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Chaka, Anne Marie. "Predicting the crystal structure of organic molecular materials." Case Western Reserve University School of Graduate Studies / OhioLINK, 1993. http://rave.ohiolink.edu/etdc/view?acc_num=case1056642240.
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Asmadi, Aldi. "Crystal structure prediction : a molecular modellling study of the solid state behaviour of small organic compounds." Thesis, University of Bradford, 2010. http://hdl.handle.net/10454/4441.
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The knowledge of the packing behaviour of small organic compounds in crystal lattices is of great importance for industries dealing with solid state materials. The properties of materials depend on how the molecules arrange themselves in a crystalline environment. Crystal structure prediction provides a theoretical approach through the application of computational strategies to seek possible crystal packing arrangements (or polymorphs) a compound may adopt. Based on the chemical diagrams, this thesis investigates polymorphism of several small organic compounds. Plausible crystal packings of those compounds are generated, and their lattice energies are minimised using molecular mechanics and/or quantum mechanics methods. Most of the work presented here is conducted using two software packages commercially available in this field, Polymorph Predictor of Materials Studio 4.0 and GRACE 1.0. In general, the computational techniques implemented in GRACE are very good at reproducing the geometries of the crystal structures corresponding to the experimental observations of the compounds, in addition to describing their solid state energetics correctly. Complementing the CSP results obtained using GRACE with isostructurality offers a route by which new potential polymorphs of the targeted compounds might be crystallised using the existing experimental data. Based on all calculations in this thesis, four new potential polymorphs for four different compounds, which have not yet been determined experimentally, are predicted to exist and may be obtained under the right crystallisation conditions. One polymorph is expected to crystallise under pressure. The remaining three polymorphs might be obtained by using a seeding technique or the utilisation of suitable tailor made additives.
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Smith, Elaine D. L. "Combined molecular modelling and powder X-ray diffraction for crystal structure solution of organic materials." Thesis, Heriot-Watt University, 2004. http://hdl.handle.net/10399/249.
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Day, G. M., T. G. Cooper, A. Cruz-Cabeza, K. E. Hejczyk, H. L. Ammon, S. X. M. Boerrigter, J. S. Tan, et al. "Significant progress in predicting the crystal structures of small organic molecules ¿ a report on the fourth blind test." International Union of Crystallography, 2009. http://hdl.handle.net/10454/4748.
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noWe report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structures of small organic molecules. There were 14 research groups which took part, using a variety of methods to generate and rank the most likely crystal structures for four target systems: three single-component crystal structures and a 1:1 cocrystal. Participants were challenged to predict the crystal structures of the four systems, given only their molecular diagrams, while the recently determined but as-yet unpublished crystal structures were withheld by an independent referee. Three predictions were allowed for each system. The results demonstrate a dramatic improvement in rates of success over previous blind tests; in total, there were 13 successful predictions and, for each of the four targets, at least two groups correctly predicted the observed crystal structure. The successes include one participating group who correctly predicted all four crystal structures as their first ranked choice, albeit at a considerable computational expense. The results reflect important improvements in modelling methods and suggest that, at least for the small and fairly rigid types of molecules included in this blind test, such calculations can be constructively applied to help understand crystallization and polymorphism of organic molecules.
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Chana, Harcharn S. "Crystal structure determination and prediction of simple organic molecules, using powder diffraction methods, and modern computational techniques." Thesis, University of Birmingham, 2006. http://etheses.bham.ac.uk//id/eprint/8849/.
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The research presented within this thesis highlights aspects of crystal structure determination from the combined use of powder X-ray, synchrotron and neutron diffraction and also computational crystal structure prediction from molecular structure only. The use of DE enabled the crystal structure of 2,4-dichloro-5-sulfamoylbenzoic acid and oxamic acid to be examined from conventional laboratory X-ray diffraction. In the case of 2,4-dichloro-5-sulfamoylbenzoic acid two comparable structures were identified each of which refined to similar extents. To correctly identify the correct crystal structure it was necessary to obtain and refine a powder neutron dataset. This presented before obscured information on the relative positions of hydrogen atoms and inevitably led to the successful elucidation of the crystal structure of 2,4-dichloro- 5-sulfamoylbenzoic acid. With reference to oxamic acid two conformations, namely 'cis' and 'trans' were identified from the refinement of laboratory X-ray diffraction. Infrared analysis and lattice energy calculations were also used to distinguish between the two conformations with some success. With respect to computational crystal structure prediction, presented here is a new computational strategy for crystal structure prediction from molecular structure only. The traditional lattice energy output from a polymorph prediction sequence is reranked in terms of hydrogen bonding and graph set merit points. My research here has to a certain extent managed to combine these attributes and enabled the successful prediction of 8 out of the initial 11 chosen test structures obtained from the Cambridge Structural Database (CSD).
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Cox, Jennifer Jane. "Structure of organic molecular thin films vapour deposited on III-V semiconductor surfaces." Thesis, Imperial College London, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.327025.
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McDonagh, James L. "Computing the aqueous solubility of organic drug-like molecules and understanding hydrophobicity." Thesis, University of St Andrews, 2015. http://hdl.handle.net/10023/6534.
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This thesis covers a range of methodologies to provide an account of the current (2010-2014) state of the art and to develop new methods for solubility prediction. We focus on predictions of intrinsic aqueous solubility, as this is a measure commonly used in many important industries including the pharmaceutical and agrochemical industries. These industries require fast and accurate methods, two objectives which are rarely complementary. We apply machine learning in chapters 4 and 5 suggesting methodologies to meet these objectives. In chapter 4 we look to combine machine learning, cheminformatics and chemical theory. Whilst in chapter 5 we look to predict related properties to solubility and apply them to a previously derived empirical equation. We also look at ab initio (from first principles) methods of solubility prediction. This is shown in chapter 3. In this chapter we present a proof of concept work that shows intrinsic aqueous solubility predictions, of sufficient accuracy to be used in industry, are now possible from theoretical chemistry using a small but diverse dataset. Chapter 6 provides a summary of our most recent research. We have begun to investigate predictions of sublimation thermodynamics. We apply quantum chemical, lattice minimisation and machine learning techniques in this chapter. In summary, this body of work concludes that currently, QSPR/QSAR methods remain the current state of the art for solubility prediction, although it is becoming possible for purely theoretical methods to achieve useful predictions of solubility. Theoretical chemistry can offer little useful additional input to informatics models for solubility predictions. However, theoretical chemistry will be crucial for enriching our understanding of the solvation process, and can have a beneficial impact when applied to informatics predictions of properties related to solubility.
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Lucas, Kaitlyn D. "Magnesium Sulfonyldibenzoates: Synthesis, Structure, Phase Transformation and Microscopic Studies." Youngstown State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ysu1391780070.
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Krug, Claudio Kristoffer [Verfasser], and J. Michael [Akademischer Betreuer] Gottfried. "Structure and Reactivity of Aromatic Molecules on Metal Single-Crystal Surfaces and at Metal/Organic Interfaces / Claudio Kristoffer Krug ; Betreuer: J. Michael Gottfried." Marburg : Philipps-Universität Marburg, 2020. http://d-nb.info/121868593X/34.
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SOUSA, JÚNIOR Joel Padilha de. "Estudo estrutural de complexos de cobre (II) como modelos de sítios metálicos de enzimas com atividade oxidativa." Universidade Federal de Goiás, 2009. http://repositorio.bc.ufg.br/tede/handle/tde/819.
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Previous issue date: 2009-04-24We present the structural study, by x-rays diffraction, of two forms on the crystalline and molecular structures of the metal-organic single-crystal compounds Dicloro[N- benzoyl-N´-(4-methylphenyl)-N´´-(2-pyridinyl)-guanidine)]copper(II). Such compound is known for the phenol oxidative catalictic bioactivity. The compound is a copper(II)-guanidine de- rivative complex. The main motivation of the present work is the polimorphism observed on such complex when the crystallization conditions are changed. The structures were sol- ved using the Direct Methods method and the structural parameters were refined with full matrix least-squares method. The copper(II) complex C19H22Cl2CuN4O crystallizes in the triclinic system in the P¯1 space group, with a single molecule in the assymetric unit and unit cell parameters: a = 8.616 (3) °A, b = 9.288 (3) °A, c = 13.623 (2) °A, α = 106.96 (2)o, β = 96.02 (3)o, γ = 100.60 (2)o, with volume 1010.3 (5) °A3 and calculated density of 1.528 Mgm−3. The same compound also crystallizes in the monoclinic system in the P21/n space group and unit cell parameters: a = 7.937 (2) °A, b = 18.727 (2) °A, c = 13.993 (2) °A, β = 102.03 (2)o, with volume 2034.2 (6) °A3 and calculated density 1.518 Mgm−3. The two isomeric molecules showed different conformations from one crystal packing to the other, due to the different intermolecular interactions. Given the different crystal packing and intermolecular interactions, we performed electronic structure calculations using the Density Functional Theory in order to derive the energetic differences, including calculations of dimers linked by hydrogen bonds, for evaluating the crystal packing influence on the complex stability in their crystal structures.
Apresentamos um estudo estrutural, por difra¸c ao de raios X, das estruturas cris- talinas e moleculares de um composto metalorg anico no estado monocristalino Dicloro [N- benzoil-N´-(4-metilfenil)-N´´-(2-piridinil)-guanidina)] Cobre(II). O qual apresenta atividade biol´ogica de cat´alise do processo de oxida¸c ao de fen´ois. O complexo ´e de cobre(II) com um derivado do grupo qu´ımico org anico guanidina. A motiva¸c ao ao exposto nesta disserta¸c ao foi a ocorr encia de duas formas polim´orficas do complexo supracitado variando-se as condi¸c oes de cristaliza¸c ao. As estruturas foram resolvidas utilizando o M´etodo Direto e para o re- finamento dos par ametros t´ermicos usou-se o m´etodo dos m´ınimos quadrados de matriz completa. O complexo de cobre(II) C19H22Cl2CuN4O foi cristalizado no sistema cristalino tricl´ınico, no grupo espacial P¯1, com uma mol´ecula independente por unidade assim´etrica e par ametros de cela: a = 8,616 (3) °A, b = 9,288 (3) °A, c = 13,623 (2) °A, α = 106,96 (2)o, β = 96,02 (3)o, γ = 100,60 (2)o com volume de 1010,3 (5) °A3 e a densidade calculada 1,528 Mgm−3. O mesmo composto cristalizou-se no sistema cristalino monocl´ınico, no grupo espacial P21/n, em que foi observada uma mol´ecula por unidade assim´etrica com par ametros cela unit´aria: a = 7,937 (2) °A, b = 18,727 (2) °A, c = 13,993 (2) °A, β = 102,03 (2)o, volume 2034,2 (6) °A3, densidade calculada 1,518 Mgm−3. Estruturalmente id enticas as mol´eculas apresentaram diferentes conforma¸c oes moleculares e seus dois empacotamento apresentaram intera¸c oes intermoleculares bastante distintas. Em fun¸c ao dos diferentes arranjos cristalinos e das diferentes intera¸c oes intermoleculares, foram feitos c´alculos de estrutura eletr onica com a Teoria do Funcional Densidade para inferir as diferen¸cas energ´eticas, incluindo d´ımeros que interagem por pontes de hidrog enio, com o objetivo de avaliar a influ encia do empacotamento cristalino na estabilidade do complexo nas estruturas cristalinas.
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Singh, Kulveer. "Structure-function studies of the oxidoreductase bilirubin oxidase from Myrothecium verrucaria using an electrochemical quartz crystal microbalance with dissipation." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:0376cc7e-f572-4e0c-96f0-43b0b4b91d99.
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This thesis presents the development and redesign of a commercial electrochemical quartz crystal microbalance with dissipation (E–QCM–D). This was used to study factors affecting the efficiency of the four electron reduction catalysed by the fuel cell enzyme bilirubin oxidase from Myrothecium verrucaria immobilised on thiol modified gold surfaces. Within this thesis, the E–QCM–D was used to show that application of a constant potential to bilirubin oxidase adsorbed to thiol-modified gold surfaces causes activity loss that can be attributed to a change in structural arrangement. Varying the load by potential cycling distorts the enzyme by inducing rapid mass loss and denaturation. Attaching the enzyme covalently reduces the mass loss caused by potential cycling but does not mitigate activity loss. Covalent attachment also changes the orientation of the surface bound enzyme as verified by the position of the catalytic wave (related to the overpotential for catalysis) and reactive labelling followed by mass spectrometry analysis. The E–QCM–D was used to show how electrostatic interactions affect enzyme conformation where high pH causes a reduction in both mass loading at the electrode and a reduction in activity. At pH lower than the enzyme isoelectric point, there is a build up of multilayers in a clustered adsorption. When enzyme adsorbs to hydrophobic surfaces there is a rapid denaturation which completely inactivates the enzyme. Changing the surface chemistry from carboxyl groups to hydroxyl and acetamido groups shows that catalysis is shifted to more negative potentials as a result of an enzyme misorientation. Further to this, increasing the chain length of the thiol modifier indicates that an increased distance between surface and enzyme reduces activity, enzyme loading and results in a conformational rearrangement that permits electron transfer over longer distances.
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Rujas, Javier Marti. "Molecular transport, reactivity and structure in organic crystals." Thesis, Cardiff University, 2005. http://orca.cf.ac.uk/56009/.
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The work presented in this thesis is based on studies concerning structural properties of molecular solids, and is composed of three different parts. First, structural aspects of solid state dimerization reactions have been studied using 1H NMR and powder X-ray diffraction. The experiments are based on the photoreactions of cinnamic acids in the solid state. These materials show photochemical behaviour upon irradiation by UV light. The /-phase (photoreactive polymorph) of 4-cMoro-/ra s-cinnamic acid was chosen as the primary material for study, and a combination of powder X-ray diffraction and solution state 1H NMR spectroscopy techniques have been used to follow the evolution of the solid-state photoreaction, and to determine the structural evolution of the photoproduct. In addition, the structure of a photoreactive material (the /-phase of 4-fluoro-/raws-cinnammic acid) that cannot be prepared as a single crystal suitable for single crystal X-ray diffraction has been determined directly from powder X-ray diffraction data. This research exploits modern developments in the application of powder X-ray diffraction techniques in order to obtain new levels of understanding of a classical solid state reaction. The second part of this thesis is based on the investigation of transport of molecules through linear tunnels in solid organic inclusion compounds (host-guest systems). This project is focused on incommensurate inclusion compounds in which guest molecules are contained within a system of one-dimensional tunnels (with a diameter of about 5.5 A) in a crystalline urea host structure. It was shown previously that net transport of guest molecules in one direction along the crystal can be achieved by insertion of new guest molecules at one end of the crystal (by dipping it into the liquid phase of another potential guest), with the original guest molecules expelled from the other end of the crystal. Such phenomena have considerable potential as the basis of selective micro-scale separation techniques, based on discrimination of molecular size, shape and chirality. In the present work, the spatial distribution of the guest molecules in the crystal has been studied together with the changes in the spatial distribution of the guest molecules as a function of time during the transport process. This process has been investigated directly by using confocal Raman microspectrometry as an in situ probe of the molecular transport process. The data obtained from such experiments have provided access to information on the kinetics of the transport process and the time-dependence of the spatial distribution of guest molecules within the channel system. A model has been developed to understand the kinetics of the transport process, leading to detailed mechanistic insights. The last part of the thesis is focused on the design of hydrogen-bonded organic complexes. Underlying all structural aspects of organic molecular crystals is the fundamental question of what factors control the molecular packing arrangement, and an important related issue is how to apply an understanding of these factors in the design of crystals with desired structural properties. The work has focused on the study of components with hydrogen bonding capability (urea/diols and /-phenylenediamine/diols), with a view to the formation of hydrogen-bonded complexes with predictable structural features. Optical microscopy, single crystal X-ray diffraction, powder X-ray diffraction and confocal Raman microspectroscopy have been applied in this work.
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Fattah, Jamila. "Structure and dynamics of some molecular crystals." Thesis, University of Oxford, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.303690.
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Coombes, David Stuart. "Towards the a priori prediction of molecular crystal structures." Thesis, University College London (University of London), 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.263300.
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Yong, Chaw Keong. "Ultrafast carrier dynamics in organic-inorganic semiconductor nanostructures." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:b2efdc6a-1531-4d3f-8af1-e3094747434c.
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This thesis is concerned with the influence of nanoscale boundaries and interfaces upon the electronic processes that occur within the inorganic semiconductors. Inorganic semiconductor nanowires and their blends with semiconducting polymers have been investigated using state-of-the-art ultrafast optical techniques to provide information on the sub-picosecond to nanosecond photoexcitation dynamics in these systems. Chapters 1 and 2 introduce the theory and background behind the work and present a literature review of previous work utilising nanowires in hybrid organic photovoltaic devices, revealing the performances to date. The experimental methods used during the thesis are detailed in Chapter 3. Chapter 4 describes the crucial roles of surface passivation on the ultrafast dynamics of exciton formation in gallium arsenide (GaAs) nanowires. By passivating the surface states of nanowires, exciton formation via the bimolecular conversion of electron-hole plasma can observed over few hundred picoseconds, in-contrast to the fast carrier trapping in 10 ps observed in the uncoated nanowires. Chapter 5 presents a novel method to passivate the surface-states of GaAs nanowires using semiconducting polymer. The carrier lifetime in the nanowires can be strongly enhanced when the ionization potential of the overcoated semiconducting polymer is smaller than the work function of the nanowires and the surface native oxide layers of nanowires are removed. Finally, Chapter 6 shows that the carrier cooling in the type-II wurtzite-zincblend InP nanowires is reduced by order-of magnitude during the spatial charge-transfer across the type-II heterojunction. The works decribed in this thesis reveals the crucial role of surface-states and bulk defects on the carrier dynamics of semiconductor nanowires. In-addition, a novel approach to passivate the surface defect states of nanowires using semiconducting polymers was developed.
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Parker, Jane Ker. "Crystal structure reactivity correlations." Thesis, University of Cambridge, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.316782.
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Campbell, Josh E. "Crystal structure prediction of organic semiconductors." Thesis, University of Southampton, 2017. https://eprints.soton.ac.uk/414008/.
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This thesis presents the use of crystal structure prediction (CSP) in the evaluation and design of novel organic semiconductors. Heteroatom substitution into common organic semiconductors (pentacene in this thesis) oers a way of modulating their crystal packing and electronic properties. Initially CSP was performed on six human designed molecules and the charge mobility of their predicted crystal structures was calculated. The packing landscapes changed signicantly from the unsubstituted pentacene. We found that seven nitrogen atoms led to a landscape showing a range of packing motifs, while seven nitrogen atoms favours the adoption of sheet-like motifs. Substitution patterns expected to result in the highest mobilities were found to perform worse than assumed, showing the importance of tuning both molecular electronic properties and crystal engineering. A genetic algorithm was then developed to generate new nitrogen substituted pentacenes. A population members tness was calculated using two molecular properties important for electron transport in organic semiconductors. Five runs of the genetic algorithm gave 12 promising candidates for CSP and mobility calculations. The packing landscapes were similar to those of the seven nitrogen substituted human designed molecules. One genetic algorithm molecule showed a high number of high mobility structures close to the global minimum, making this molecule an attractive target for synthesis. Extensions to include CSP within the tness function of the genetic algorithm represents possible future work. Addition work included the design and testing of structure generator for the generation of trial crystal structures during a CSP. The novel structure generator performed well in locating the experimental structures of three test molecules and was used in the group's submission to the 6th blind test, of which one molecule is also presented here. The experimental structure of this molecule was located in lists ranked by lattice energy and free energy, though the free energy list ranked the experimental structure as the global minimum.
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Täuber, Daniela, Katrin Radscheit, Rafael Camacho, Ivan Scheblykin, and Borczyskowski Christian von. "Guest molecule diffusion and conformation influenced by local liquid crystal structure." Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-183950.
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Täuber, Daniela, Katrin Radscheit, Rafael Camacho, Ivan Scheblykin, and Borczyskowski Christian von. "Guest molecule diffusion and conformation influenced by local liquid crystal structure." Diffusion fundamentals 20 (2013) 103, S. 1-2, 2013. https://ul.qucosa.de/id/qucosa%3A13692.
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Nyman, Jonas. "Computational predictions of structures, inclusion behaviour and properties of organic molecular crystals." Thesis, University of Southampton, 2017. https://eprints.soton.ac.uk/416439/.
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This thesis is about the computational prediction of crystal structures and their properties. Polymorphism, where the same molecule crystallizes in more than one structure is investigated. Several structures of polymorphs and clathrates, porous crystals that adsorb gases, are predicted without prior experimental data. Rigid-molecule lattice dynamics in an anisotropic force field is used to calculate temperature-dependent properties of large sets of crystals. Using the lattice-vibrational free energy as scoring function incrystal structure prediction is discussed. Brillouin zone sampling and convergence difficulties of lattice dynamics calculations are addressed, with a kernel density estimationmethod offered as a solution. The advantage of computationally affordable force field methods over electronic structure methods will be described. I demonstrate that multipole-based force fields canbe comparable in accuracy to dispersion-corrected generalized gradient approximation density functional theory and that such force fields are very suitable for crystal structure prediction as they allow the calculation of realistic free energies for hundreds ofstructures at a relatively small computational cost. For the prediction of clathrate structures, I show that a combination of the free energy and the guest-to-cavity volume ratio can be a suitable scoring function. I suggest thatporous structures in predicted crystal energy landscapes should be interpreted as possible solvates, clathrates and hydrates, and that these should be carefully considered in theanalysis of prediction results.
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Bucar, Dejan-Kresimir. "Crystal engineering of organic and metal-organic solids: design, structure and properties." Diss., University of Iowa, 2010. https://ir.uiowa.edu/etd/3435.
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Crystal engineering has recently emerged as a method of choice for the design and the construction of functional materials. Solid-state synthesis, of the most commonly studied aspects of crystal engineering, has been shown to provide access to molecular targets that are hardly obtainable using principles of conventional (i.e. solution-based) organic synthesis. Reactions in the solid state are, however, not routinely used in organic synthetic chemistry. The scarce use of solid-state reactions can be attributed to the difficulty of predicting molecular arrangements in the solid state, as well as to the lack of methodologies to control crystal packing. Template-directed solid-state synthesis is a recently developed modus operandi that enables control over reactivity within multi-component crystals. The thesis is focused on the application of template-directed solid-state approach to [2+2] photocycloaddition reactions in the solid state, as well as on the understanding of intermolecular interactions in crystals. Synthetic templates have been utilized to construct cocrystals that enable a class of hitherto underdeveloped organic solid-state reactions, namely [2+2] cross-photoaddition reactions. In addition, products derived form templated solid state reactions, namely tetrapyridylcyclobutanes, have been utilized to generate exceptional materials, such as thixothropic hydrogels based on nano-dimensional metal-organic particles. The utility of crystal engineering has also been expanded to the nanoscience and the development of nanomaterials. A crystallization method for the preparation of nano-dimensional cocrystals has been developed. The method has been shown to enable single-crystal-to-single-crystal [2+2] photodimerizations of olefins. In addition, nano-dimensional cocrystals have been shown to exhibit distinctive mechanical properties upon single-crystal-to-single-crystal transformations.
In addition to solid-state reactions and materials derived therefrom, we systematically studied hierarchies of supramolecular synthons in pharmaceutical cocrystals comprised of multi-functional molecules. Pharmaceutical cocrystals have been recently shown to exhibit physical properties superior to those of parent drugs. Our studies involved xanthine alkaloids as pharmaceutical agents and a series of hydroxylated benzoic acids as cocrystal formers. Synthon hierarchies have been established for three xanthine alkaloids. We also discovered pharmaceutical salts that formed where cocrystallization was expected to occur. Reasons contributing to such unexpected salt formation were investigated using X-ray crystallography and computational methods. The established synthon hierarchies are expected to contribute to a better understanding of self-assembly processes in cocrystals that is crucial for the development of state-of-art drugs, and the design of organic reactions in the solid state.
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Krause, Bärbel. "Growth and structure of the organic molecule PTCDA on Ag(111)." [S.l. : s.n.], 2002. http://www.bsz-bw.de/cgi-bin/xvms.cgi?SWB10361096.
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Mohamed, S. "Computational crystal structure prediction and experimental characterisation of organic salts." Thesis, University College London (University of London), 2011. http://discovery.ucl.ac.uk/1318096/.
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Approximately half of all pharmaceutical drugs are marketed as salts. This thesis pioneers the application of computational crystal structure prediction to organic salts containing the commonly used chloride or carboxylate counterions, and assesses the extent to which the theoretical calculations can be used to aid experimental efforts targeting organic salts. A screen for multi-component solid forms of pyridine and 4- dimethylaminopyridine (DMAP) using a range of dicarboxylic acids led to one novel cocrystal of pyridine and six novel salts of DMAP. All novel crystal structures were solved using single crystal X-ray diffraction. At a simplistic level, salts differ from cocrystals in the position of the acidic proton within the crystal. For a selected set of structures, periodic ab initio calculations were shown to be useful in suggesting the observed N+-H (salt) or O-H (cocrystal) covalent bond as the preferred atomic connectivity. Modelling the same crystal structures by lattice energy minimisation using a distributed multipole based electrostatic model proved successful if the correct proton connectivity was used. The observed structures of a model salt, cocrystal and disordered salt-cocrystal system were found to be the most stable or almost equienergetic with the most stable structure in the predicted crystal energy landscapes. When the predictions were repeated using molecular structures with the wrong proton connectivity, the energetic ranking of the structure got worse. The computational model of crystal structure prediction was successfully used to rationalise the different polymorphic and hydration behaviour of the pharmacologically active amantadine hydrochloride and memantine hydrochloride salts. Finally, a similar methodology was applied to 1,8-naphthyridinium fumarate and the calculations performed as part of the fifth international blind test of crystal structure prediction. Overall, the success in modelling the crystal structures of carboxylate and chloride salts illustrates the promise of crystal structure prediction in aiding experimental efforts of organic salt selection.
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Hansson, Anders. "Electronic Structure and Transport Properties of Carbon Based Materials." Doctoral thesis, Linköpings universitet, Beräkningsfysik, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-7544.
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In the past decade the interest in molecular electronic devices has escalated. The synthesis of molecular crystals has improved, providing single crystals or thin films with mobility comparable with or even higher than amorphous silicon. Their mechanical flexibility admits new types of applications and usage of electronic devices. Some of these organic crystals also display magnetic effects. Furthermore, the fullerene and carbon nanotube allotropes of carbon are prominent candidates for various types of applications. The carbon nanotubes, in particular, are suitable for molecular wire applications with their robust, hollow and almost one-dimensional structure and diverse band structure. In this thesis, we have theoretically investigated carbon based materials, such as carbon nanotubes, pentacene and spiro-biphenalenyl neutral radical molecular crystals. The work mainly deals with the electron structure and the transport properties thereof. The first studies concerns effects and defects in devices of finite carbon nanotubes. The transport properties, that is, conductance, are calculated with the Landauer approach. The device setup contains two metallic leads attached to the carbon nanotubes. Structural defects as vacancies and bending are considered for single-walled carbon nanotubes. For the multi-walled carbon nanotubes the focus is on inter-shell interaction and telescopic junctions. The current voltage characteristics of these systems show clear marks of quantum dot behaviour. The influence of defects as vacancies and geometrical deformations are significant for infinite systems, but in these devices they play a minor role. The rest of the studies concern molecular crystals, treated with density-functional theory (DFT). Inspired by the enhance of the electrical conductivity obtained experimentally by doping similar materials with alkali metals, calculations were performed on bundles of single-walled carbon nanotubes and pentacene crystals doped with potassium. The most prominent effect of the potassium intercalation is the shift of Fermi level in the nanotube bands. A sign of charge transfer of the valence electrons of the potassium atoms. Semi-conducting bundles become metallic and metallic bundles gain density of states at the Fermi level. In the semi-conducting pristine pentacene crystals structural transitions occur upon doping. The herringbone arrangement of the pristine pentacene molecules relaxes to a more π-stacked structure causing more dispersive bands. The charge transfer shifts the Fermi level into the lowest unoccupied molecular orbital band and turns the crystal metallic. Finally, we have studied molecular crystals of spiro-biphenalenyl neutral radicals. According to experimental studies, some of these materials show simultaneous electrical, optical and magnetical bistability. The electronic properties of these crystals are investigated by means of DFT with a focus on the possible intermolecular interactions of radical spins.
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Mohamed, Tahir Mohamed Ibrahim. "Combination of single crystal X-ray diffraction & ¹³C CP/MAS solid state NMR spectroscopy : studies of structures & dynamics of molecular organic crystals." Thesis, University of Oxford, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.249427.
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Jia, Yuanyuan Wu Yue. "Structure analysis of titanate nanotube/organic molecule hybrid and self-healing polymer." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2007. http://dc.lib.unc.edu/u?/etd,799.
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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2007.Title from electronic title page (viewed Dec. 18, 2007). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Department of the Department of Physics and Astronomy." Discipline: Physics and Astronomy; Department/School: Physics and Astronomy.
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Friedman, Mark Richard. "Novel thermotropic liquid crystals possessing a benzo[b]furan unit." Thesis, University of Hull, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342980.
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Bissonnette, Martine C. "Ion/radical and ion/molecule complexes and ion structure assignments in the gas phase." Thesis, University of Ottawa (Canada), 1991. http://hdl.handle.net/10393/7731.
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The fragmentation mechanism of ionized neopentanol, (CH$\sb3$)$\sb3$CCH$\sb2$OH$\sp{+-}$, has been studied in great detail along with other C$\sb5$H$\sb $H$\sp{+-}$ isomers. The use of $\sp $C and D labelling was found an essential tool to establish the relation between the other species involved in the dissociation of neopentanol. The involvement of (CH$\sb3$)$\sb2$C$\sp{\cdot}$CH$\sb2\sp+$(O)HCH$\sb3$, (CH$\sb3$)$\sb3$C$\sp+$(O)HCH$\sb2$ and (CH$\sb3$)$\sb2$($\sp\cdot$CH$\sb2$)CCH$\sb2\sp+$OH$\sb2$ was essential to explain the H/D label exchange occurring upon fragmentation of neopentyl alcohol. An ion-dipole complex between methanol and ionized methyl propene is proposed as the final intermediate which leads directly to the products, methanol and ionized methyl propene. The results of the investigation of C$\sb7$H$\sb5\sp+$ ions from various precursor molecules are also described. The following compounds, which all produce C$\sb7$H$\sb5\sp+$ ions, were studied: benzyl acetate, benzyl formate, benzyl alcohol, 2-bromocyclopropabenzene, 1,6-heptadiyne and 1,5-decadiyne. According to the metastable ion (MI) mass spectra and the He collision induced dissociation (CID) of m/z 89 ions, it is suggested that four structures exist. (Abstract shortened by UMI.)
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Clough, Andrew James. "Synthesis and crystal structure determination of novel lithium metal-organic frameworks." Thesis, California State University, Long Beach, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=1524184.
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In this thesis, three new lithium homometallic metal-organic frameworks are discussed. An introduction to lightweight metal-organic framework is given, followed by a detailed analysis of each new structure's topology, composition, novel secondary building units, and potential for gas adsorption. Special attention is given to the formation of new lithium secondary building units and the synthetic conditions that create them. These novel secondary building units are discussed in the context of the current lithium metal-organic framework literature, and compared when appropriate to known structures. Crystallography data is also discussed, with an emphasis on the connectivity of these lithium secondary building units.
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McManus, Gregory J. "Structural diversity in metal-organic materials." [Tampa, Fla] : University of South Florida, 2008. http://purl.fcla.edu/usf/dc/et/SFE0002596.
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Petit, Samuel. "Structures de complexes dans le système (cuivre (II)-oxine-sulfoxine-eau), étude expérimentale et modélisation moléculaire de la cristallisation et de transitions de phases." Rouen, 1994. http://www.theses.fr/1994ROUES025.
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La résolution structurale d'une nouvelle variété anhydre d'oxinate de cuivre(II) (noté X) a été effectuée d'après le diagramme de diffraction X sur poudre. L'étude des filiations structurales et la prise en compte des données cinétiques, thermodynamiques et physico-chimiques ont mené à proposer un modèle pour les transitions solide-solide entre variétés dihydratées et anhydres d'oxinate de cuivre(II) (déshydratations et transitions polymorphiques). La résolution de structure sur monocristal et sur poudre de deux variétés hydratées de sulfoxinate de cuivre(II) a permis une étude par modélisation moléculaire de la nucléation homogène en solution aqueuse des variétés de structure connue. La croissance cristalline des sulfoxinates de cuivre(II) a été envisagée, conduisant à considérer la croissance d'une face associée à une tranche contenant deux molécules de conformations différentes. Le concept de sous-tranches non équivalentes par les opérations de symétrie du groupe d'espace est défini. Deux approches complémentaires ont été utilisées en vue d'expliquer l'influence de la sulfoxine sur l'évolution des oxinates de cuivre(II). D'une part, une étude des molécules d'oxine et de sulfoxine par les méthodes de chimie théorique a permis d'interpréter leur comportement en milieu aqueux. D'autre part, une étude expérimentale des complexes mixtes cuivre-oxine-sulfoxine a été entreprise
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Tsuboi, Chiaki. "X-ray crystal structure analyses of magnetically oriented microcrystalline suspensions." Kyoto University, 2016. http://hdl.handle.net/2433/216190.
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Kyoto University (京都大学)0048
新制・課程博士
博士(農学)
甲第19936号
農博第2186号
新制||農||1044(附属図書館)
学位論文||H28||N5009(農学部図書室)
33022
京都大学大学院農学研究科森林科学専攻
(主査)教授 木村 恒久, 教授 西尾 嘉之, 教授 髙野 俊幸
学位規則第4条第1項該当
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Lafuente, Hernández Mª Pilar. "Computational Study of the Mechanisms that Stabilize Organic Molecule‐Based Magnets." Doctoral thesis, Universitat de Barcelona, 2016. http://hdl.handle.net/10803/400864.
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The objective of this PhD thesis has been the study of the mechanisms that stabilize high-spin states in organic molecule-based magnetic materials. These materials require organic radicals with permanent magnetic moment as building units. Additionally, these molecules need to interact ferromagnetically, and expand that interaction along all three directions of the space.
We have carried out our studies using computational chemistry techniques, mostly ab- initio methods (MP2, CASSCF and CASMP2), and DFT-based methods (B3LYP or M06L). Besides, we have also used the hybrid Molecular Mechanics Valence Bond method (MMVB) for alternant hydrocarbons with high number of active electrons.
We have demonstrated that in organic radicals the energy gap between two spin states is usually higher when the stabilization of the spin centers occurs by means of through- bond (TB) instead of through-space (TS) interactions. As a result, alternant hydrocarbons (π-delocalized, with TB interactions) are more stable than non-alternant hydrocarbons (π-localized, with TS interactions). Therefore, alternant hydrocarbons would be preferable in the design of permanent molecular magnets.
Polymerization of high-spin radicals leads to high-spin systems. However, our research showed that the gap of energy between the first and second spin states decreases with the number of units bonded when these are alternant hydrocarbons. On the other hand, it has been proved that, when the synthesis of macro-radicals follows the SU-CU- SU methodology (SU=spin-containing unit; CU=coupling unit), the SU and CU units keep their multiplicity once coupled. In that case, the energy gap between the spin states of the system can be described considering the energy gap of the spin states of the constitutive units.
McConnell-I theory is widely applied to describe ferromagnetic intermolecular interactions. Our research has revised systematically this approach. We have explored the existence of a magneto-structural relationship using pairs of well-known radicals (H2NO·, ·CH3 and ·C3H5) at different geometrical orientations. We demonstrated that McConnell-I model predicts correctly the spin preference of the ground state when the interacting spin-containing radical centers are placed in parallel planes and there are mainly TS interactions between them. However, in other cases, the prediction of the spin preference becomes very complex, and more detailed quantum calculations are required. Overall, we have demonstrated that this model must be used carefully when predicting the multiplicity of the through-space interaction between two radicals. Further, we evaluated whether McConnell-I theory could be applied to assess the magnetic character of real crystals on the subset of experimentally FM crystals of the α- nitronyl nitroxide (α-NN) family. We analyzed the closest contacts between two intermolecular ONCNO groups (atoms where the spin densities are mainly located) for
each chosen crystal. We concluded that the ONCNO interactions do not describe entirely the observed macroscopic magnetic property for all the systems. Consequently, TS interactions not considered in the simplistic ONCNO model must play an important role defining the magnetic character. Secondly, we proved there is not a simple magneto-structural relationship, such as the one suggested in McConnell-I model, that can be applied to all through-space interactions in the crystals. This conclusion was reached after a twofold statistical analysis (namely, factor and cluster analyses) of the geometrical parameters as a function of the calculated energy gap ΔES-T.
Charge-transfer salts are successful examples of molecular magnets. However, the formation of diamagnetic dimers of the donor species, [D]22+, or the acceptor species, [A]22-, causes the loss of the magnetic properties. We studied the causes of this dimerization studying the formation of TCNE dimers, [TCNE]22-], as a prototypical example of an organic acceptor. The Eint of two charged molecules has two components: the Coulomb contribution (Ecoul > 0, for molecules with the same charge) and the bonding energy (Ebond < 0). If the repulsion energy is higher than the bonding energy in absolute value (|Ecoul|>|Ebond|) the two molecules will repel and the formation of the dimer will not be stable (Eint > 0). However, if there is any force that counterbalances the repulsion between the two charged molecules, the bonding energy could overcome the repulsion energy in absolute value (|Ecoul|<|Ebond|), and the metastable minima would become stable (Eint < 0). The calculations performed described three metastable minima that agree with those observed experimentally. Besides, the spectroscopic features of each class of these three dimers have been calculated and are in agreement with the
available experimental data. Extended calculations performed in the presence of cations or polar solvents resulted in the stabilization of the dimers, which demonstrates that counterbalance of the repulsive energy is needed for the formation of these long multicenter bonds. The two electrons - four centers (2e-/4c) bond described is unique since it involves 2e- and takes place among four carbon atoms chemically equivalent.El objetivo de esta tesis ha sido estudiar computacionalmente las bases teóricas del magnetismo molecular para poder utilizar el conocimiento adquirido en el diseño de materiales magnéticos moleculares. Hemos analizado los mecanismos a través del enlace (TB: through-bond) y a través del espacio (TS: through-space) que estabilizan moléculas de alto spin (radicales) y sus interaccionan intermoleculares ferromagnéticas. Para llevar a cabo dichos estudios se han utilizado métodos híbridos como el Molecular Mechanics Valence Bond (MMVB), métodos DFT como el B3LYP y métodos ab-initio como MP2, CASSCF, y CASMP2. Así pues, por un lado, se ha estudiado la estabilidad de moléculas orgánicas de alto spin y su posible polimerización manteniendo su alta multiplicidad de spin. Se ha llegado a la conclusión que el mecanismo TS es de menor coste energético que el TB. Por lo tanto, los radicales cuyos centros de spin se estabilizan a través del enlace TB son más estables. Asimismo, compuestos que presentan ambos mecanismos, los estados de spin de los estados fundamental y primer excitado vendrán determinados por el mecanismo TS. Por otro lado, se estudiaron las interacciones intermoleculares entre radicales, con el objetivo de establecer las condiciones que favorecen las que son ferromagnéticas. En este contexto, se evaluó la teoría denominada McConnell-I. Tras metódicos estudios de la interacción entre dos radicales (H2NO·, ·CH3 y ·C2H6) en diferentes orientaciones en el espacio, se concluyó que el ámbito de aplicación de esta teoría está limitado a cuando los centros de spin interaccionan en planos paralelos y existe una interacción TS predominante. Estudios adicionales en cristales de la familia α-nitronil nitróxido demostraron que la teoría de McConnell-I no se puede aplicar de forma general a cualquier interacción intermolecular entre radicales. Se observó que esta teoría no predice correctamente el comportamiento magnético de cristales cuando se analiza sólo la interacción entre los átomos que contienen mayoritariamente la densidad de spin (ONCNO). Así pues, el estudio se debe ampliar a otros contactos entre las moléculas para poder describir correctamente el comportamiento magnético observado. Finalmente hemos establecido que, en sales de transferencia de carga, se dan casos de dimerización de las especies constituyentes, por ejemplo tetracianoetileno (TCNE), cuando la repulsión entre especies de la misma carga se minimiza por la presencia de contra-iones o disolventes polares. De esta manera, se favorece la formación del enlace en el dímero al permitir la interacción de los electrones desapareados.
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Chan, Hin Chung Stephen. "Polymorph prediction of organic (co-) crystal structures from a thermodynamic perspective." Thesis, University of Bradford, 2012. http://hdl.handle.net/10454/5530.
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A molecule can crystallise in more than one crystal structure, a common phenomenon in organic compounds known as polymorphism. Different polymorphic forms may have significantly different physical properties, and a reliable prediction would be beneficial to the pharmaceutical industry. However, crystal structure prediction (CSP) based on the knowledge of the chemical structure had long been considered impossible. Previous failures of some CSP attempts led to speculation that the thermodynamic calculations in CSP methodologies failed to predict the kinetically favoured structures. Similarly, regarding the stabilities of co-crystals relative to their pure components, the results from lattice energy calculations and full CSP studies were inconclusive. In this thesis, these problems are addressed using the state-of-the-art CSP methodology implemented in the GRACE software. Firstly, it is shown that the low-energy predicted structures of four organic molecules, which have previously been considered difficult for CSP, correspond to their experimental structures. The possible outcomes of crystallisation can be reliably predicted by sufficiently accurate thermodynamic calculations. Then, the polymorphism of 5- chloroaspirin is investigated theoretically. The order of polymorph stability is predicted correctly and the isostructural relationships between a number of predicted structures and the experimental structures of other aspirin derivatives are established. Regarding the stabilities of co-crystals, 99 out of 102 co-crystals and salts of nicotinamide, isonicotinamide and picolinamide reported in the Cambridge Structural Database (CSD) are found to be more stable than their corresponding co-formers. Finally, full CSP studies of two co-crystal systems are conducted to explain why the co-crystals are not easily obtained experimentally.
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Schulz, Benjamin, Daniela Täuber, Jörg Schuster, Thomas Baumgärtel, and Borczyskowski Christian von. "Influence of mesoscopic structures on single molecule dynamics in thin smectic liquid crystal films." Universitätsbibliothek Chemnitz, 2013. http://nbn-resolving.de/urn:nbn:de:bsz:ch1-qucosa-122240.
Full textAbstract:
Mesoscopic structures in liquids have an impact on the diffusion dynamics of the constituting molecules. Smectic 8CB liquid crystals on silicon wafers show the formation of mesoscopic structures on the μm scale at a film thickness of 200 nm. Depending on the kind of substrate (thermally grown or native SiOx), we observed the formation of focal conic domains (FCDs) and a new type of terraced holes, respectively. Dynamics are described via single perylene diimide tracer molecule tracking of translational diffusion and in the case of FCDs by a combination of translation and rotation detected via fluorescence correlation spectroscopy. Tailoring perylene diimide molecules such that the optical transition dipole moment follows the liquid crystal director allows mapping out FCDs and investigating the dynamics within a single FCD.
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Fu, Jie. "Molecular Structure-Nonlinear Optical Property Relationships for a Series of Polymethine and Squaraine Molecules." Doctoral diss., University of Central Florida, 2006. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/3941.
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This dissertation reports on the investigation of the relationships between molecular structure and two-photon absorption (2PA) properties for a series of polymethine and squaraine molecules. Current and emerging applications exploiting the quadratic dependence upon laser intensity, such as two-photon fluorescence imaging, three-dimensional microfabrication, optical data storage and optical limiting, have motivated researchers to find novel materials exhibiting strong 2PA. Organic materials are promising candidates because their linear and nonlinear optical properties can be optimized for applications by changing their structures through molecular engineering. Polymethine and squaraine dyes are particularly interesting because they are fluorescent and showing large 2PA. We used three independent nonlinear spectroscopic techniques (Z-scan, two-photon fluorescence and white-light continuum pump-probe spectroscopy) to obtain the 2PA spectra revealing 2PA bands, and we confirm the experimental data by comparing the results from the different methods mentioned. By systematically altering the structure of polyemthines and squaraines, we studied the effects of molecular symmetry, strength of donor terminal groups, conjugation length of the chromophore chain, polarity of solvents, and the effects of placing bridge molecules inside the chromophore chain on the 2PA properties. We also compared polymethine, squaraine, croconium and tetraon dyes with the same terminal groups to study the effects of the different additions inserted within the chromophore chain on their optical properties. Near IR absorbing squaraine dyes were experimentally observed to show extremely large 2PA cross sections ([approximately equal to] 30000GM). A simplified three-level model was used to fit the measured 2PA spectra and detailed quantum chemical calculations revealed the reasons for the squaraine to exhibit strong 2PA. In addition, two-photon excitation fluorescence anisotropy spectra were measured through multiple 2PA transitions. A theoretical model based on four-levels with two intermediate states was derived and used for analysis of the experimental data.Ph.D.
Other
Optics and Photonics
Optics
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McGregor, Pamela A. "Crystal structure studies of low-melting point organic compounds at low temperature and high pressure." Thesis, University of Edinburgh, 2003. http://hdl.handle.net/1842/11125.
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Hay, Duncan A. "Design and synthesis of small molecule chemical probes for bromodomain-containing proteins." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:04f6c56d-72de-4c32-b0fd-cc4bcdc996a8.
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Bromodomains (BRDs) are protein modules which bind to acetylated lysines on histones and transcriptional regulating proteins. BRD-containing proteins are involved in a large variety of critical cellular processes and their misregulation, or mutation of the genes encoding for them, has been linked to pathogenesis in humans. The generation of chemical probes (potent, selective and cell permeable small molecules) in cellular experiments to investigate the biological role of the BRDs is thus desirable. A chemical probe for the CREB (cyclic-AMP response element binding protein) binding-protein (CBP) and E1A binding protein (p300) BRDs was developed, starting from a low molecular weight, weak and non-selective dimethylisoxazole benzimidazole compound. Parallel synthesis was used to optimise the initial hit into a weak, but selective CBP inhibitor. Further modification of the two N-1 and C-2 moieties of the benzimidazole scaffold, led to highly potent and selective CBP inhibitors. Structure-guided design was then applied to optimise the selectivity of the series for CBP over the first domain of bromodomain-containing protein 4 BRD4(1). A strategy to reduce the flexibility of the N-1 and C-2 ethylene linker groups through the incorporation of conformational constraints led to inhibitors with increased selectivity. The optimal compound was highly potent for the CBP and p300 BRDs (Kd 21 nM and 32 nM, respectively) and selective over BRD4(1) (40-fold and 27-fold, respectively). On-target cellular activity was observed in a fluorescence recovery after photobleaching (FRAP) assay (0.1 μM), a p53 reporter gene assay (IC50 1.5 μM) and a Förster resonance energy transfer (FRET) assay (5 μM). A weak indolizine bromodomain-containing protein 9 (BRD9) inhibitor was used as the starting point for the development of a BRD9/BRD7 chemical probe. Analogues were synthesised via [3+2] cycloadditions. An optimised compound was found to be highly potent (68 nM) and selective over BRD4(1) (34-fold). On-target cellular activity was observed in a FRAP assay (5 μM). Efforts were made to improve the cellular activity through the introduction of an ionisable centre to aid solubility. A selection of piperazine analogues were shown to be potent and selective, and these compounds warrant further investigation of their selectivity and cellular activity. Overall, the work has led to the first potent and selective inhibitors of the CBP/p300 and BRD9 BRDs. It also highlights the role of structural analysis in the development of inhibitors that modulate protein-protein interactions.
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Leng, Siwei. "From Crystal to Columnar Discotic Liquid Crystal Phases: Phase Structural Characterization of Series of Novel Phenazines Potentially Useful in Organic Electronics." Akron, OH : University of Akron, 2009. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=akron1247614330.
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Dissertation (Ph. D.)--University of Akron, Dept. of Polymer Science, 2009."August, 2009." Title from electronic dissertation title page (viewed 9/23/2009) Advisor, Stephen Z. D. Cheng; Committee members, Alexei P. Sokolov, Gustavo A. Carri, Darrell H. Reneker, Weiping Zheng; Department Chair, Ali Dhinojwala; Dean of the College, Stephen Z. D. Cheng; Dean of the Graduate School, George R. Newkome. Includes bibliographical references.
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Schulz, Benjamin, Daniela Täuber, Jörg Schuster, Thomas Baumgärtel, and Borczyskowski Christian von. "Influence of mesoscopic structures on single molecule dynamics in thin smectic liquid crystal films." Soft Matter, 2011,7, S. 7431-7440, 2011. https://monarch.qucosa.de/id/qucosa%3A19943.
Full textAbstract:
Mesoscopic structures in liquids have an impact on the diffusion dynamics of the constituting molecules. Smectic 8CB liquid crystals on silicon wafers show the formation of mesoscopic structures on the μm scale at a film thickness of 200 nm. Depending on the kind of substrate (thermally grown or native SiOx), we observed the formation of focal conic domains (FCDs) and a new type of terraced holes, respectively. Dynamics are described via single perylene diimide tracer molecule tracking of translational diffusion and in the case of FCDs by a combination of translation and rotation detected via fluorescence correlation spectroscopy. Tailoring perylene diimide molecules such that the optical transition dipole moment follows the liquid crystal director allows mapping out FCDs and investigating the dynamics within a single FCD.
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Hammer, Sebastian Tobias [Verfasser], and Jens [Gutachter] Pflaum. "Influence of Crystal Structure on Excited States in Crystalline Organic Semiconductors / Sebastian Tobias Hammer ; Gutachter: Jens Pflaum." Würzburg : Universität Würzburg, 2021. http://d-nb.info/1240614845/34.
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Halut, Desportes Sabine. "Etude de complexes du MG2+ avec le méthanol et la pyridine par diffraction des rayons X et spectroscopie vibrationnelle." Paris 6, 1986. http://www.theses.fr/1986PA066408.
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Synthèse et caractérisation de differents complexes solides. Structures de MG CH3OH6 BR::(2), (MGPY::(4)CL::(2)), (MGPY::(4)BR::(2))PY::(2) (MG(H::(2)O)::(4)PY::(2))CL::(2), (MG(H::(2)O)::(3)PY::(3)) BR::(2)PY::(2) ET (MG(H::(2)O)::(2)PY::(4))I::(2)PY::(2). Analyse des spectres IR de M(ROH)::(6) X::(2), M(ROH)::(4)X::(2) (AVEC M = MG,CA; R = CH::(3),C::(2)H::(5); X = CL,BR) ET DE MG(PY)::(4) CL::(2) ET M(PY)::(4)X::(2)PY::(2) (M = CA,MG)
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Semyonov, Alexander N. "Design, Synthesis and Characterization of Fluorescent Dyes and Liquid Crystal Semiconductors." Kent State University / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=kent1153556141.
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Essandoh, Ernest. "Structural studies of organic crystals of pharmaceutical relevance : correlation of crystal structure analysis with recognised non-bonded structural motifs in the organic solid state." Thesis, University of Bradford, 2009. http://hdl.handle.net/10454/4444.
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Pharmaceutical solids tend to exist in different physical forms termed as polymorphs. Issues about pharmaceutical systems are mainly concerned with the active ingredient's physico-chemical stability and bioavailability. The main aim of this study is to investigate the non-bonded interactions in pharmaceutical solids that govern the physical pharmaceutics performance of such materials and through the use of structural techniques and correlation of these results with crystal structural database to establish the presence of physical motifs in selected systems. Structural motifs were identified by the use of single crystal and crystal packing analysis on diverse range of pharma-relevant materials including chalcones, cryptolepines, biguanides and xanthines. These selected systems were validated using functional group and molecular analysis and correlating them to the Cambridge Structural Database. Crystallization studies are done on these selected systems as well as exploiting those using synthetic analogues. A total of 51 crystal structures were investigated including 16 new structure determinations. Addition synthesis of new xanthines to investigate novel intermolecular patterns was also undertaken. The understanding and exploitation of intermolecular interactions involving hydrogen bonds and coordination complexation during packing can be used in the design and synthesis of solid state molecular structures with desired physical and chemical properties.
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Byrichetti, Kiranmai. "Synthesis and Structure of a Substituted Pyridazine." TopSCHOLAR®, 2011. http://digitalcommons.wku.edu/theses/1080.
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Pyridazines are heterocyclic compounds with an N-N bond in their ring structure. Heterocyclic aromatic compounds are of great interest as a result of their novel properties and commercial applications. Our current research is focused on the potential role of pyridazines in next generation electronic devices that utilize organics as the semiconducting material. The synthesis of 5, 6-fused ring pyridazines beginning from fulvenes (Scheme 1) is described herein. These fused heterocycles will serve as synthetic models and building blocks for potential organic or organometallic conducting polymers.
Our goal was to modify the route of Snyder et al. previously reported for the direct synthesis of pyridazine 2. This required improved synthesis of fulvene 1 and higher yields of 5. Additionally, a thorough analysis of the x-ray data was obtained to better understand the 3D aspects of this compound (pyridazine 2).This route was quite general and features an efficient and convenient synthesis.
Single crystal X-ray analysis confirms the molecular structure of pyridazine 2. Full synthesis and characterization of newly formed pyridazine 2 and Fulvene 1 are reported.
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Combet, Jérôme. "Désordre moléculaire dans les composés d'inclusion du tano : une approche par diffusion des rayons X et diffusion quasi élastique incohérente des neutrons." Université Joseph Fourier (Grenoble ; 1971-2015), 1997. http://www.theses.fr/1997GRE10185.
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Le nitroxide c#9h#1#6no#2 (tano) forme des composes d'inclusion a canaux avec une grande variete de chaines lineaires (alcanes, monobromo alcanes. . . ). Les molecules de tano (reseau hote) s'organisent de facon a creer des canaux dans lesquels les molecules viennent s'inserer. A temperature ambiante, les molecules de tano et les chaines invitees sont dynamiquement desordonnees. Les cliches de diffraction de rayons x revelent la presence de plans diffus, perpendiculaires a l'axe b, caracteristiques de la nature des molecules incluses et typiques de la diffusion par des chaines de molecules non correlees. L'analyse du profil de diffusion met en evidence l'existence d'un ordre positionnel a courte distance le long des canaux. Les composes monobromes presentent de plus un ordre substitutionnel a courte portee. La projection de la structure parallelement a l'axe des canaux montre un desordre orientationnel des chaines autour de leur axe. Ce phenomene est egalement observe en diffusion quasi elastique incoherente des neutrons. Outre le desordre des molecules incluses, les molecules de tano peuvent adopter l'une ou l'autre des deux formes enantiomeres par inversion dynamique du cycle piperidinique. Chacun des groupements methyles effectue egalement des reorientations de 120 autour de leur position d'equilibre. Cette structure hautement desordonnee est marquee par l'apparition d'une ou deux transitions de phase selon la longueur des molecules incluses. Le mecanisme de transition est relie au blocage simultane des molecules de tano (inversion du cycle) et des molecules incluses, resultant de fortes correlations entre les deux sous reseaux.
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Garg, Akhilesh. "Organic Self-Assembled Films for Nonlinear Optics: Film Structure, Composition and Kinetics of Film Formation." Diss., Virginia Tech, 2008. http://hdl.handle.net/10919/28872.
Full textAbstract:
Organic materials exhibiting second-order non-linear optical (NLO) properties are a key to the development of advanced electro-optic (EO) modulators used in fiber-optic communications system. This work addresses the fabrication and characterization of organic materials with NLO properties using a self-assembly approach by alternately dipping a charged substrate into positively and negatively charged polymers to build up layer-by-layer (LbL) films.
The effect of solution pH on the formation of LbL films fabricated using the polycation poly(allylamine hydrochloride) (PAH) and the polyanion poly{1-[p-(3–-carboxy-4–-hydroxyphenylazo)benzenesulfonamido]-1,2-ethandiyl} (PCBS) was studied using a quartz crystal microbalance with dissipation (QCM-D) monitoring, ellipsometry, absorbance, and second harmonic generation (SHG) measurements. PCBS has an azo-benzene chromophore side group that, when sufficiently oriented, results in measurable SHG. Films of PAH/PCBS fabricated at neutral pH where both PAH and PCBS are highly charged led to thin bilayers, ~1 nm, with a 1:1 molar ratio of PCBS:PAH. This molar ratio was found to be important for long-range polar ordering of PCBS in these films. Increasing the rate of convection was found to reduce the time required for complete adsorption of the polyion. This can have a significant impact on fabrication of films with high bilayer numbers.
A variation of the above technique, which involves adsorbing one of the constituents electrostatically and another covalently, was studied using PAH and a reactive dye, Procion Brown (PB), which has a significantly higher hyperpolarizability than PCBS. It was found that a high pH, ~10.5, was important for achieving covalent attachment of the PB to the underlying PAH films. This resulted in much higher SHG intensities compared to when PB was deposited pH at 8.5-9.5 where the attachment of PB was due to a combination of electrostatic and covalent interactions. QCM-D results for PAH/PB films revealed the presence of a high percentage of unreacted amine groups in the underlying PAH film. A rate constant value for PB attachment step to the underlying PAH was also calculated.
To enhance the SHG intensity of these films, silver nanoprisms were synthesized and deposited onto films using physisorption. An enhancement in the SHG intensity was observed for both PAH/PCBS and PAH/PB films.Ph. D.
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Zhang, Teng. "Synchrotron radiation study of free and adsorbed organic molecules." Licentiate thesis, Uppsala universitet, Molekyl- och kondenserade materiens fysik, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-307787.
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In this licentiate thesis, organic molecules, namely Cobalt Phthalocyanine (CoPc) and Biphenylene, have been studied by means of synchrotron radiation-based spectroscopic methods (Photoemission Spectroscopy (PES) and X-ray Absorption Spectroscopy (XAS) in combination with Density Functional Theory (DFT) calculations. Paper I is a combined experimental and theoretical investigation of electronic structure of CoPc. addressing the atomic character of the Highest Occupied Molecular Orbital (HOMO) and the electronic configuration of the molecular ground state. Both these aspects are still under discussion since different experimental and theoretical studies have given controversial results. Previous works have indicated the CoPc ground state to either be described by the 2A1g or 2Eg, or by a mix of the two electronic configurations. Regrading the debated the atomic character of the HOMO of CoPc, it has been suggested to be either metal 3d-like and localized on the central Co atom or originating in the organic ligand of the molecule. In this thesis the valence photoemission results for CoPc in gas phase and as adsorbed films on Au(111) together with the DFT simulations, consistently indicate that the HOMO is derived only by the organic ligand, with mainly contribution from the carbon atoms with no metal character. Moreover, the good agreement between the experimental and theoretical results, confirms that the ground state of CoPc is correctly described by the 2A1g configuration. In Paper II, PES and XAS have been used to investigate the occupied and empty density of states of biphenylene films of different thicknesses, deposited onto a Cu(111) crystal. The results have been compared to previous gas phase spectra and single molecule Density Functional Theory (DFT) calculations to get insights into the possible modification of the molecular electronic structure in the film induced by the adsorption on a surface. Furthermore, XAS measurements allowed the characterizion of the variation of the molecular arrangement with the film thickness and helped to clarify the substrate-molecule interaction.
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Zhang, Shi-Yuan. "Homochiral Metal-Organic Materials: Design, Synthetic and Enantioseletive Separation." Scholar Commons, 2014. https://scholarcommons.usf.edu/etd/5163.
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Owing to the growing demand for enantiopurity in biological and chemical processes, tremendous efforts have been devoted to the synthesis of homochiral metal-organic materials (MOMs) because of their potential applications in chiral separation and asymmetric catalysis. In this dissertation, the synthetic strategies for homochiral MOMs are discussed keeping the focus on their applications. Two distinct approaches have been taken to synthesize chiral structures with different topologies and accessible cavities. The chiral MOMs have been utilized in enantioselective separation of racemates.
Chiral variants of the prototypal metal-organic framework MOF-5, δ-CMOF-5 and [lambda]-CMOF-5, have been synthesized by preparing MOF-5 in the presence of L-proline or D-proline, respectively. CMOF-5 crystallizes in chiral space group P213 instead of Fm-3m as exhibited by MOF-5. The phase purity of CMOF-5 was validated by single crystal and powder X-ray diffraction, IR spectroscopy, TGA, N2 adsorption, microanalysis and solid-state CD. CMOF-5 undergoes a reversible single crystal to single crystal phase change to MOF-5 when immersed in a variety of organic solvents although N-methyl-2-pyrolidone, NMP, does not induce loss of chirality. Indeed, MOF-5 undergoes chiral induction when immersed in NMP, affording racemic CMOF-5.
A pair of homochiral network materials (CNMs), [Co2(S-man)2(bpy)3](NO3)2·guests (1S) and [Co2(R-man)2(bpy)3](NO3)2·guests (1R) based upon S-mendelic acid and R-mendelic acid were synthesized and characterized, respectively. The cationic networks contain 1D homochiral channels with the cross section of 8.0 Å × 8.0 Å. The chiral amphiphilic channel surfaces lined with hydrophilic nitrate anions and hydrophobic phenyl groups are capable for multiple interactions with guest species. Chiral resolution of 1-phenyl-1-propanol (PP) enantiomers was performed utilizing the homochiral porosity of 1S and 1R through different time period at different temperatures with/without additives. The mechanism for enantioselective separation of PP was fully investigated through single crystal structural analysis of guest exchanged 1S and 1R. Chiral resolution of PP revealed enhanced performance with additive, which can significantly improve the ee value from 32% to 60%.
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Kress, Brian J. "Synthesis of Novel Small Molecule PPARδ Agonists for Controlling Mesenchymal Stem Cell Osteogenesis." University of Toledo Health Science Campus / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=mco1564751044043639.
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