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This thesis describes the development of new osmium-mediated methodologies providing novel applications through the use of a third generation of reoxidant for osmium. Chapter 1, The introduction: Summary of past and present methodologies towards the synthesis of the 1,2 amino alcohol motif. Chapter 2, Intramolecular processes: The studies of the tethered aminohydroxylation (TA) of amide and urea derivatives are being investigated. Chapter 3, Investigations towards an intermolecular process: The transposition of the TA methodology to an intermolecular process and the requirements involved are discussed. The role of acetamide is being investigated. Chapter 4, Successful transition to an intermolecular process: Amino acid derivatives became for the first time possible nitrogen sources and were efficiently employed through osmium-mediated reaction to afford interesting biological scaffolds. Chapter 5, Experimental: Full experimental procedures and characterisation of compounds are reported. References: A complete list of citations employed in the previous five chapters is provided. Appendix: Full documentation of X-ray crystal structures, key NMR spectra and HPLC traces is provided.

Water and methanol are common solvents used in liquid chromatographic (LC) separations. It is highly desirable to model .the interactions of these solvents in order to better understand the nature of analyte solvation and its effect on retention. Therefore, structure and frequencies of complexes of these solvent molecules have been studied from a theoretical perspective as a first step in this direction. Specifically, cluster structures have been optimized at the RHF and MP2 levels in various flexible basis sets and with the counterpoise correction for basis set superposition error, and trends in the structure and binding energies of several clusters are described. Good agreement wasobtained for the water dimer with the experimental value for the binding energy of D20 using MP2 energies from 6-3 11G**/6-3 l+G** basis sets in conjunction with counterpoise optimizations and full counterpoise corrections. In this investigation harmonic frequencies have been calculated and corrected for the effects of anharmonicity by several methods, two of which are original. The first new method fits a Morse potential function to the energy computed along each normal mode. A second new method is based on fitting a quartic polynomial to energies computed along each normal mode. In cases where the quartic potential function is not very different from the harmonic well, a second order perturbation formula provides a reasonable approximation to the anharmonic vibrational frequencies. When the quartic potential is very far from the harmonic potential, a variational treatment of the vibrations is required. We find that the Morse method delivers reasonable estimates of frequencies of anharmonic motions at lower cost than multi-point potential mapping/multiple geometry optimization/Taylor series methods, and is more successful at predicting intermolecular frequencies than the anharmonic VSCF methods found in GAMESS software. Variational calculations using the quartic polynomials produce estimates of frequencies comparable to the more costly VSCF method. Both the Morse method and polynomial method are very fast computationally relative to these and other methods found in the literature.

Doctor of Philosophy / Department of Chemistry / Christer B. Aakeroy / A family of three 2-aminopyrazine derivatives were prepared and co-crystallized with thirty carboxylic acids. Our theoretical charge calculations and experimental results from 90 reactions demonstrated that decreasing the charge on the hydrogen-bond acceptor sites results in a decrease of the supramolecular yield (the frequency of occurrence of the desired outcome). However, synthon crossover (undesired connectivity) was observed 7/12 times and was unavoidable due to competitive binding sites present in the N-heterocyclic bases chosen. To avoid synthon crossover, we used a strategy based on geometric bias. We utilized hydrogen-bonding two-point contacts and halogen-bonding single-point contacts for supramolecular reactions with the 2-aminopyrazine family of compounds. The desired two-point contact and single-point contact (N•••I or N•••Br) appeared in 9/9 times even in the presence of other potentially interfering intermolecular interactions. In addition, the role of charge in controlling the presence/absence of proton transfer was also highlighted. To establish a hierarchy in halogen-bonding interactions we designed and synthesized a library of eight molecules equipped with two different halogen bond donors and combined with variety of halogen-bond acceptors. 11 Halogen-bonded co-crystals were obtained; however, positional disorder of I/Br atoms obscures a complete analysis. This problem was solved by introducing asymmetry in the halogen-bond donor molecules. Finally, successfully demonstrated an unprecedented hierarchy in halogen-bond interactions based on electrostatics. We developed high-yielding Suzuki-Miyaura coupling reactions of tetraboronic pinacolyl ester cavitand to iodoarenes with a range of functional groups (electron withdrawing/donating group and a heterocycle) that show robustness and versatility, making it a ‘launch pad’ for the synthesis of many new cavitands in a facile manner. We have also successfully demonstrated cavitand functionalization from tetraaldehyde to tetraoximes using ‘solvent assisted grinding’, irrespective of the position of the aldehyde. Finally, we prepared tetra-substituted pyridyl and carboxylic acid cavitands having an ellipsoidal cavity capable of encapsulating asymmetric guest molecules and was subsequently obtained the first of its kind, C[subscript]2v symmetric molecular capsule with encapsulated asymmetric guest molecule.

A study of Molecular Dynamics using computational methods and modeling provides the understanding on the interaction of the atoms, properties, structure, and motion and model phenomenon. There are numerous commercial tools available for simulation, analysis and visualization. However any particular tool does not provide all the functionalities. The main objective of this work is the development of the visualization tool customized for our research needs to view the three dimensional orientation of the atom, process the simulation results offline, able to handle large volume of data, ability to display complete frame, atomic trails, and runtime response to the researchers' query with low processing time. This thesis forms the basis for the development of such an in-house tool for analysis and display of simulation results based on Open GL and MFC. Advantages, limitations, capabilities and future aspects are also discussed. The result is the system capable of processing large amount of simulation result data in 11 minutes and query response and display in less than 1 second. / by Meha Garg. / Thesis (M.S.C.S.)--Florida Atlantic University, 2010. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2010. Mode of access: World Wide Web.

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O tema interações intermoleculares é um conceito central dentro do conhecimento químico por permitir, por exemplo, a interpretação de uma série de transformações e propriedades físicas dos materiais. Considerando a carência de estudos que investigam especificamente os processos de ensino e aprendizagem em nível superior, a presente pesquisa objetivou analisar o aprendizado de graduandos em química durante uma disciplina de química geral I, relacionando-o as aulas ministradas aos alunos e a abordagem do tema nos livros didáticos sugeridos para estudo. Para isso, as aulas da disciplina, oferecidas aos alunos ingressantes do curso de química do Instituto de Química da Universidade de São Paulo, foram acompanhadas e gravadas em vídeo; os estudantes responderam alguns questionários para o levantamento das principais dificuldades e lacunas na aprendizagem e os livros didáticos sugeridos foram analisados através de mapas conceituais. A análise dos livros mostrou a complexidade e amplitude do tema por apresentar uma rede de relações conceituais extensa e distribuídas ao longo de diferentes capítulos. Nas análises dos livros e das aulas chamou atenção a abordagem classificatória com que o tema é tratado começando pelas interações que envolvem moléculas polares e depois interações entre moléculas apolares. Na análise das explicações dos alunos foi possível perceber a presença de várias dificuldades ou lacunas como na interpretação das equações das energias potenciais das interações e identificação dos tipos de interações que atuam em distintos contextos. A partir das análises foi feita uma triangulação dos dados que permitiu elencar ideias fundamentais que os alunos precisam compreender sobre o tema sendo essas relacionadas a: uma melhor compreensão da estrutura molecular considerando a geometria da molécula e a distribuição da densidade eletrônica na mesma, parâmetro expresso pelos conceitos polaridade, polarizabilidade e nuvem eletrônica (propriedades moleculares); necessidade de fazer uma correta diferenciação entre as interações intermoleculares e as ligações químicas; compreender que as mudanças de estado físico estão correlacionadas aos diferentes tipos de interações intermoleculares que atuam nos sistemas; entender que vários tipos de interações intermoleculares podem estar atuando no mesmo sistema e que as forças dispersivas de London são universais; interpretar as equações das energias potenciais que são diretamente proporcionais a propriedade molecular e inversamente a distância; interpretar os valores de energia típicos das interações e também relacionar a intensidade e o alcance; considerar nas ligações de hidrogênio a direcionalidade da interação e a necessidade de sítios para esse tipo de interação (pares de elétrons livres). Essas ideias integraram sugestões para o ensino do tema que vão desde a repensar a forma como as interações intermoleculares são ensinadas na química geral até uma possível retomada da abordagem do tema em disciplinas mais avançadas ampliando e ressignificando a compreensão dos conceitos. Defende-se aqui a necessidade de superar o ensino classificatório do tema interações intermoleculares abordando separadamente os tipos de interações intermoleculares: íon-dipolo, dipolo-dipolo, dipolo-dipolo induzido, forças dispersivas de London e ligação de hidrogênio para um ensino com ênfase na estrutura molecular e propriedades moleculares. / The subject of intermolecular interactions is a central concept within the chemical knowledge because it allows, for example, the interpretation of a series of transformations and physical properties of the materials. Considering the lack of studies that specifically investigate teaching and learning processes at the higher level, the present study is aimed at analyzing the chemistry students\' learning in during a general chemistry course, relating the classes given to the students and the approach to the subject suggested textbooks for study. For this, the classes of the course, offered to the incoming chemistry\'s course students of the Institute of Chemistry of the University of São Paulo, were accompanied and recorded in video; the students answered some questionnaires to survey the main difficulties and gaps in learning and the suggested textbooks were analyzed through concept maps. The analysis of the books showed the complexity and amplitude of the theme by presenting a network of extensive conceptual relationships distributed throughout different chapters. In the analysis of books and classes, the classificatory approach with which the topic is treated, starting with the interactions involving polar molecules and then interactions between apolar molecules, was called attention. In the analysis of the students\' explanations, it was possible to perceive the presence of several difficulties or gaps as in the interpretation of the equations of the potential energies of the interactions and identification of the types of interactions that operate in different contexts. From the analyzes, a triangulation of the data was made which allowed to list fundamental ideas that the students need to understand about the subject being related to: a better understanding of the molecular structure considering the geometry of the molecule and its distribution of the electronic density in, expressed parameter by the concepts polarity and polarizability and electronic cloud (molecular properties); the need to make a proper differentiation between intermolecular interactions and chemical bonds; to understand that the changes of physical state are correlated to the different types of intermolecular interactions that operate in the systems; to understand that various types of intermolecular interactions may be operating in the same system and that London\'s dispersive forces are universal; interpret the equations of potential energies that are directly proportional to the molecular property and inversely the distance; interpret the energy values typical of the interactions and also relate intensity and range; to consider in the hydrogen bonds the directionality of the interaction and the need of sites for this type of interaction (free electron pairs). These ideas have included suggestions for teaching the subject, ranging from rethinking how intermolecular interactions is taught in general chemistry to a possible resumption of the subject approach in more advanced courses by broadening and redefining the understanding of concepts. It is argued here the need to overcome classificatory teaching of intermolecular interactions by addressing separately the types of intermolecular interactions: ion-dipole, dipole-dipole, dipole-induce dipole, London\'s dispersive forces and hydrogen bonding for teaching with an emphasis on molecular structure and molecular properties.

We have used ab initio computational simulation techniques to investigate both intra- and intermolecular interactions in a novel family of ionic organophosphonate molecular crystals. We have examined the influence of various numerical approximations on the computed geometry and binding energies of a selection of well-characterised hydrogen bonded systems. It was found that numerical basis sets provided the efficiency required to study the large hydrogen bonded dimer anions present in the organophosphonate system, while also producing accurate geometries and binding energies. We then calculated the relaxed structures and binding energies of phenylphosphonic acid dimer in the two arrangements in which it is present in the bulk crystal. The computed geometries were in excellent agreement with the experimental structures and the binding energies were consistent with those found for other ionic hydrogen bonded systems. Electron density maps were used to gain insight into the nature of the hydrogen bonding interaction between phenylphosphonic acid dimers. We also examined the effect of aromatic ring substituents on the geometry and energetics of the hydrogen bonding interaction. The nitro-substituted dimer was predicted to have a stronger binding energy than its unsubstituted parent while the methyl-substituted dimer was predicted to have a similar binding energy to its unsubstituted parent. An analysis of crystal field effects showed that the structure of the phenylphosphonic acid dimers in the organophosphonates is a complex product of competing intra- and intermolecular forces and crystal field effects. Cooperative effects in the organophosphonate system were also investigated and it was found that the interactions were mostly one-body (local) in nature. We have examined the intramolecular charge-transfer interaction between copper-halogen cations in the organophosphonate materials. The origin of geometric differences between the Cu(I) starting material and Cu(II) product cations was attributed to the electronic configuration of the Cu ion, not crystal field effects. To gain further insight into the difference in electronic structure between the starting material and product, we attempted to simulate the step-by-step dissociation of the [CuI]+ system. Although this investigation was not successful, we were able to expose some of the pitfalls of simulating dissociating odd-electron systems. We also analysed and compared the charge-transfer interaction in the chloro-, bromo- and iodo-forms of the organophosphonate family. The charge-transfer interaction was predicted to increase on going from the chloro- to the iodo-form, consistent with solid-state UV-visible data. Finally, we used the highly accurate Quantum Monte Carlo (QMC) method to investigate the hydrogen bonding interaction in water dimer and to calculate the dissociation energy. The accuracy of the experimental estimate for the dissociation energy has recently been questioned and an alternative value has been put forward. Our results lend support to the validity of the alternative value and are also in excellent agreement with those from other high-level calculations. Our results also indicate that QMC techniques are a promising alternative to traditional wavefunction techniques in situations where both high accuracy and efficiency are important.

<p>This work presents first-principles calculations of long-range intermolecular dispersion energies between two atoms or molecules as expressed in terms of the C₆ dipole-dipole dispersion coefficients. In a series of publications, it has been shown by us that the complex linear polarization propagator method provides accurate <em>ab initio</em> and first-principles density functional theory values of the C₆ dispersion coefficients in comparison with those reported in the literature. The selected samples for the investigation of dispersion interactions in the electronic ground state are the noble gases, <em>n</em>-alkanes, polyacenes, azabenzenes, and C₆₀. It has been shown that the proposed method can also be used to determine dispersion energies for species in their respective excited electronic states. The C₆dispersion coefficients for the first <em>π</em> → <em>π*</em> excited state of the azabenzene molecules have been obtained with the adopted method in the multiconfiguration self-consistent field approximation. The dispersion energy of the <em>π</em> → <em>π*</em> excited state is smaller r than that of the ground state. It is found that the characteristic frequencies ω₁ defined in the London approximation of <em>n</em>-alkanes vary in a narrow range and that makes it possible to construct a simple structure-to-property relation based on the number of -bonds for the dispersion interaction in these saturated compounds. However, this simple approach is not applicable for the interactions of the <em>π</em>-conjugated systems since their characteristic frequencies <em>ω</em>₁ vary strongly depending on the systems.</p> / Report code: LIU-TEK-LIC-2006:2

The virial equation of state p = ρRT[ 1 + B(T) ρ + C(T) ρ2 + · · ·] for high pressure and density gases is used for computing chemical equilibrium properties and mixture compositions of strong shock and detonation waves. The second and third temperature-dependent virial coefficients B(T) and C(T) are included in tabular form in computer codes, and they are evaluated by polynomial interpolation. A very accurate numerical integration method is presented for computing B(T) and its derivatives for tables, and a sophisticated method is introduced for interpolating B(T) more accurately and efficiently than previously possible. Tabulated B(T) values are non-uniformly distributed using an adaptive grid, to minimize the size and storage of the tables and to control the maximum relative error of interpolated values. The methods introduced for evaluating B(T) apply equally well to the intermolecular potentials of Lennard-Jones in 1924, Buckingham and Corner in 1947, and Rice and Hirschfelder in 1954.