the polarized and depolarized Raman spectra of various modes in the following dihalomethanes: dibromomethane, dichloromethane, dichloromethane-d2, and bromochloromethane. Among other observed trends, we have found the following: Vibrational dephasing times calculated from the bend) and (C-Br stretch) lineshapes are of the same magnitude in CI^B^. The vibrational dephasing time of [C-D(H) stretch] is twice as long in CD2Cl2 as in CH-^C^, and the relaxation time of (C-Cl stretch) is greater in CI^C^ than in CD2CI2. Isotropic relaxation times for all three stretching vibrations are significantly shorter in C^BrCl than in CI^C^ or CI^B^. Application of the Kubo model revealed that derived modulation times are close to equal for equivalent vibrations in the various dihalomethanes. Thus, the more efficient relaxation of the A^ modes in CE^BrCl can be attributed almost entirely to the broader mean squared frequency perturbation of the vibrations in this molecule.
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Pounds, Andrew J. "A generalized discrete dynamical search method for locating minimum energy molecular geometries." Diss., Georgia Institute of Technology, 1994. http://hdl.handle.net/1853/27144.
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Swann, Andrew Thomas. "Characterization of polymer-supported homogeneous catalysts by molecular modeling." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/26702.
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Thesis (Ph.D)--Chemical Engineering, Georgia Institute of Technology, 2009.<br>Committee Chair: Ludovice, Pete; Committee Member: Grover, Martha; Committee Member: Jones, Christopher; Committee Member: Realff, Matthew; Committee Member: Sherrill, David. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Allen, Benjamin C. P. "Molecular similarity calculations using two dimensional molecular representations." Thesis, University of Oxford, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.289585.
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Jensen, C. H. "Molecular dynamics and complexity analysis of molecular systems." Thesis, University of Cambridge, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.605591.
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In this thesis, Complexity Analysis, which is defined as the use of Markov models and Computational Mechanics, is applied to Molecular Dynamics simulations of peptides. To achieve this, the trajectories from the Molecular Dynamics simulations are clustered into conformational states and by investigating the time series of these states, statistical models are constructed. A basic property of a Markov model is that the probability distribution of the subsequent states depends only on the current state and not the history. This has previously been used to develop a method for testing the model which is based on calculating and comparing eigenvalues for Markov models constructed at different time steps. Here, the method is applied to a simulation of the four residue peptide VPAL and it is found that the Markov model is accurate at a minimum time step of 100ps. The determination of the time step using this test is, however, subjective, so I have developed a method which is based on Computational Mechanics to determine the minimum time step at which the dynamics are Markovian. An important part of the application of a Markov model is the clustering of the Molecular Dynamics simulation into conformational states. The effect of varying the clustering of the simulation is investigated by calculating the mean first passage times between conformational states as the cluster boundaries are varied. It is found that the mean first passage times are sensitive to specific clustering, and to reduce the model sensitivity to variations in clustering, it is especially important to exclude sparsely populated states from the model. Finally, it is demonstrated that the folding time of a slow folding protein can be very sensitive to changes in the Markov model transition matrix. This implies that folding times calculated using Molecular Dynamics cannot meaningfully be compared to folding times obtained from experiments.
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Khan, Sajida A. "Investigation of Molecular Wires: Molecular Superconductors to Proteins." Ohio University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1414756747.
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Alaparthi, Madhubabu. "Molecular Recognition Involving Anthraquinone Derivatives and Molecular Clips." Thesis, University of South Dakota, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10285748.
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<p> In the past, we have demonstrated that 1,8-anthraquinone-18-crown-5 (1) and its heterocyclic derivatives act as luminescent hosts for a variety of cations of environmental and clinical concern. We report here a series of heteroatom-substituted macrocycles containing an anthraquinone moiety as a fluorescent signaling unit and a cyclic polyheteroether chain as the receptor. Sulfur, selenium, and tellurium derivatives of 1,8-anthraquinone-18-crown-5 (<b>1</b>) were synthesized by reacting sodium sulfide (Na<sub>2</sub>S), sodium selenide (Na<sub>2</sub>Se) and sodium telluride (Na<sub>2</sub>Te) with 1,8-bis(2-bromoethylethyleneoxy)anthracene - 9,10-dione in a 1:1 ratio (<b>2,3,</b> and <b>6</b>). These sensors bind metal ions in a 1:1 ratio (<b>7</b> and <b>8</b>), and the optical properties of the new complexes were examined and the sulfur and selenium analogues show that selectivity for Pb(II) is markedly improved as compared to the oxygen analogue <b>1</b> which was competitive for Ca(II) ion. </p><p> Selective reduction of <b>1</b> yields secondary alcohols where either one or both of the anthraquinone carbonyl groups has been reduced (<b> 15</b> and <b>9</b>). A new mechanism for the fluorescence detection of metal cations in solution is introduced involving a unique keto-enol tautomerization. Reduction of <b>1</b> yields the doubly reduced secondary alcohol, <b> 9. 9</b> acts as a chemodosimeter for Al(III) ion producing a strong blue emission due to the formation of the anthracene fluorophore, <b>10,</b> via dehydration of the internal secondary alcohol in DMSO/aqueous solution. The enol form is not the most thermodynamically stable form under these conditions however, and slowly converts to the keto form <b>11.</b> </p><p> Currently we are focusing on cucurbituril derivatives, also described as molecular clips due to their folded geometry used as molecular recognition hosts. We first investigated the synthesis and characterization of aromatic methoxy/catechol terminated cucurbituril units that act as hosts for small solvent molecules, such as CH<sub>2</sub>Cl<sub>2</sub>, CH<sub>3</sub>CN, DMF, and MeOH, through dual pi…H-C T-shaped interactions. We have calculated the single-point interaction energies of these non-covalent interactions and compared them to the dihedral angle formed from the molecular clip. We have also synthesized a molecular clip that contains terminal chelating phenanthroline ligands. This tetradentate ligand shows 2:3 metal:ligand binding with Fe(II) and 1:2 metal:ligand binding with Co(II) and Ni(II) cations.</p><p>
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Eckel, Rainer. "Single molecules and nanocrystals: molecular recognition forces and optomechanical switching." [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=978888227.
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Samorí, Paolo. "Self-assembly of conjugated (macro)molecules nanostructures for molecular electronics /." [S.l. : s.n.], 2000. http://deposit.ddb.de/cgi-bin/dokserv?idn=962281530.
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Roberts, Darren Leslie. "Molecular characterisation of the pro-apoptotic molecules APAF1 and Smac." Thesis, University of Leicester, 2001. http://hdl.handle.net/2381/30757.
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Apoptosis is a key process involved in cell number regulation and a range of pathological disorders. It is a highly structured process that removes the cell from the body without damage to surrounding cells. The mitochondria has been shown to play a key role in apoptosis induced by a wide range of stimuli and can trigger the apoptotic pathway by release of apoptogenic factors. One of these factors is cytochrome c, a protein that normally functions in the electron transport chain but upon release it binds to the first mammalian homologue of CED-4, Apoptotic Protease Activating Factor 1 (APAF1) and induces the formation of a large caspase-activating complex. Another protein released from the mitochondria is Smac, a pro-apoptotic protein that functions by antagonising Inhibitor of Apoptosis Protein function. The data presented in this thesis demonstrates the existence of multiple splice forms of both APAF1 and Smac and investigated their roles in the apoptotic pathway. APAF1 forms the large molecular weight complex known as the apoptosome in 293 cells although epitope tagged APAF1 formed an incorrectly formed this complex in the absence of additional stimuli. APAF1 was also found to be cleaved by Caspase-3 during apoptosis and that the resulting 30 kDa fragment is associated with the inactive complex. Data also indicates that caspase-9 recruitment to the apoptosome occurs via interactions between both the CARD and the CED-4 homologous regions of APAF1. The pro-apoptotic protein Smac exists as several forms due to alternative slicing and one of these forms, Smac , is pro-apoptotic even though it lacks the N-terminal Inhibitor of Apoptosis protein binding domain. Smac is localised to the cell cortex and does not redistribute upon induction of apoptosis. These data demonstrate that Smac is able to induce apoptosis independently of Inhibitor of Apoptosis Protein binding. A polyclonal antibody to Smac / Smac was also developed and characterised.
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Stoer, Marcell. "Molecular beam laser Stark spectroscopy of highly vibrationally excited molecules." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ34285.pdf.
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Jenny, Nicolas [Verfasser]. "Synthesis of New Functional Molecules for Molecular Electronics / Nicolas Jenny." München : Verlag Dr. Hut, 2012. http://d-nb.info/1026652278/34.
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Comben, E. R. "The study of small molecules by high resolution molecular spectroscopy." Thesis, University of Oxford, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.375245.
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Aitken, Craig George. "Electron impact ionisation of molecular clusters and spatially oriented molecules." Thesis, University of Canterbury. Chemistry, 1995. http://hdl.handle.net/10092/7613.
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A pulsed supersonic molecular beam apparatus has been used to determine the appearance energies of the cluster ions (CO₂)n+ (2≤n≤4), (N₂O)n+ (2≤n≤4), (NH₃)nNH⁺₄ (0≤n≤7) and the cluster ion fragments (N₂O.O)⁺ and (N₂O.NO)⁺ by electron impact ionisation. The measured appearance energies were used to estimate cluster ion binding energies and to deduce possible mechanisms for the formation of the cluster fragment ions (N₂O.O)⁺ and (N₂O.NO)⁺.
A discussion is given on the transformation of the molecular beam machine to accommodate the study of electron impact ionisation of spatially oriented molecules. Characterisation of the inhomogeneous electrostatic hexapole field is described. Electron impact ionisation asymmetry results were measured for CH₃Cl, CH₃Br, CF₃Br and CHCl₃ using a quadrupole mass spectrometer and mass insensitive rotatable particle multiplier. Measurement of the asymmetry effect for formation of the molecular ions CH₃Cr, CH₃Br⁺ and the fragment ions CH₃+ from CH₃Cl and CH₃Br, CF₃⁺ from CF₃Br and CHCl₂+ from CHCl₃ are determined and discussed. Each molecule showed a preference for electron impact to occur at the positive end of the molecule. The effect of hexapole voltage and electron energy on the asymmetry effect is also discussed. A simple model is presented for electron impact ionisation at either end of a molecule which accounts qualitatively with the asymmetry results determined.
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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 <I>ab initio</I> 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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Freitas, Rodrigo Moura 1989. "Molecular simulation = methods and applications = Simulações moleculares : métodos e aplicações." [s.n.], 2013. http://repositorio.unicamp.br/jspui/handle/REPOSIP/278440.
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Orientador: Maurice de Koning<br>Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin<br>Made available in DSpace on 2018-08-23T00:50:21Z (GMT). No. of bitstreams: 1
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Previous issue date: 2013<br>Resumo: Devido aos avanços conceptuais e técnicos feitos em física computacional e ciência dos materiais computacional nos estamos aptos a resolver problemas que eram inacessíveis a alguns anos atrás. Nessa dissertação estudamos a evolução de alguma destas técnicas, apresentando a teoria e técnicas de simulação computacional para estudar transições de fase de primeira ordem com ênfase nas técnicas mais avançadas de calculo de energia livre (Reversible Scaling) e métodos de simulação de eventos raros (Forward Flux Sampling) usando a técnica de simulação atomística da Dinâmica Molecular. A evolução e melhora da e ciência destas técnicas e apresentada junto com aplicações a sistemas simples que permitem solução exata e também ao caso mais complexo da transição de fase Martenstica. Também apresentamos a aplicação de métodos numéricos no estudo do modelo de Pauling para o gelo. Nos desenvolvemos e implementamos um novo algoritmo para a criação e ciente de estruturas de gelo desordenadas. Este algoritmo de geração de cristais de gelo nos permitiu criar células de gelo Ih de tamanhos que não eram possíveis antes. Usando este algoritmo abordamos o problema de efeitos de tamanho finito não estudados anteriormente<br>Abstract: Due to the conceptual and technical advances being made in computational physics and computational materials science we have been able to tackle problems that were inaccessible a few years ago. In this dissertation we study the evolution of some of these techniques, presenting the theory and simulation methods to study _rst order phase transitions with emphasis on state-of-the-art free-energy calculation (Reversible Scaling) and rare event (Forward Flux Sampling) methods using the atomistic simulation technique of Molecular Dynamics. The evolution and efficiency improvement of these techniques is presented together with applications to simple systems that allow exact solution as well as the more the complex case of Martensitic phase transitions. We also present the application of numerical methods to study Pauling\'s model of ice. We have developed and implemented a new algorithm for efficient generation of disordered ice structures. This ice generator algorithm allows us to create ice Ih cells of sizes not reported before. Using this algorithm we address finite size effects not studied before<br>Mestrado<br>Física<br>Mestre em Física
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Wright, Patricia Ann. "Understanding MS/MS fragmentation pathways of small molecular weight molecules." Thesis, University of Greenwich, 2015. http://gala.gre.ac.uk/18134/.
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Fragmentation of molecules by collision-induced dissociation (CID) is not well-understood, making interpretation of MS/MS spectra difficult and limiting the effectiveness of software tools intended to aid mass spectral interpretation. An approach is required which is tailored to each individual molecule and improves the ‘chemical sense’ of the software. It was hypothesised that the bonds which break during CID of protonated molecules are the bonds which are elongated, and hence weakened, as a result of conformational changes induced by protonation. Bond length changes for a test set of molecules were calculated using quantum chemistry software. Density Functional Theory (DFT) or Austin Model 1 (AM1) or both were used to energy minimise the structures of the neutral molecules and their corresponding protonated molecules (protonated at all possible sites). Bonds which elongated to the greatest extent after protonation were compared to the bonds which were found to cleave to give the product ions in the CID spectra of these compounds. Quantum chemistry modelling was also applied to the deprotonated molecules. AM1 calculated bond lengths were found to be similar to those generated by DFT and have the advantage of being rapidly obtained. All the polarised bonds which cleaved were calculated to elongate significantly, thus achieving a 100% success rate in the prediction of bond cleavage as a result of protonation on a heteroatom. The proton is mobile across the molecule, leading to fragmentation when the proton reaches a site where it causes significant bond elongation, provided the molecule has sufficient internal energy. Cleavage of carbon-carbon bonds was not predicted. The success rate for predicting bond cleavage in deprotonated molecules was 48%, suggesting this approach cannot be applied reliably for these anions. AM1 calculated bond length change acts as a descriptor for predicting polarised bond cleavage in protonated pseudo-molecular ions having the potential to be incorporated in mass spectral interpretive software to increase the accuracy of prediction of CID spectra.