Thesis (Ph.D)--Chemistry and Biochemistry, Georgia Institute of Technology, 2010. / Committee Chair: Weck, Marcus; Committee Member: Breedveld, Victor; Committee Member: Fahrni, Christoph; Committee Member: Kelly, Wendy; Committee Member: Lyon, L. Andrew. Part of the SMARTech Electronic Thesis and Dissertation Collection.

Thesis (Ph. D.)--University of Chicago, Department of Chemistry, August 2002. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--University of Chicago, Department of Chemistry, August 2002. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--Ohio State University, 2009. / Title from first page of PDF file. Includes vita. Includes bibliographical references (p. 152-162).

Thesis (Ph. D.)--Ohio State University, 2005. / Title from first page of PDF file. Includes bibliographical references (p. 193-213).

This thesis describes the synthesis of macrocyclic and interlocked receptors which exploit halogen- and hydrogen-bonding intermolecular interactions for anion recognition. <strong>Chapter One</strong> introduces the field of supramolecular chemistry, with particular focus on applications of host–guest chemistry to anion coordination and anion templation in the construction of mechanically interlocked molecules. <strong>Chapter Two</strong> details the synthesis of a series of cyclic and cage-like porphyrin-based receptors which bind anions through halogen- and hydrogen-bonding interactions. The ability of these receptor systems to bind and sense anionic guest species is investigated and comparisons between hydrogen- and halogen-bonding are discussed. <strong>Chapter Three</strong> reports anion-templated pseudorotaxane assemblies stabilised by both halogen- and hydrogen-bonding. The related catenanes are also prepared and their affinity for anions is investigated. The first examples of interpenetrated and interlocked architectures constructed by a single charge-assisted halogen bond are also reported. <strong>Chapter Four</strong> describes the synthesis of a 1,3-dialkyl-1,2,3-triazolium-containing threading component, whose anion binding properties are studied and compared with other threading molecules. The ability of this novel thread to form pseudorotaxanes is investigated and the preparation of the related rotaxane species is outlined. <strong>Chapter Five</strong> discusses attempts to prepare rotaxanes with improved anion binding affinities through increasing the lipophilicity of the anion binding clefts. Several novel rotaxanes are described and their anion binding properties are probed. <strong>Chapter Six</strong> describes the experimental procedures used in this work and the characterisation of compounds presented in chapters two to five. <strong>Chapter Seven</strong> summarises the conclusions of this thesis.

Bidentate ligands are a commonly used class of ligands in catalysis that generate highly-active and selective catalysts. Such bidentate ligands, however, often suffer from synthetic challenges, which can be alleviated by the use of simpler monodentate ligands that assemble through non-covalent interactions to mimic the structure of bidentate ligands at the metal center. To produce a strongly assembled catalyst complex, the Hamilton receptor motif was utilized. Hamilton receptors form six hydrogen bonds with complementary guests and have binding affinities for barbiturates of up to 104 M-1 in CDCl3. Complete bifurcation of the Hamilton scaffold produces a modular ligand structure that allows for modification of either end of the supramolecular ligand structure. Similarly, the barbiturate guest can be synthetically altered creating both chiral guests and guests with differing amounts of steric bulk. Both experimental titration data and density functional theory calculations show that steric bulk discourages binding of the guest while a pre-organized host encourages guest inclusion. Electronic effects on the bifurcated Hamilton system were studied by varying the electron donating or withdrawing ability of the benzamide moiety on the host molecule. Electron withdrawing moieties produce more acidic amide hydrogens on the host which are able to participate in stronger hydrogen bonds with the guest resulting in a stronger host-guest complex. The effects of substitutions on the barbiturate guest were examined as well, and increased steric bulk on the guest resulted in decreased affinities with the host. The bifurcated Hamilton receptor ligands were examined in the palladium-catalyzed Heck reaction of iodobenzene with butyl acrylate. Pd2(OAc)4 was used as a control and all reaction yields with the diphenylphosphine ligand-stabilized Pd were greater than or equal to those obtained with Pd2(OAc)4 alone. The reaction rates did not correlate with the determined binding constants, suggesting that phosphine substitution on the guest plays a larger role than affinity of the complex for the guest. Reaction temperatures were varied, and at lower temperatures the yields increased implying that the strength of the hydrogen bonds between the metal complex and the guest does play a secondary role in the catalysis. This dissertation includes previously published co-authored material.

abstract: This thesis is devoted to the theoretical and computational study of electron transport in molecular junctions where one or more hydrogen bonds are involved in the process. While electron transport through covalent bonds has been extensively studied, in recent work the focus has been shifted towards hydrogen-bonded systems due to their ubiquitous presence in biological systems and their potential in forming nano- junctions between molecular electronic devices and biological systems. This analysis allows us to significantly expand our comprehension of the experimentally observed result that the inclusion of hydrogen bonding in a molecular junc- tion significantly impacts its transport properties, a fact that has important implications for our understanding of transport through DNA, and nano-biological interfaces in general. In part of this work I have explored the implications of quasiresonant transport in short chains of weakly-bonded molecular junctions involving hydrogen bonds. I used theoretical and computational analysis to interpret recent experiments and explain the role of Fano resonances in the transmission properties of the junction. In a different direction, I have undertaken the study of the transversal conduction through nucleotide chains that involve a variable number of different hydrogen bonds, e.g. NH···O, OH···O, and NH···N, which are the three most prevalent hydrogen bonds in biological systems and organic electronics. My effort here has fo- cused on the analysis of electronic descriptors that allow a simplified conceptual and computational understanding of transport properties. Specifically, I have expanded our previous work where the molecular polarizability was used as a conductance de- scriptor to include the possibility of atomic and bond partitions of the molecular polarizability. This is important because it affords an alternative molecular descrip- tion of conductance that is not based on the conventional view of molecular orbitals as transport channels. My findings suggest that the hydrogen-bond networks are crucial in understanding the conductance of these junctions. A broader impact of this work pertains the fact that characterizing transport through hydrogen bonding networks may help in developing faster and cost-effective approaches to personalized medicine, to advance DNA sequencing and implantable electronics, and to progress in the design and application of new drugs. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2017

Submitted by Irene Nascimento (irene.kessia@ufpe.br) on 2016-07-21T15:56:16Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Machado CMB_Configuração Absoluta e Deslocamentos Químicos de Moléculas Organicas por GIAO DFT.pdf: 4055624 bytes, checksum: 78784f0f10b901b4372dd2e2a038b173 (MD5) / Made available in DSpace on 2016-07-21T15:56:16Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Machado CMB_Configuração Absoluta e Deslocamentos Químicos de Moléculas Organicas por GIAO DFT.pdf: 4055624 bytes, checksum: 78784f0f10b901b4372dd2e2a038b173 (MD5) Previous issue date: 2016-04-06 / Facepe / Nesta dissertação, estudamos quatro moléculas quirais através do emprego de quatro funcionais da densidade diferentes com vinte funções de base para encontrar uma combinação que melhor descrevesse o ângulo de rotação óptica destas moléculas. Analisamos também como a ligação de hidrogênio pode influenciar no ângulo de rotação óptica e quais seriam os efeitos dessa ligação de hidrogênio nas propriedades de diferentes sistemas envolvendo compostos nitrogenados cíclicos e ácidos carboxílicos. Os funcionais empregados foram: B3LYP, PBE, PBE0 e ωB97XD; e as funções de base foram: 6-31G, 6-31+G, 6-31++G, 6-31G*, 6-31+G*, 6-31++G*, 6-31G**, 6-31+G**, 6-31++G**, cc-pVDZ, cc-pVTZ, cc-pVQZ, aug-cc-pVDZ, aug-cc-pVTZ, aug-cc-pVQZ, def2-TZVP, def2-TZVPD, def2-TZVPP, def2-TZVPPD e 6-311+G**. As moléculas quirais estudadas para a atribuição da configuração absoluta foram a R,R-dimetiloxirano, S-metiloxirano, S-halotano e (S)(+)4-fenil-2-oxazolidinona. As moléculas estudadas para a espectroscopia de RMN de 1H e cálculos GIAO foram a 1,10-fenantrolina, 2,2-bipiridina, 4,4’-difenil-2,2’-bipiridina e os ácidos carboxílicos: fórmico, acético e benzoico. As geometrias de todas as moléculas e complexos foram otimizadas para que não houvesse nenhuma frequência harmônica imaginária e, a partir delas, o ângulo de rotação óptica foi calculado. Para a molécula (S)(+)4-fenil-2-oxazolidinona, foi observada a possibilidade de formação de dímeros que podem influenciar no valor do ângulo de rotação óptica. As conformações possíveis para esse dímero foram encontradas utilizando mecânica molecular (MMFF - Merck Molecular Force Field) pelo programa SPARTAN 14, tendo suas geometrias sido na sequência otimizadas. As energias de estabilização de todos os complexos foram corrigidas levando em consideração os erros de sobreposição do conjunto de base (BSSE) e da energia do ponto zero (ZPE). O cálculo do ângulo de rotação óptica foi feito com o uso da média de Boltzmann. Todas as moléculas quirais foram estudadas no modo isolado e em clorofórmio através do método PCM. Observamos que moléculas simples, rígidas e sem possibilidade de formação de ligação de hidrogênio, não precisam de funcionais sofisticados para a otimização de sua geometria, mas precisam destes para o cálculo do ângulo de rotação óptica. Para moléculas flexíveis, é necessário um funcional mais sofisticado também para a otimização de geometria. Assim, a melhor combinação de método e base para moléculas mais rígidas para a otimização de geometria foi ωB97XD com a base 6-31G**. Já para moléculas flexíveis, para a otimização de geometria, a melhor base foi def2-TZVP. Em ambos os casos, para o cálculo do ângulo de rotação óptica, a melhor combinação foi ωB97XD com a base def2-TZVP. Para os complexos de ligação de hidrogênio estudados, o deslocamento químico do núcleo do hidrogênio ácido nos complexos envolvendo a 1,10-fenantrolina, como aceitador de elétrons foi mais fortemente afetado em comparação aos complexos correspondentes da 2,2’-bipiridina e 4,4-difenil-2,2’-bipiridina. Os cálculos GIAO estão de acordo com os experimentos de RMN de 1H na previsão da blindagem eletrônica do hidrogênio ácido durante a ligação de hidrogênio existente nos complexos estudados. / In this dissertation, we studied four chiral molecules using four distinct density functionals, and twenty basis functions, searching for a combination that could best describe the optical rotation angle of these molecules. We also analyzed how hydrogen bonding influences the optical rotation angle and what are the effects of hydrogen bonding on the properties of different systems involving cyclic nitrogenated compounds and carboxylic acids. The functionals employed were B3LYP, PBE, PBE0 and ωB97XD. The basis functions employed were: 6-31G, 6-31+G, 6-31++G, 6-31G* 6-31+G*, 6-31++G*, 6-31G**, 6-31+G**, 6-31++G**, cc-pVDZ, cc-pVTZ, cc-pVQZ, aug-cc-pVDZ, aug-cc-pVTZ, aug-cc-pVQZ, def2- TZVP, def2-TZVPD, def2-TZVPP, def2-TZVPPD and 6-311+G**. The chiral molecules studied for the assignment of their absolute configuration were R,R-dimethyloxirane, S-methyl oxirane, S-halothane and (S)(+)4-phenyl-2-oxazolidinone. The molecules studied for the GIAO calculation of 1H NMR spectroscopy were 1,10-phenanthroline, 2,2-bipyridine, 4,4'-diphenyl-2,2'-bipyridine and the carboxylic acids: formic, acetic and benzoic. The geometries of all molecules and complexes were optimized so that there were no imaginary harmonic frequencies and, from them, the optical rotation angle was calculated. For the (S)(+)4-phenyl-2-oxazolidinone molecule, the possibility of dimer formation was observed which can influence the value of the optical rotation angle. The possible conformations for this dimer were found using molecular mechanics by SPARTAN program, and their geometries optimized. The energies of stabilization of all complexes were corrected for the basis set superposition error (BSSE) and zero point energy (ZPE). The calculation of optical rotation angle was made using a Boltzmann average. All chiral molecules were studied, both isolated and in chloroform by the PCM method.We note that simple molecules, rigid and with no possibility of hydrogen bond formation, do not need sophisticated functionals for geometry optimization. However, these sophisticated functionals are indeed needed for the optical rotation angle to be calculated. For flexible molecules, more sophisticated functionals are also necessary for the geometry optimization step. Thus, the best combination method and basis set for the geometry optimization of more rigid molecules found was ωB97XD to the base 6-31G **. As for the geometry optimization of flexible molecules, the best basis set was def2-TZVP. On the other hand, for calculating the optical rotation angle in both cases, the best combination found was ωB97XD with the def2-TZVP.For the hydrogen bonding complexes studied, the chemical shift of the acidic hydrogen nucleus in the complex involving 1,10-phenanthroline as electron acceptor was more strongly affected compared to the corresponding complexes of 2,2'-bipyridine and 4,4'-diphenyl-2,2'-bipyridine. The GIAO calculations agree with the NMR 1H experiments in predicting the electronic shielding of the acidic hydrogen during hydrogen bonding in the studied complexes.

Orientador: Pedro Faria dos Santos Filho / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-11T11:58:23Z (GMT). No. of bitstreams: 1 Reis_AdrianodeSouza_M.pdf: 1594474 bytes, checksum: 4085fd3be588cce4f866d8ebc2f1c832 (MD5) Previous issue date: 2008 / Resumo: O enfoque deste trabalho é o ensino de química, abordando situações cotidianas de pessoas comuns, visando a interpretação destas situações do ponto de vista químico. O principal objetivo é a elaboração de um material que seja útil para graduandos e professores, particularmente os professores de química que atuam no nível médio e superior. As ligações hidrogênio e suas propriedades compõem a maior parte da discussão deste texto. Vários contextos são utilizados, tais como, química ácido-base, capilaridade, formação do DNA e mutações genéticas, água líquida e sua contribuição em diversos fenômenos, química da sensação dos sabores doce e amargo, além de outras situações corriqueiras. As situações abordadas não são utilizadas como objetos de estudo, mas como forma de discutir alguns aspectos, propriedades e características das ligações hidrogênio. Além disso, o texto discute a melhor forma de entender ligação hidrogênio em diferentes níveis. A seqüência do texto coloca, gradualmente, as principais propriedades das ligações hidrogênio em diferentes contextos. Inicialmente o modelo puramente eletrostático é utilizado para explicar algumas situações interessantes. Em seguida, o modelo puramente eletrostático tradicional é questionado e observa-se que ele não é conveniente para explicar todos os fenômenos, sendo então questionado e repensado ao longo do texto. Novos argumentos são usados para explicar a ligação hidrogênio, agora usando o conceito de modelo eletrostático com uma componente covalente. Esta contribuição torna o modelo mais complexo que o anterior e inclui outras idéias além dos ¿pontinhos¿ (X ¿ H ....... X), normalmente usados para representar a contribuição puramente eletrostática desta interação. Muitas propriedades das ligações hidrogênio são apresentadas e discutidas ao longo do texto, utilizando este novo conceito / Abstract: The focus of this work is chemistry teaching, approaching common people's daily situations, and seeking the interpretation of these situations in a chemical point of view. The main goal is the elaboration of an useful didactic material for high school and undergraduate teachers and also for the students. The chemical interactions, particularly hydrogen bonding, compose the major discussion of the text. Several contexts are used, such as acid-base chemistry, capillarity, DNA formation and genetic mutations, liquid water and its contribution in several phenomena, sweet and bitter flavor sensation chemistry, among other existing situations. All approached situations are not used as study cases, but as a way to discuss some aspects, properties and characteristics of the hydrogen bonding. Besides, the text discusses the best way for hydrogen bonding understanding in different levels. The sequence of the text set gradually the main properties of the hydrogen bonding in different contexts. The merely electrostatic model is used to explain some interesting situations. On the other hand, the text also shows that the conventional electrostatic model is not convenient to explain all phenomena, being this model questioned and rethought along the text. New arguments are used to explain the hydrogen bonding, now using the concept of electrostatic model associated to a covalent component. This approach makes more complex the original model and shows other ideas - besides the "dots¿ (X ¿ H .... X) - usually used to represent the purely electrostatics contribution of this interaction. Several properties of the hydrogen bonding using this new concept are presented and discussed along the text / Mestrado / Quimica Inorganica / Mestre em Química