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1
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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Brooke, Carly. "Synthesis, characterisation and single molecule conductance measurements of organic molecules." Thesis, University of Liverpool, 2012. http://livrepository.liverpool.ac.uk/9397/.
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The use of single molecules to construct electronic devices is an exciting prospect, and one that has long provided a driving force for research in the area of molecular scale electronics. In order for this emerging field to advance a deep understanding of the fundamental mechanisms that govern electron conduction at the molecular level is imperative. Recent developments in areas such as scanning tunnelling microscopy, have facilitated the determination of the electrical properties of single molecules tethered between two metallic contacts. The analysis and potentially tailoring of structure-property relationships is hugely important and could lead to new and unforeseen applications for this emerging field. The work presented herein details two major studies. The first is an investigation of the transport properties of a series of analogous molecules, which consist of a single benzene ring sandwiched between two alkyl chains of varying length. Prior to the work in this thesis one such molecule, and various substituted analogues thereof, had shown behaviour similar to what would be expected of a molecular equivalent of a double tunnelling barrier. The data presented here demonstrates a remarkably low dependence of this system on molecular length; this result contradicts the behaviour expected of a coherent transport mechanism. Moreover, the study of the orbital energies and densities of these molecules provides further evidence of a mechanism of conduction that is very different to that previously suggested for this system. The second study centres around the investigation of the conductance behaviour of 4,4’-bipyridine and some substituted analogues thereof; this study is presented in two parts. The first details attempts to synthesise planar analogues of 4,4’-bipyridine, as well the synthesis and reactivity of novel substituted bipyridines. The second part reports conductance data, electrochemical studies and theoretical calculations of properties of these molecules. The data presented provides new information regarding the relationship between electronic structure and conductance behaviour in this type of system.
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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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Edman, Lars. "Single molecule dynamics /." Stockholm, 2000. http://diss.kib.ki.se/2000/91-628-4025-8/.
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Szumski, Douglas Stewart. "Single molecule spintronics." Thesis, University of Bristol, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.535471.
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Davies, Eva Melari. "Single molecule microscopy." Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-173355.
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Kirstein, Johanna, Christophe Jung, Christian Hellriegel, and Christoph Bräuchle. "Single molecule spectroscopy." Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-196553.
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Aubin, Sheila Marie Josée. "Single-molecule magnets /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 1997. http://wwwlib.umi.com/cr/ucsd/fullcit?p9820882.
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Martínez, Rodríguez Luis. "Molecule and catalyst design for recognition and activation of small molecules." Doctoral thesis, Universitat Rovira i Virgili, 2016. http://hdl.handle.net/10803/398693.
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Sikor, Martin. "Single-molecule fluorescence studies of Protein Folding and Molecular Chaperones." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-138521.
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Grätz, Fabian [Verfasser]. "Molecule-Surface Scattering with Velocity-Controlled Molecular Beams / Fabian Grätz." Berlin : Freie Universität Berlin, 2014. http://d-nb.info/1060717735/34.
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Ökten, Zeynep. "Single molecule mechanics and the myosin family of molecular motors." [S.l.] : [s.n.], 2006. http://www.diss.fu-berlin.de/2006/6/index.html.
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Palaiokostas-Avramidis, Michail. "Molecular dynamics simulations of small molecule permeation through lipid membranes." Thesis, Queen Mary, University of London, 2017. http://qmro.qmul.ac.uk/xmlui/handle/123456789/31859.
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Passive permeation through biological membranes is an important mechanism for transporting molecules and regulating the cellular content. Studying and understanding passive permeation is also extremely relevant to many industrial applications, including drug design and nanotechnology. In vivo membranes typically consist of mixtures of lamellar and nonlamellar lipids. Lamellar lipids are characterised by their tendency to form lamellar bilayer phases, which are predominant in biology. Nonlamellar lipids, when isolated, instead form non-bilayer structures such as inverse hexagonal phases. While mixed lamellar/nonlamellar lipid membranes tend to adopt the ubiquitous bilayer structure, the presence of nonlamellar lipids is known to have profound effects on key membrane properties, such as internal distributions of stress and elastic properties. This dissertation examines permeation through lamellar and nonlamellar lipid membranes by utilising atomistic molecular dynamics simulations in conjunction with two di erent methods, the z-constraint and the z-restraint, in order to obtain transfer free energy profiles, diffusion profiles and permeation coefficients. An assessment of these methods is performed in search for the optimal, with the goal to create an automated, accurate and robust permeation study framework. Part of the dissertation involves the creation of the corresponding software. Furthermore, this work examines the effect of changing the lamellar vs. nonlamellar lipid composition on the passive permeation mechanism of a series of 13 small molecules and drugs. These nonlamellar lipids are known to affect the lateral pressure distribution inside the membranes. This work investigates the hypothesis that the differences in lateral pressure should increase the resistance to permeation. The results indicate that, upon addition of nonlamellar lipids, permeation is hindered for small molecules but is facilitated for the largest. All results are in agreement with previous experimental and computational studies. This work represents an advancement towards the development of more realistic in silico permeability assays, which may have a substantial future impact in the area of rational drug design.
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Zhao, Xiaotao. "The synthesis and single-molecule conductance of conjugated molecular wires." Thesis, Durham University, 2014. http://etheses.dur.ac.uk/10634/.
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The past decades have seen the fast development of electronic devices in the industrial sector. There is increasingly rapid growth in the demand for alternative electronic building blocks to compliment, and possibly replace, the conventional silicon-based products. Electronic devices based on organic molecules, especially those based on single molecules, receive intense studies both theoretically and experimentally. In this presented work, a new family of oligo(aryleneethenylene)s (OAE)s with molecular lengths (N…N distance) of ca. 2-6 nm were designed to investigate the length dependence of conductance at the single molecule level. X-ray molecular structures of OAEs with a molecular length up to 5.3 nm were successfully analysed and presented. Secondly, four groups of pyridyl terminated oligo(phenyleneethylene) (OPE) derivatives were studied for the quantum interference effects. A dramatic destructive quantum interference effect was observed which decreased the single molecule conductance by several orders of magnitude. Unsymmetrical molecules with only one anchor group were noticed to form π-π stacking between two molecules. Thirdly, amino terminated OPEs bearing various substituents on the central phenyl rings were explored to present the robustness of the central OPE backbone towards various functionalising substituents. Fourthly, diaryloligoynes with different anchor groups were synthesised and the single-molecule conductances were studied. The stability of the tetrayne compounds is discussed and X-ray crystal structures of the stable tetraynes are presented. Finally, pyridyl terminated OAE derivatives bearing an anthraquinone core were synthesised to investigate the charge transport through the central anthraquinone core, with special purpose of investigating quantum interference effects and the switching process of the central anthraquinone core.
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Pantos, Stefan D. "New refinement strategies for meso-molecular and small molecule crystallography." Thesis, University of Oxford, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.490343.
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CRYSTALS is a well known and widely used software package for the refinement of x-ray crystallographic data and the solution of crystal structures containing small to medium size molecules in the unit cell. Its development at the Chemical Crystallography Laboratory in Oxford has been in progress for several years, initiated by J.R. Carruthers and further developed by many others most notably RW. Betteridge, R.L Cooper, K. Front, and D.J. Watkin assisted by a number of postgraduate students.
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Halbert, Jason Paul. "A New Chromophoric Organic Molecule Toward Improved Molecular Optoelectronic Devices." Thesis, University of North Texas, 2012. https://digital.library.unt.edu/ark:/67531/metadc177207/.
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The characterization of 2,3,6,7,10,11-hexabromotriphenylene, Br6TP, is presented toward its potential use as an n-type organic semiconductor and metal-free room temperature phosphor. The crystal structure shows both anisotropic two-dimensional BrBr interactions and inter-layer ?-stacking interactions. Photophysical characteristics were evaluated using solid-state photoluminescence and diffuse reflectance spectroscopies, revealing significantly red-shifted excitations in the visible region for the yellow solid material (compared to ultraviolet absorption bands for the colorless dilute solutions). Correlation of spectral, electrochemical, and computational data suggest the presence of an n-type semiconducting behavior due to the electron-poor aromatic ring. The material shows excellent thermal stability as demonstrated by thermogravimetric analysis and infrared spectra of a thin film deposited by thermal evaporation. The potential for Br6TP and its analogues toward use in several types of photonic and electronic devices is discussed.
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Peiris, Malwattage Chandramalika Rukmali. "Covalently linked molecule–electrode contacts toward robust molecular-electronics circuits." Thesis, Curtin University, 2020. http://hdl.handle.net/20.500.11937/84186.
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The use of molecules as active components in electronic devices is a trend in current electronics and a potential alternative to the semiconductor-based nanoelectronics. This thesis provides a step forward in terms of potential chemistries for molecular electronics on silicon. Different molecule-electrode contacts were investigated at the macro and nano-scale using electrochemical techniques and single-molecule circuits. The work also explored the potential of silicon oxide layers as alternative materials in molecular electronics, as both a static and dynamic material.
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Mitsari, Efstratia. "Guest-molecule dynamics and conductivity effects in carbon-based molecular solids." Doctoral thesis, Universitat Politècnica de Catalunya, 2016. http://hdl.handle.net/10803/397721.
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Disordered systems are abundant in everyday life and so their study is of importance from a scientific and a technological point of view. The most common non-crystalline solid phases are structural glasses (e.g. window glass), in which both translational and orientational degrees of freedom are disordered. While at low temperature (in the glass state) the disorder is static, at higher temperature a viscous state is reached, where the disorder is dynamic (as in a liquid). Other systems exist, namely molecular solids, which display different types of disorder (either static or dynamic depending on temperature) due to the larger variety of microscopic degrees of freedom compared to atomic solids(ch. 1). For instance, molecular solids display phases in which the molecules' average centers of mass occupy lattice positions while their orientations are disordered (orientationally disordered phases). Such phases are usually formed by small molecules or molecules with a globular shape like the carbon-only fullerene molecule (C60). Molecular solids display low electrical conductivities due to localization of valence electrons on single molecules, so that electron hopping is the main charge transport mechanism. The type of disorder, and whether it is static or dynamic, are both factors that have an important impact on the conductivity. This thesis is an experimental study of the dynamic disorder and conduction properties of molecular solids, focusing in particular on hydrated molecular materials and on fullerene systems. The experimental technique of choice, which allows studying simultaneously molecular dynamics and electrical conductivity, is broadband dielectric spectroscopy (ch. 2 and 3). Studying water inside organic systems is of great importance in several contexts, ranging from the study of food texture and the stability of biotechnology products and pharmaceuticals to the investigation of macromolecular function in biochemical systems for which hydration water plays a preeminent role. Fullerene solids are relatively simple systems to study the impact of water and in general of heterogeneous species inside an organic matrix. Hydrophilic or hygroscopic fullerene derivatives can be obtained by functionalization with oxygen or hydroxyl groups, as in the case of the fullerenol molecule (ch. 5). We show in this thesis that water molecules not only display interesting orientational dynamics, but they also contribute to the enhancement of the conductivity due to proton hopping through surface hydration layers. These phenomena are not specific to functionalized fullerenes (ch. 5) but also to other organic materials, as we show for the case of an organic dye of the rhodamine family (ch. 4). As for the dynamics of the fullerene molecules themselves, it is well known that the solid phase of pure C60 exhibits order-disorder orientational transition. We show that a derivative of C60 functionalized with oxygen-containing groups also displays several orientational transitions,reminescent of that of solid C60 (ch. 6). Finally, we analyze the structural and dynamic orientational disorder in a co-crystal of C60 with a small ethane derivative (C60:(1,1,2)-trichloroethane (ch. 7). We are able to observe two distinct orientational dynamics of the ethane molecules. To the best of our knowledge, ours is the first-ever report of the relaxation dynamics of guest molecules intercalated inside C60. Considering the very broad variety of (partially) disordered structures that can be obtained in binary systems containing fullerene molecules, these solids may represent model systems to investigate the impact of disorder and of the interaction geometry on the molecular dynamics of heterogeneous systems. The results of this thesis represent a first step in the direction of extending the current experimental knowledge of disordered solid phases to more complex systems of relevance in organic organic chemistry and biology, or with possible commercial applications.Los sistemas desordenados son muy comunes en nuestra vida cotidiana y su estudio tiene por tanto un impacto importante. Las fases sólidas más comunes son los vidrios estructurales (e.g. los vidrios típicos) en los que tanto los grados de libertad de orientación como de translación están desordenados. A bajas temperaturas (estado vítreo) el desorden es estático, mientras que a temperaturas más altas se alcanza un estado fluido viscoso, donde el desorden es dinámico (como en un líquido). Existen también otros sistemas sólidos, formados por moléculas, que pueden presentar diferentes tipos de desorden (estático o dinámico) debido a la gran variedad de los grados de libertad moleculares en comparación con los sólidos formados exclusivamente por átomos (ch.1). Así existen sólidos moleculares que presentan fases en los que las moléculas tienen movimientos de reorientación manteniendo invariables sus centros de masa (fases orientacionalmente desordenadas). Estas fases pueden estar formadas por moléculas pequeñas o por moléculas con forma globular, como la molécula de fulereno (C60). La baja conductividad eléctrica de los sólidos moleculares es debida a la localización de los electrones de valencia en cada molécula individual, de modo que el mecanismo principal de transporte de carga es el salto (''hopping'') de los electrones entre las moléculas. El tipo de desorden, y si el desorden es estático o dinámico, son factores que tienen un impacto importante en la conductividad del material. Esta tesis es un estudio experimental del desorden dinámico y de las propiedades de conducción en los sólidos moleculares, y está especialmente dirigida al estudio en materiales moleculares hidratados y en sistemas con fulereno. La técnica de caracterización que permite un estudio de la dinámica molecular y de la conductividad eléctrica de manera simultánea es la espectroscopia dieléctrica (ch. 2 y 3). La tesis presta también una especial atención al estudio de la influencia del agua en sistemas orgánicos moleculares, debido a la importancia en muchas aplicaciones, desde la textura de los alimentos, o la estabilidad de productos biotecnológicos, hasta la investigación de la función macromolecular en sistemas bioquímicos, en los que el agua de hidratación tiene un papel fundamental. Los sólidos de fulereno son sistemas sencillos para estudiar el impacto de especies moleculares heterogéneas en el interior de una matriz orgánica. Tanto los derivados higroscópicos como hidrofóbicos del fulereno se pueden obtener por funcionalización con grupos de oxígeno, como en el caso de la molécula de fullerenol (ch. 5). Esta tesis demuestra que las moléculas de agua tienen una dinámica orientacional muy variada y, además, que su presencia contribuye a la conductividad debido a los saltos de los protones a través de los diferentes niveles de hidratación de la superficie. Estos fenómenos se detectan también en otros materiales orgánicos, como es el caso de un colorante orgánico de la familia de la rodamina (ch. 4). En cuanto a la propia dinámica de las moléculas del fulereno, es conocido que la fase sólida de C60 tiene una transición orientacional orden-desorden. De forma paralela, se demuestra la existencia de transiciones similares en un derivado de C60 (oxC60, ch.5). Por último, se estudia también el desorden orientacional, estructural y dinámico, en un cristal mixto formado por C60 y 1,1,2-tricloroetano (ch.7).). En este sistema se observan dinámicas orientacionales asociadas a las conformaciones moleculares del tricloroetano, representando así un estudio sobre la dinámica de moléculas huéspedes intercaladas estructuralmente en una matriz de C60. Los resultados de esta tesis representan un primer paso para profundizar en el conocimiento de sólidos con fases desordenadas y para el progreso en sistemas más complicados y relevantes en el campo de la química y de la biología orgánica, o con posibles aplicaciones comerciales.
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Inverarity, Iain Andrew. "Marked small molecule libraries : a new approach to molecular probe design." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/14147.
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This thesis documents a new approach for the identification of a small biologically active molecule’s site of interaction, through the rapid synthesis of molecular probes. A marked library approach has been developed whereby a biocompatible marker is attached onto the small molecule’s molecular scaffold. This marker plays no role in the screening process itself, but facilitates the formation of a range of molecular probes from active marked library members. As an example of molecular probe formation, site selective biotinylation will be discussed in the introduction. This marked library concept has been applied to the natural product anisomycin A. Investigations focused on development of a detailed structure activity relationship for anisomycin’s activation of the stress activated protein kinase (SAPK) pathway, along with the synthesis of a number of marked library analogues. The active marked library members were then converted to a range of functional molecular probes utilising the copper(I) catalysed Huisgen cycloaddition as the key coupling step. These molecular probes are being used in the elucidation of anisomycin’s biological target for activation of the SAPK pathway. In a further demonstration of this strategy, a focused library of marked steroids has been synthesised based on the functionalisation of dehydroepiandrosterone B. Directed by the results of preliminary biological screening, a number of marked library members have been converted into fluorescent molecular probes. These probes will be used in future applications to probe the biological action of the dehydroepiandrosterone.
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Liu, Jing. "Heterocyclic small molecule peptidomimetics." [College Station, Tex. : Texas A&M University, 2008. http://hdl.handle.net/1969.1/ETD-TAMU-3125.
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Wan, Yanjun. "Simple Molecule Mercury Sensor." NCSU, 2008. http://www.lib.ncsu.edu/theses/available/etd-08082008-132023/.
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Several molecules previously produced from a nitrile-based cascade cyclization were examined as potential mercury sensors. Various analytical parameters, including fluorescence quantum yield, UV shift, fluorescence quenching, binding constant, binding ratio, and lowest detection limit, were measured. The best mercury sensor molecule was found to be molecule 3c, which could be easily synthesized in gram quantities (3 steps, 55% overall yield). This molecule has a very high fluorescence quantum yield (Φ = 0.87), high sensitivity and selectivity towards mercury ion in both organic and aqueous media. The overall performance of molecule 3c is as good as, or better than, the majority of organic dye based mercury sensors reported to date.
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Lillehei, Peter Thomas. "Single molecule mechanical testing." Diss., Georgia Institute of Technology, 2001. http://hdl.handle.net/1853/31044.
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Cooper, James Neil. "Positron hydrogen molecule scattering." Thesis, University of Nottingham, 2009. http://eprints.nottingham.ac.uk/12240/.
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In this thesis, we present Kohn variational calculations of scattering and annihilation parameters for very low energy interactions of positrons with molecular hydrogen. Our analysis includes the first application of the Kohn method for this system in which the interelectronic potential in the molecular target is treated explicitly. All previous Kohn calculations on positron hydrogen molecule scattering have avoided this complication by the use of the method of models. The advantage of the explicit treatment over the method of models is that it allows approximate target wavefunctions of a very high accuracy to be admitted more easily to the Kohn calculations. We find that the accuracy of the approximate target wavefunction is an extremely important factor in obtaining reliable results from the calculations. We carry out an extensive investigation of anomalous, nonphysical behaviour in the results of our Kohn calculations. Our explanations of how these anomalies arise and how they may be avoided significantly improves upon the discussions of these phenomena given in earlier accounts of positron hydrogen molecule scattering calculations by other authors. As with all previous models of positron hydrogen molecule scattering, we find discrepancies between the experimental value of the annihilation parameter, Z effective, and the theoretical value of this quantity as determined from our Kohn calculations. Limitations of the model that could explain these discrepancies are discussed and suggestions for future improvements are proposed.
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Phillips, Laurie James. "Molecule-inserted silicon nanogaps." Thesis, Bangor University, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.540412.
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Wadoos, Abdul. "Lysozyme-small molecule interactions." Thesis, University of Glasgow, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264109.
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Pugh, Sara Dorothy. "Single molecule protein folding." Thesis, University of Leeds, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.441320.
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Marsden, David Michael. "3D small-molecule microarrays." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611660.
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Cluzel, Philippe. "L'adn, une molecule extensible." Paris 6, 1996. http://www.theses.fr/1996PA066519.
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Dans la partie i, il s'agit essentiellement de l'observation sous microscope de molecules d'adn fluorescentes isolees. On decrit une transition de phase de conformation de l'adn : la molecule est etiree dans un ecoulement visqueux et adopte une forme de batonnet. Si l'on arrete l'ecoulement, la molecule relaxe par ses extremites qui changent de conformation, et adoptent une forme de pelote. Dans la partie ii on mesure, grace a un nouvel appareil (le picodynamometre), la reponse elastique d'une molecule unique d'adn quand elle estsoumise a un etirement extreme. Nous montrons qu'un fort etirement de l'adn induit une transition de phase de structure. Nous discutons egalement le role biologique de cette nouvelle structure, la forme s, qui pourrait avoir un role primitif dans l'evolution des especes. La partie iii est prospective mais decrit cependant, une experience de diffraction aux rayons x qui permet de caracteriser des etats tres condenses de l'adn. Il est montre que sous etirement, un etat semi-cristallin de molecules d'adn transite vers un etat cristallin.
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Kirk, Sarah Ruth. "RNA-small molecule interactions /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2000. http://wwwlib.umi.com/cr/ucsd/fullcit?p9979970.
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Maleki, Parastoo. "Investigation of G-quadruplex and Small Molecule Interactions at the Single Molecule Level." Kent State University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=kent1543944037378098.
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Howle, Christopher Roy. "Decay processes of photoexcited molecules in the VUV : comparison with ion/molecule reactions." Thesis, University of Birmingham, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.421712.
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Rüttinger, Steffen. "Confocal microscopy and quantitative single molecule techniques for metrology in molecular medicine." [S.l.] : [s.n.], 2006. http://opus.kobv.de/tuberlin/volltexte/2007/1434.
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Sikor, Martin [Verfasser]. "Single-molecule fluorescence studies of Protein Folding and Molecular Chaperones / Martin Sikor." München : Verlag Dr. Hut, 2012. http://d-nb.info/1020298650/34.
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Tampi, Girish. "Investigating small molecule modulators of bio-molecular interactions : an in-silico study." Thesis, University of Leeds, 2015. http://etheses.whiterose.ac.uk/12511/.
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Small molecule inhibitors are commonly used to target protein targets that assist in the spread of diseases such as AIDS, cancer and deadly forms of influenza. Despite drug companies spending millions on R&D, the number of drugs that pass clinical trials is limited due to difficulties in engineering optimal non-covalent interactions. As many protein targets have the ability to rapidly evolve resistance, there is an urgent need for methods that rapidly identify effective new compounds. The thermodynamic driving force behind most biochemical reactions is known as the Gibbs free energy and it contains opposing dynamic and structural components that are known as the entropy (ΔS°) and enthalpy (ΔH°) respectively. ΔG° = ΔH° - TΔS°. Traditionally, drug design focussed on complementing the shape of an inhibitor to the binding cavity to optimise ΔG° favourability. However, this approach neglects the entropic contribution and phenomena such as Entropy-Enthalpy Compensation (EEC) often result in favourable bonding interactions not improving ΔG°, due to entropic unfavorability. Similarly, attempts to optimise inhibitor entropy can also have unpredictable results. Experimental methods such as ITC report on global thermodynamics, but have difficulties identifying the underlying molecular rationale for measured values. However, computational techniques do not suffer from the same limitations. MUP-I can promiscuously bind panels of hydrophobic ligands that possess incremental structural differences. Thus, small perturbations to the system can be studied through various in silico approaches. This work analyses the trends exhibited across these panels by examining the dynamic component via the calculation of per-unit entropies of protein, ligand and solvent. Two new methods were developed to assess the translational and rotational contributions to TΔS°, and a protocol created to study ligand internalisation. Synthesising this information with structural data obtained from spatial data on the binding cavity, intermolecular contacts and H-bond analysis allowed detailed molecular rationale for the global thermodynamic signatures to be derived.
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Mowrey, Richard Carlton. "Theoretical studies of inelastic molecule-surface and resonant electron-atom and electron-molecule scattering /." The Ohio State University, 1985. http://rave.ohiolink.edu/etdc/view?acc_num=osu148725958026243.
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McHugh, Toni. "Single molecule mechanics of Kif15." Thesis, University of Warwick, 2015. http://wrap.warwick.ac.uk/77516/.
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Kinesin-12 is a motor protein that has a role in the processes of mitotic spindle formation and maintenance. The human Kinesin-12, Kif15, has been shown to have some functional redundancy with Eg5, a Kinesin-5 that plays key roles in the formation of the bipolar spindle and is a potential target for anti-cancer drugs. Eg5 is thought to contribute to spindle formation by cross-linking and sliding microtubules, however little is known about the mechanism of Kif15. We have used laser tweezers to investigate the mechanical properties of Kif15 compared to those of kinesin-1. We have found that Kif15 is plus end directed and takes multiple steps along the microtubule without detaching. Full-length Kif15 walks faster and supports more load than full-length Eg5. Kif15 is less processive under load than kinesin-1, although it has a similar stall force. A second, diffusive, microtubule binding site in Kif15 supports processivity at zero load, and slows flyback following a detachment in the optical trap. The microtubule-associated protein, Tpx2, is necessary for the localisation of Kif15 to spindle microtubules. We find that Tpx2 binding arrests the motion of Kif15 and creates a stable binding state that resists both assisting and hindering loads. We also find evidence of a tail-mediated auto-inhibitory mechanism that creates a stable MT binding state and causes pausing during processive runs. C-terminal truncation of the Kif15 tail relieves this inhibition leading to faster overall stepping and abrogates the effects of Tpx2. We examined the detachment behaviour of Kif15 from microtubules, under assisting and hindering loads. We find that assisting loads cause single Kif15 and Kinesin-1 motors to detach from the microtubule more easily than hindering loads. Kif15 shows a much more asymmetric response to load in low levels of ATP than Kinesin-1, and both show more asymmetry than Eg5: previous work has shown that the behaviour of Eg5 does not change dramatically with differing loading directions. This has interesting implications for the roles of Kif15 and Eg5 motors in both parallel and anti-parallel microtubule bundles. Overall our data supports an in vivo mechanism for Kif15 that it distinct from that of Eg5. We investigated the load-dependent detachment of Kinesin-1 and Kif15 in millimolar concentrations of ADP, AMPPNP and micromolar concentrations of ATP. Kinesin-1 in ADP detached at low loads, and in AMPPNP at two different loads, both higher than in ADP. These two AMPPNP states of Kinesin1 likely corresponding to single and double headed microtubule binding, as proposed by Ishiwata and colleagues. Kif15 behaved broadly similarly. At micromolar ATP concentrations and hindering loads, both Kinesin-1 and Kif15 again showed two different high load detachment states. This is inconsistent with the model proposed by Ishiwata and possible modifications are discussed.
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O'Sullivan, Antoinette C. "Modelling of cellulose-molecule interactions." Thesis, Bangor University, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.296178.
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Pánek, Dalibor. "Developments for single molecule studies." Thesis, University of Strathclyde, 2010. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=16933.
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Single molecule fluorescence spectroscopy has attracted considerable attention over the past two decades. Measurement on a single entity provides an opportunity to avoid ensemble averaging which is always present in conventional bulk fluorescence measurements. This makes single molecule spectroscopy particularly interesting for biophysics and biochemistry where heterogeneous systems are often encountered. The general interest of this thesis is in studies of single immobilised molecules carried out at room temperature. One of t.he major issues of single molecule spectroscopy is finding a suitable immobilising medium. Inorganic silica matrices prepared by the sol-gel method have a great potential to provide a close- to-natural immobilising environment even for sensitive biomolecules and thus allow investigation of their natural behaviour on the most fundamental level. In order to be able to tailor both physical and chemical properties of the final gel, it is of great importance to develop reliable methods to control each stage of polymerisation. In one part of this thesis, applications of fluorescent probes to investigation of sol-gels properties, as well as monitoring the gel assembly process, are discussed. The thesis further presents studies of the genetically engineered glucose binding protein labelled with the environmentally sensitive dye badan. This system was developed in a search for an appropriate recognition-reporter unit to serve as a part of fluorescence-based sensor for continuous blood glucose monitoring. This labelled biomolecule represents an interesting subject for a single molecule study. Due to technical reasons however, single molecule spectroscopy could not be applied in this case. Therefore, conventional ensemble fluorescence spectroscopy methods were used to characterise behaviour of the labelled protein at different glucose concentrations. The last part of the thesis deals with instrumental aspects of single molecule imaging and spectroscopy. The aim of the work was to assess the applicability of a freshly installed commercial microscope a-SNOM (WITec GmbH) in single molecule fluorescence studies and at the same time to adopt the technique for future experiments in our research group.
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Jeranko, Timo. "Photodissociation of the oxygen molecule." Thesis, University of Bristol, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.492508.
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The aim of this work was to determine the distribution of photofragments of the O2 molecule in the Schumann-Runge continuum and bands, as well as their vector correlations and alignment parameters. Pontential energy curves were calculated ab initio using variational methods both in the equilibrium geometry and in the long range dissociation limit. To obtain the distribution of products, the molecule was dissociated in a molecular dynamics calculation, and the resulting vibrational wavepackets were analysed in the long range to obtain absorption cross-sections, yielding product distribution for the atomic |LS) states. Th
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Lu, Siran. "Single molecule kinetic isotope effect." Thesis, University of Oxford, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.526483.
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Hanna, Thomas Mark. "Dynamics of Feshbach molecule production." Thesis, University of Oxford, 2008. http://ora.ox.ac.uk/objects/uuid:676c8932-9c30-4776-a264-67405fe61c0c.
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The variation of a magnetic field in the vicinity of a zero-energy resonance allows highly vibrationally excited molecules (‘Feshbach molecules’) to be produced from an ultracold atomic gas. In this thesis, we study the dynamics of this process. We begin by studying the dissociation of Feshbach molecules, showing that in the limit of a sudden jump the shape of the spectrum of dissociated atoms can act as a probe of the zero-energy resonance. For some resonances, such jumps are within reach of current experiments. We also study the intermediate region between sudden jumps and asymptotically wide, linear ramps. It is shown from a precise derivation how the latter limit leads to a universal spectrum with a shape independent of the implementation of the two-body physics, provided that the near-resonant scattering properties are correctly modelled. We then turn to the dynamics of Feshbach molecule production from thermal and condensed gases. Our microscopic quantum dynamics approach includes the exact twobody evolution as an input to the many-body calculations. We show that in the long-time limit, and the Markov limit for the interactions, the non-Markovian Boltzmann equation (NMBE) we derive for the one-body density matrix reduces to the normal Boltzmann equation. In the limit of short times and small depletion of the atomic gas, the molecule production efficiency can be calculated by thermally averaging the two-body transition probability density. This thermal averaging technique is applied to studies of the formation of Feshbach molecules using a magnetic field modulation that is near-resonant with the molecular bound state energy. The continuum is shown to have a significant effect on both the dynamics and efficiency of this process. We examine the dependence of the molecule production efficiency on the duration, amplitude and frequency of the modulation, as well as the temperature and density of the gas. This method of producing molecules is effective for a wide range of bound state energies, but requires sufficient variation of the two-body energy levels with magnetic field. Lastly, we implement the NMBE for the case of a fast linear ramp across a Feshbach resonance. The solution of this equation is made feasible by including a large part of the required computation in the kernel, which is calculated in advance. The NMBE allows predictions of the molecule production efficiency which go beyond the thermal averaging technique by accounting for the depletion and rethermalisation of the continuum. In the limit of small depletions, the two approaches give the same results. As the depletion increases, the two approaches differ due to many-body effects limiting the maximum possible molecule production efficiency. We have observed this in our simulations by considering higher-density gases. We have therefore shown the suitability and practicability of this beyond mean-field approach for application to further problems in the production of Feshbach molecules from ultracold gases.
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Boxwell, Clive. "Small molecule models of metalloproteins." Thesis, University of York, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.323507.
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Napoleon, Raeanne L. "Understanding small molecule-protein interactions." Thesis, Boston University, 2012. https://hdl.handle.net/2144/31592.
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Thesis (Ph.D.)--Boston UniversityPLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.
The binding of small molecules to a protein is among the most important phenomena in the chemistry of life; the activity and functionality of many proteins depend critically on binding small molecules. A deep understanding of protein-small molecule interactions and the interplay between ligation and function can give valuable insight into key systems of interest. The complete characterization of any small molecule-protein interaction requires quantification of many interactions and the pursuit of such information is the purpose of this body of work. The discovery of binding regions on proteins, or "hot spots," is an important step in drug development. To this end, a highly regarded and robust fragment-based protocol has been developed for the detection of hot spots. Firstly, we use this protocol in conjunction with other computation techniques, such as homology modeling, to locate the allosteric binding site of £-phenylalanine in Phenylalanine Hydroxylase. Secondly, computational fragment mapping was employed to locate the site of allostery for Ras, an important signaling protein. Lastly, the identification of hot spots for many unligated protein targets is presented highlighting the importance of a reliable way to predict druggability computationally. The second part of this dissertation shifts focus to the development of electrostatic models of small molecules. It is widely believed that classical potentials can describe neither vibrational frequency shifts in condensed phases nor the response of vibrational frequencies to an applied electric field, the vibrational Stark effect. In this work, an improved classical molecular electrostatic model for the CO ligand was developed to faithfully model these phenomena. This model is found to predict the vibrational Stark effect and Fe-CO binding energy with unprecedented accuracy for such a classical model. As an extension of this work, a geometrically dependent water potential was developed. This work has shown that comparison of results obtained from current water models against experimentally determined proton momentum distributions is an invaluable benchmark
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Rabinovich, Daniel. "A molecule for football fans." Revista de Química, 2016. http://repositorio.pucp.edu.pe/index/handle/123456789/99465.
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Una molécula para los aficionados al fútbol (El descubrimiento de los Fullerenos y su aparición en las estampillas del Reino Unido)A molecule for football fans (The discovery of fullerenes and their appearance on stamps UK)
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Bhasin, Deepak. "Small Molecule Inhibitors asAnticancer Agents." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1305826098.
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Li, Yang. "Single Molecule Spintronics and Friction." Ohio University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou151561792063398.
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Luccarelli, James. "Small Molecule Modulators of Apoptosis." Thesis, Harvard University, 2017. http://nrs.harvard.edu/urn-3:HUL.InstRepos:32676118.
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Control of cell survival relies on a delicate balance between pro-apoptotic and anti-apoptotic signalling. In humans, the key regulatory proteins are those of the BCL-2 family, which include effector proteins such as BAX and BAK, anti-apoptotic proteins including BCL-2 and MCL-1, and pro-apoptotic proteins including BID and BIM. Dysregulation of apoptosis is among the Hallmarks of Cancer, and modulation of apoptosis holds promise as an effective therapeutic strategy for a range of malignancies. This thesis advances new strategies for modulating apoptosis using small molecules.
The first section explores the properties of stapled peptides. These molecules incorporate two non-natural amino acids with olefin sidechains that are then covalently linked. The resulting “staple” modifies the biophysical properties of the molecule. This chapter shows how stapling results in greater serum stability of the peptides, improves binding affinity for anti-apoptotic targets, and allows for facile transformation of a native sequence into an improved peptide, as demonstrated by stapling a SOS1 peptide to target KRAS.
The second section targets MCL-1, an antiapoptotic BCL-2 family protein that has emerged as a major pathogenic factor in human cancer. MCL-1 bears a surface groove whose function is to sequester the BH3 killer domains of proapoptotic BCL-2 family members, but successful drugging of this groove has not been achieved. This chapter develops an alternative strategy using a small molecule that covalently modifies C286 at a novel interaction site distant from the BH3-binding groove. This allosteric mechanism results in reduced BH3 binding capacity of MCL-1 and impairs the oncogenic anti-apoptotic activity of the protein.
The final chapter targets BAX, a critical executioner protein in the apoptotic pathway whose oligomerization causes permeabilization of the mitochondrial outer membrane. Using STD-NMR, a library of nearly 1,000 fragments was screened for binding to full-length BAX. This resulted in the discovery of a compound BIF-44 that sensitizes BAX by engaging a noncanonical hydrophobic pocket formed by the junction of the α3-α4 and α5-α6 hairpins. Biochemical and structural analyses indicate that the molecule sensitizes BAX by allosterically mobilizing the α1-α2 loop, a mechanism implicated in the initiation of BH3-mediated direct BAX activation. The identified compound thus informs the mechanism for initiation of BAX activation, and provides a new opportunity to reduce the apoptotic threshold for potential therapeutic benefit.