Orientador: Susanne Rath / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-16T00:51:54Z (GMT). No. of bitstreams: 1 Barros_LeonardoAugustode_M.pdf: 2516979 bytes, checksum: 9e6340ca4d81c25d9929cae4417e6fbf (MD5) Previous issue date: 2010 / Resumo: Esse trabalho teve como objetivo principal sintetizar um polímero de impressão molecular (MIP) para ser empregado em processo de extração em fase sólida (SPE), visando a determinação de resíduos de fenitrotiona (FNT) em tomates. Os reagentes da síntese foram selecionados a partir de estudos de modelagem molecular, usando para tanto o programa computacional Gaussian 03. As energias eletrônicas de ligação para a interação entre o monômero funcional e a FNT, no vácuo e no solvente, foram calculadas através do método DFT, no nível B3LYP e conjunto de base 6-31G(d). Os reagentes de síntese foram: FNT (molde), ácido metacrílico (monômero funcional), etilenoglicol dimetacrilato (reagente de ligação cruzada), AIBN (iniciador radicalar) e tolueno (solvente porogênico). Também foi sintetizado um polímero não-impresso (NIP). Por meio de estudos de adsorção foi avaliado o meio de melhor reconhecimento molecular. Foram construídas as isotermas de adsorção para cada um dos polímeros impresso e não impresso e foi avaliada a seletividade do MIP frente a análogos da FNT. Os polímeros foram caracterizados por infravermelho com transformada de Fourier, ressonância magnética nuclear de C, microscopia de varredura eletrônica e porosimetria de sorção de nitrogênio (BET). O MIP foi empregado como fase estacionária em SPE. Foi desenvolvido e validado um método para a determinação de FNT em tomates, usando a cromatografia líquida de alta eficiência. A eficiência de extração foi de 96%. A faixa linear foi de 130 a 2000 ng g, com uma linearidade superior a 0,99. A precisão intra-ensaio e inter-ensaio foram inferiores a 7,0% e 8,1%, respectivamente (níveis de fortificação 250, 500 e 1000 ng g). A exatidão foi superior a 89% no nível de fortificação em torno do limite máximo de resíduo de 500 ng g / Abstract: This work aimed the synthesis of a molecularly imprinted polymer (MIP) to be employed in process of solid phase extraction (SPE), for the determination of residues of fenitrothion (FNT) in tomatoes. The synthesis reagents were selected from molecular modeling, using the Gaussian 03 software. The electronic binding energies for the interaction between the functional monomer and the FNT, in vacuum and in solvent, were calculated by the DFT method in B3LYP level and 6-31G(d) basis set. The reagents of the synthesis were: FNT (template), methacrylic acid (functional monomer), ethyleneglycol dimethacrylate (cross-linker), AIBN (initiator) and toluene (porogenic solvent). Also, was synthesized a non-imprinted polymer. Through batch rebinding studies were evaluated the medium of the best molecular recognition. The adsorption isotherms for each imprinted and non-imprinted polymer were constructed and the selectivity of the MIP in relation to FNT analogues evaluated. The polymers were characterized by Fourier transform infrared, C nuclear magnetic resonance, scanning electron microscopy and nitrogen sorption porosimetry (BET). The MIP was employed as stationary phase in SPE. A method for the determination of FNT in tomatoes was developed and validated, using high performance liquid chromatography. The extraction efficiency was 96%. The linear range was 130 to 2000 ng g, with a linearity greater than 0.99. The intra-day and inter-day precision were lower than 7.0% and 8.1%, respectively (fortification levels 250, 500 e 1000 ng g). The accuracy was higher than 89% for a concentration level around the maximum residue limit of 500 ng g / Mestrado / Quimica Analitica / Mestre em Química

As anfetaminas, grupo de moléculas derivadas da anfetamina, são fármacos estimulantes do sistema nervoso central, e possuem, entre outras, atividade antidepressiva sendo sua ação baseada na inativação da enzima monoamina oxidase (MAO) a qual catalisa a desaminação oxidativa de neurotransmissores, como por exemplo, a serotonina e a noradrenalina. Esta enzima pode ser encontrada em duas diferentes isoformas, a MAO A e MAO B. Este trabalho teve como objetivo o estudo de uma série de derivados anfetamínicos os quais apresentam diferente seletividade e diferentes valores de IC50, variando desde moléculas muito potentes, pouco potentes, até inativas, através da aplicação de técnicas de química-quântica no cálculo de descritores moleculares, bem como a aplicação da mecânica clássica na descrição das interações ligante-receptor a partir de estudos de docking e simulações de dinâmica molecular. Inicialmente, foram aplicados os métodos de química-quântica AM1, HF, DFT (com os funcionais B3LYP e BP86) e MP2 para a determinação do nível de teoria mais apropriado para a otimização da geometria desta série de compostos a partir da comparação entre os resultados teóricos e de raios-X obtidos para a molécula MDMA. O método HF/6-31G(d,p) mostrou os melhores resultados. Desta forma, este método foi utilizado na obtenção das geometrias de mínimo das demais moléculas em estudo. Posteriormente, estes métodos foram utilizados no cálculo das propriedades estruturais, eletrônicas e físico-químicas, distribuição de cargas derivadas do potencial eletrostático, momento dipolar, energia total, energia dos orbitais de fronteira, GAP de energia entre o orbital ocupado de mais alta energia (HOMO) e o orbital desocupado de mais baixa energia (LUMO), dureza, potencial químico, eletronegatividade, eletronegatividade absoluta e eletrofilicidade. Assim, foram verificadas possíveis relações entre os descritores calculados e a atividade biológica determinada por Scorza et al, Hurtado-Guzmán et al and Sterling et al.esta para esta série de compostos. A análise destes resultados foi feita através da aplicação da técnica quimiométrica de análise de componentes principais para, desta forma, verificar-se o agrupamento dos compostos segundo a presença ou ausência de atividade biológica na série estudada. Entretanto, não foi possível se identificar um padrão de agrupamento para as moléculas ativas e inativas, sugerindo assim, que estes descritores não são os mais adequados para a descrição da atividade antidepressiva destes compostos. Em uma segunda etapa, foram feitos estudos de docking para seis diferentes estruturas da MAO B (1OJA, 1OJ9, 2BK3, 2V5Z, 2V60 e 2V61) e cinco da MAO A (2BXR, 2BXS, 2Z5X e 2Z5Y) todas disponíveis no banco de dados de proteína, PDB, no qual se avaliou o modo de interação do ligante no sitio ativo da proteína. Os resultados de docking para a MAO B mostraram que o tamanho do inibidor é importante para uma correta interação no sítio ativo da enzima, tendo-se em vista que o tamanho da cavidade catalítica é dependente da conformação do aminoácido isoleucina 199 e, que a conformação deste aminoácido está relacionada com o tamanho do ligante. Desta forma, a escolha correta da estrutura da proteína torna-se importante para uma correta descrição do sistema. Os resultados sugerem ainda que o átomo do ligante, no qual ocorre a reação com o receptor, deve estar a uma distância média de 3,5 Å do sitio reativo. Os resultados de MD mostraram que este aminoácido é flexível na ausência de um inibidor, onde sua conformação varia entre as chamadas formas aberta e fechada ao longo do tempo, porém, quando o estudo é feito na presença de um ligante, sua conformação perrnanece, de modo geral, constante. / The amphetamine family of drugs is central nervous system stimulant drugs. Amphetamine inhibits the monoamine oxidase enzyme (MAO, isoforms A and B) which catalyzes the oxidative deamination of the neurotransmitter, e. g., serotonin and noradrenalin. In the present study, the aim was to understand the main features of a series of amphetamines derivatives, which have different substrate selectivity and a good range of activity varying from very potent to low potent compounds, even inactive molecules by the application of quantum chemistry techniques to calculate the molecular descriptors, as well as the application of a classical mechanics to describe the ligand-receptor interactions from docking studies and molecular dynamics (MD) simulation. First of all, was applied the AM1, HF, DFT (B3LYP and BP86 functionals) and MP2 quantum chemical methods to analyze which theoretical level is more appropriated for the molecular geometry optimization of this series of compounds from a comparison between the theoretical results for MDMA molecule and it\'s X-ray data. The HF/6-3lG** calculations produced results in close agreement with X-ray crystallography. Thus, was employed the same method for the molecular optimization of the other compounds in the series under investigation. Furthermore, the same method was applied to calculate quantum-chemical parameters (atomic charges, total energy, highest occupied molecular orbital -HOMO- lowest unoccupied molecular orbital -LUMO- dipole moments, hardness, electronegativity, chemical potential, absolute electronegativity and electrophilicity). It was examined possible correlations between the theoretical parameters as calculated by us with the biological activity results as reported by Scorza et al, Hurtado-Guzman et al and Sterling et al. The chemometric technique of Principal Component Analysis for the quantum chemical parameters of these compounds was employed in order to identify some pattern of grouping between the active and inactive molecules. However, it was not possible to identify a pattern between active and inactive compounds suggesting that these above-mentioned parameters are not the best descriptors to evaluate the antidepressant activity for this group of molecules. Later, a docking study was performed for six different PDB structure of MAO B (1OJA, 1OJ9, 2BK3, 2V5Z, 2V60 e 2V61) and five different structure of MAO A (2BXR, 2BXS, 2Z5X e 2Z5Y). It was possible to analyze the ligand-receptor interaction and, according to the bind site size, the activity molecules showed a 3.5A distance between the reactive atoms of the inhibitor and of the protein. Because the conformation of the isoleucine 199 (Ile 199) amino acid can change, the chosen of the correct PDB structure is important for a write description of that interaction. The MD results for the 1OJA structure showed that the Ile199 is flexible in the absence of an inhibitor, where its conformation varies between so-called closed and open forms over the simulation time. However, when the study was done in the presence of a ligand, its conformation remains by generally constant.

Orientador: Wanda Pereira Almeida / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-24T01:24:55Z (GMT). No. of bitstreams: 1 Silva_GiseleSilvestreda_M.pdf: 8524593 bytes, checksum: e3f6789232b8b6dc82852428db406fbf (MD5) Previous issue date: 2013 / Resumo: A Doença de Alzheimer (DA) é uma doença neurodegenerativa, que compromete as funções cognitivas. A acetilcolinesterase (AChE), enzima responsável pela hidrólise da acetilcolina (ACh), é um importante alvo para o desenvolvimento de candidatos a fármacos para tratar a DA. A AChE possui dois sítios ligantes: o catalítico e o periférico, envolvidos com a hidrólise da AChE e com o processo de formação de fibrilas do peptídeo b-amilóide, respectivamente. Neste trabalho propusemos a síntese e avaliação biológica de dois híbridos, ambos contendo porção tetraidroacridina baseado na estrutura da tacrina O hibrido I contem uma subunidade indanona baseado na donepezila e o híbrido II contém uma porção anti-inflamatória do ibuprofeno. O híbrido I e o híbrido II comportaram-se como um simples ligante e um híbrido molecular multipotente, respectivamente. Em ambos os casos foram escolhidos híbridos contendo duas unidades metilênicas. Um intermediário tetraidroacridínico contendo um grupo aminoálcool (6), que também se liga ao sítio catalítico da AChE, foi sintetizado a partir do ácido antranílico em uma sequência de três etapas. Todas as tentativas de acoplar este intermediário ao ibuprofeno fracassaram. Face a estes resultados, voltamos nossa atenção para as quinolonas, compostos planares que como a tacrina poderiam interagir com o sítio catalítico da AChE. Assim, nós sintetizamos quatro derivados da 4-quinolona. A síntese envolveu a ciclização catalisada por TFA do aduto de Morita-Baylis-Hillman, derivado do 2-nitrobenzaldeído, levando ao correspondente N-óxido (32). Em seguida, ele foi tratado com hexacarbonilmolibdato para fornecer a 3- carboetoxi-4-quinolona (38) em 33 % de rendimento global. O ácido carboxílico correspondente e derivados N-etilados também foram preparados. O efeito de três destes derivados quinolônicos sobre a atividade da acetilcolinesterase foi estudado. A N-alquil-3- carboetoxi-4-quinolona (40) foi o mais ativo dos derivados (IC50 ~84mmol/L). Estudo de docking molecular corroboraram nossas observações / Abstract: AlzheimerLs disease (AD) is a neurodegenerative pathology, which compromises the cognitive functions. Acetylcholinesterase (AChE) is the enzyme involved in the hydrolysis of neurotransmitter acetylcholine (ACh) and has been highlighted as an important target for the design of drugs to treat AD. AChE has two binding sites: a catalytic site and the peripheral one, which are involved in the acetylcholine hydrolysis and the formation of Ab42 peptide fibrils, respectively. In this work we proposed the synthesis and biological evaluation of two hybrids based on the tacrine structure, both containing portion tetrahydroacridine based on the structure of tacrine. The hybrid I has donepezil moieties and the hybrid II has anti-inflammatory portion. The hybrid I and hybrid II behave as a simple ligand and molecular hybrid, respectively. We have found that linkers with two and three methylene units generate suitable hybrids to bind to the catalytic site of the AChE. A key tetrahydroacridine bearing an amino alcohol function (6) also binds to the catalytic site of the AChE. It was synthesized from anthranilic acid in three steps sequence. All attempts to couple 6 and ibuprofen failed. In view of these results, we turn our attention to other planar structures which could interact with the catalytic site of the AChE. Thus, we synthesized four 4-quinolone derivatives. The synthesis involved a TFA mediated cyclization of the Morita-Baylis-Hillman adduct, derived from 2-nitrobenzaldehyde, leading to the corresponding N-Oxide (32). Then, it was treated with hexacarbonyl molibdate to afford 3-carboethoxy-4-quinolone (38) in 33% overall yield. We have also prepared: the corresponding carboxylic acid and the N-ethyl derivatives. The effect of three of them on the acetylcholinesterase activity was evaluated. The N-alkyl-3-carboethoxy-4- quinolone (40) was the most active (IC50 ~84mmol/L). Molecular docking studies corroborated our observations / Mestrado / Quimica Organica / Mestra em Química

As anfetaminas, grupo de moléculas derivadas da anfetamina, são fármacos estimulantes do sistema nervoso central, e possuem, entre outras, atividade antidepressiva sendo sua ação baseada na inativação da enzima monoamina oxidase (MAO) a qual catalisa a desaminação oxidativa de neurotransmissores, como por exemplo, a serotonina e a noradrenalina. Esta enzima pode ser encontrada em duas diferentes isoformas, a MAO A e MAO B. Este trabalho teve como objetivo o estudo de uma série de derivados anfetamínicos os quais apresentam diferente seletividade e diferentes valores de IC50, variando desde moléculas muito potentes, pouco potentes, até inativas, através da aplicação de técnicas de química-quântica no cálculo de descritores moleculares, bem como a aplicação da mecânica clássica na descrição das interações ligante-receptor a partir de estudos de docking e simulações de dinâmica molecular. Inicialmente, foram aplicados os métodos de química-quântica AM1, HF, DFT (com os funcionais B3LYP e BP86) e MP2 para a determinação do nível de teoria mais apropriado para a otimização da geometria desta série de compostos a partir da comparação entre os resultados teóricos e de raios-X obtidos para a molécula MDMA. O método HF/6-31G(d,p) mostrou os melhores resultados. Desta forma, este método foi utilizado na obtenção das geometrias de mínimo das demais moléculas em estudo. Posteriormente, estes métodos foram utilizados no cálculo das propriedades estruturais, eletrônicas e físico-químicas, distribuição de cargas derivadas do potencial eletrostático, momento dipolar, energia total, energia dos orbitais de fronteira, GAP de energia entre o orbital ocupado de mais alta energia (HOMO) e o orbital desocupado de mais baixa energia (LUMO), dureza, potencial químico, eletronegatividade, eletronegatividade absoluta e eletrofilicidade. Assim, foram verificadas possíveis relações entre os descritores calculados e a atividade biológica determinada por Scorza et al, Hurtado-Guzmán et al and Sterling et al.esta para esta série de compostos. A análise destes resultados foi feita através da aplicação da técnica quimiométrica de análise de componentes principais para, desta forma, verificar-se o agrupamento dos compostos segundo a presença ou ausência de atividade biológica na série estudada. Entretanto, não foi possível se identificar um padrão de agrupamento para as moléculas ativas e inativas, sugerindo assim, que estes descritores não são os mais adequados para a descrição da atividade antidepressiva destes compostos. Em uma segunda etapa, foram feitos estudos de docking para seis diferentes estruturas da MAO B (1OJA, 1OJ9, 2BK3, 2V5Z, 2V60 e 2V61) e cinco da MAO A (2BXR, 2BXS, 2Z5X e 2Z5Y) todas disponíveis no banco de dados de proteína, PDB, no qual se avaliou o modo de interação do ligante no sitio ativo da proteína. Os resultados de docking para a MAO B mostraram que o tamanho do inibidor é importante para uma correta interação no sítio ativo da enzima, tendo-se em vista que o tamanho da cavidade catalítica é dependente da conformação do aminoácido isoleucina 199 e, que a conformação deste aminoácido está relacionada com o tamanho do ligante. Desta forma, a escolha correta da estrutura da proteína torna-se importante para uma correta descrição do sistema. Os resultados sugerem ainda que o átomo do ligante, no qual ocorre a reação com o receptor, deve estar a uma distância média de 3,5 Å do sitio reativo. Os resultados de MD mostraram que este aminoácido é flexível na ausência de um inibidor, onde sua conformação varia entre as chamadas formas aberta e fechada ao longo do tempo, porém, quando o estudo é feito na presença de um ligante, sua conformação perrnanece, de modo geral, constante. / The amphetamine family of drugs is central nervous system stimulant drugs. Amphetamine inhibits the monoamine oxidase enzyme (MAO, isoforms A and B) which catalyzes the oxidative deamination of the neurotransmitter, e. g., serotonin and noradrenalin. In the present study, the aim was to understand the main features of a series of amphetamines derivatives, which have different substrate selectivity and a good range of activity varying from very potent to low potent compounds, even inactive molecules by the application of quantum chemistry techniques to calculate the molecular descriptors, as well as the application of a classical mechanics to describe the ligand-receptor interactions from docking studies and molecular dynamics (MD) simulation. First of all, was applied the AM1, HF, DFT (B3LYP and BP86 functionals) and MP2 quantum chemical methods to analyze which theoretical level is more appropriated for the molecular geometry optimization of this series of compounds from a comparison between the theoretical results for MDMA molecule and it\'s X-ray data. The HF/6-3lG** calculations produced results in close agreement with X-ray crystallography. Thus, was employed the same method for the molecular optimization of the other compounds in the series under investigation. Furthermore, the same method was applied to calculate quantum-chemical parameters (atomic charges, total energy, highest occupied molecular orbital -HOMO- lowest unoccupied molecular orbital -LUMO- dipole moments, hardness, electronegativity, chemical potential, absolute electronegativity and electrophilicity). It was examined possible correlations between the theoretical parameters as calculated by us with the biological activity results as reported by Scorza et al, Hurtado-Guzman et al and Sterling et al. The chemometric technique of Principal Component Analysis for the quantum chemical parameters of these compounds was employed in order to identify some pattern of grouping between the active and inactive molecules. However, it was not possible to identify a pattern between active and inactive compounds suggesting that these above-mentioned parameters are not the best descriptors to evaluate the antidepressant activity for this group of molecules. Later, a docking study was performed for six different PDB structure of MAO B (1OJA, 1OJ9, 2BK3, 2V5Z, 2V60 e 2V61) and five different structure of MAO A (2BXR, 2BXS, 2Z5X e 2Z5Y). It was possible to analyze the ligand-receptor interaction and, according to the bind site size, the activity molecules showed a 3.5A distance between the reactive atoms of the inhibitor and of the protein. Because the conformation of the isoleucine 199 (Ile 199) amino acid can change, the chosen of the correct PDB structure is important for a write description of that interaction. The MD results for the 1OJA structure showed that the Ile199 is flexible in the absence of an inhibitor, where its conformation varies between so-called closed and open forms over the simulation time. However, when the study was done in the presence of a ligand, its conformation remains by generally constant.

In this study, an attempt was made to identify the electronic and steric properties of the precatalyst ligands that determine the characteristics of phosphine ligated Grubbs-type precatalysts for alkene metathesis by means of molecular modelling. It was found from studying the literature that the possibilities for synthesising a wide range of phosphine ligands are almost unlimited. Additionally, it was found that there is no easy method to determine the electronic and steric properties of the precatalyst ligands in existence. Molecular modelling might provide a method to study potential ligands and precatalysts before tedious synthesis methods are attempted. It was found that the theoretically calculated structures of the commercially available precatalysts compared well with the experimental data reported in literature. It is also shown that the energy profiles for alkene metathesis of simplified model systems do not compare well with non-simplified systems. Correlations between these simplified model systems and experimental work have to be regarded as serendipitous at best. When the energy profiles of the various new and commercially available precatalysts are compared, similarities in the energy trends for 1-octene metathesis are observed. These similarities raise questions about the significance of the differences in the energy barriers. In an effort to better understand this, two low activity precatalysts were also investigated in an attempt to identify the area or trend of poor catalysis. Instead of providing the desired different result, trends very similar to that of the highly active precatalysts were observed. This led to the observation that, without a sufficiently large dataset, great care should be taken before conclusions are drawn from theoretical work. Since the electronic investigation did not provide the desired result of finding a fast and effective method of determining which ligand merits further investigation, some steric aspects were studied. Once again, the precatalysts proved to be remarkably similar and no definitive answer for the observed differences in the various precatalysts could be determined. A preliminary experimental study into the feasibility of the synthesis of the new potential ligands was done. The multi-step synthesis route resulted in low yields in some cases, with the need for large volumes of solvents to purify the products. The toxicity of phenylphosphine also has to be taken into account when considering these types of ligands. A new precatalyst obtained by using a new ligand should show a remarkable improvement over the current commercially available precatalysts to justify the additional cost to synthesise a new ligand. It would seem that for future projects more consideration should be given to the deactivation mechanism of the Grubbs-type precatalysts, since this seems to be the logical starting point to look for the answers to the experimentally observed differences. A deeper understanding of the mechanism of alkene metathesis can only be obtained if all aspects are investigated in as much detail as possible. While the results did not provide the initially expected outcome, some valuable insights were gained that challenge the current way of thinking about the alkene metathesis mechanism. It is also clear that to oversimplify a very complex reaction and using limited data will lead to false assumptions being made. / PhD (Chemistry), North-West University, Potchefstroom Campus, 2014

In this study, an attempt was made to identify the electronic and steric properties of the precatalyst ligands that determine the characteristics of phosphine ligated Grubbs-type precatalysts for alkene metathesis by means of molecular modelling. It was found from studying the literature that the possibilities for synthesising a wide range of phosphine ligands are almost unlimited. Additionally, it was found that there is no easy method to determine the electronic and steric properties of the precatalyst ligands in existence. Molecular modelling might provide a method to study potential ligands and precatalysts before tedious synthesis methods are attempted. It was found that the theoretically calculated structures of the commercially available precatalysts compared well with the experimental data reported in literature. It is also shown that the energy profiles for alkene metathesis of simplified model systems do not compare well with non-simplified systems. Correlations between these simplified model systems and experimental work have to be regarded as serendipitous at best. When the energy profiles of the various new and commercially available precatalysts are compared, similarities in the energy trends for 1-octene metathesis are observed. These similarities raise questions about the significance of the differences in the energy barriers. In an effort to better understand this, two low activity precatalysts were also investigated in an attempt to identify the area or trend of poor catalysis. Instead of providing the desired different result, trends very similar to that of the highly active precatalysts were observed. This led to the observation that, without a sufficiently large dataset, great care should be taken before conclusions are drawn from theoretical work. Since the electronic investigation did not provide the desired result of finding a fast and effective method of determining which ligand merits further investigation, some steric aspects were studied. Once again, the precatalysts proved to be remarkably similar and no definitive answer for the observed differences in the various precatalysts could be determined. A preliminary experimental study into the feasibility of the synthesis of the new potential ligands was done. The multi-step synthesis route resulted in low yields in some cases, with the need for large volumes of solvents to purify the products. The toxicity of phenylphosphine also has to be taken into account when considering these types of ligands. A new precatalyst obtained by using a new ligand should show a remarkable improvement over the current commercially available precatalysts to justify the additional cost to synthesise a new ligand. It would seem that for future projects more consideration should be given to the deactivation mechanism of the Grubbs-type precatalysts, since this seems to be the logical starting point to look for the answers to the experimentally observed differences. A deeper understanding of the mechanism of alkene metathesis can only be obtained if all aspects are investigated in as much detail as possible. While the results did not provide the initially expected outcome, some valuable insights were gained that challenge the current way of thinking about the alkene metathesis mechanism. It is also clear that to oversimplify a very complex reaction and using limited data will lead to false assumptions being made. / PhD (Chemistry), North-West University, Potchefstroom Campus, 2014

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: see full text for abstract. / AFRIKAANSE OPSOMMING: Sien volteks vir die opsomming.

<p>Molecular modelling strategies for evaluation of enzyme selectivity wereinvestigated with a focus on principles of how molecular interactionscould be evaluated to provide information about selectivity. Althoughmolecular modelling provides tools for evaluation of geometrical andenergy features of molecular systems, no general strategies for evaluationof enzyme selectivity exist. Geometrical analyses can be based uponinspection and reasoning about molecular interactions, which provide aneasily accessible way to gain information, but suffer from the risk of biasput in by the modeller. They can also be based on geometrical features ofmolecular interactions such as bond lengths and hydrogen-bond formation.Energy analyses are appealing for their modeller independenceand for the possibility to predict not only stereopreference, but also itsmagnitude.In this thesis, four examples of enantio- or regioselective serinehydrolase-catalysed reaction systems are presented together with developedmodelling protocols for explanation, prediction or enhancement ofselectivity. Geometrical as well as energy-based methodology were used,and provided an understanding of the structural basis of enzymeselectivity. In total, the protocols were successful in making qualitative explanationsand predictions of stereoselectivity, although quantitative determinationswere not achieved.</p>

The biosynthesis of the steroid precursor molecule lanosterol is a remarkable process in which the enzyme-bound substrate 2,3-S-oxidosqualene forms four new carbocyclic rings by a cascade of cation-alkene addition reactions, followed by a series of 1,2-methyl and hydride shifts. The work presented in this thesis is a computational study of the reactions of compounds designed to model the oxidosqualene-lanosterol cyclisation in order to establish details of the mechanism of this amazing cyclisation. The initiation of oxidosqualene cyclisation has been modelled by the intermolecular reaction of protonated oxirane and methylpropene. The SN2-like ring opening of the protonated epoxide is strongly exothermic with a low barrier to reaction; the geometry of the gas phase reaction has been found to be significantly affected by hyperconjugative stabilisations and low energy steric interactions. The energy profile and geometry of this reaction can now be compared to analogous intramolecular reactions such as the formation of the lanosterol A-ring. The competing five- and six-membered cyclisations of a series of substituted A-ring model compounds was investigated. It has been found that the facile cleavage of the protonated epoxide causes the reaction to behave more as an electrophilic addition than as a nucleophilic ring-opening substitution. This behaviour accounts for the general preference of protonated epoxides to react at the more substituted carbon atom, while epoxides in neutral or basic media react at the least sterically hindered carbon. With consideration for Baldwin's rules for ring closure, it is seen that the series of model compounds generally favours six-membered ring formation endo at the epoxide. The formation of the lanosterol B-ring was studied using a bicyclic model system. Previous computational studies had predicted the B-ring to close with readily with an activation energy of less than 1 kcal mol-1, however the present study has found a significant barrier to cyclisation of ca. 5-7 kcal mol-1 in this gas-phase model at the HF/6-31G(d) level of theory. This barrier is thought to arise from the closure of the B-ring in a sterically hindered twist-boat conformation.

A conhecida regra do acoplamento em W, que estabelece que núcleos na conformação em W planar exibem valores significativos de constantes de acoplamento através de quatro ligações, tem sido uma ferramenta útil para a determinação estrutural desde o início do uso da RMN para essa finalidade. Muitas configurações e conformações foram decididas com base nessa regra. A contínua evolução do equipamento de RMN, porém, resulta em modificações na qualidade e no número dos dados experimentais obtidos, obrigando os químicos a freqüentes revisões de seus pontos de vista sobre a importância relativa dos dados que podem ser obtidos dos espectros de RMN. O equipamento mais recente tem uma resolução maior e várias características adicionais que obscurecem um pouco os conceitos mais antigos: por um lado, o alto valor informativo de algumas técnicas modernas tais como NOE DIFF e outros métodos multi-dimensionais reduzem a importância das constantes de acoplamento; por outro lado, agora é possível determinar um número muito maior de constantes de acoplamento, devido principalmente à maior resolução. Uma conseqüência natural é que o químico agora pode explorar o uso de desdobramentos sutis em análise conformacional. Como parte de nosso trabalho de pesquisa na síntese de produtos naturais, preparamos há algum tempo um número apreciável de derivados de ciclopentanos. Nossa atenção foi fortemente atraída para certas constantes de acoplamento a longa distância (4JHH) que ocorriam em alguns destes compostos, já que uma conformação W planar não parece ser possível em ciclopentanos. Decidimos então iniciar um estudo mais detalhado dos espectros de RMN desses compostos, com vistas a uma interpretação mais clara dos dados. Inicialmente fizemos as atribuições para todos os hidrogênios, incluindo a estéreo-química de cada um, e medimos todos os valores de J para os compostos; para tanto fizemos extenso uso dos espectros de RMN tanto de 1H (300 MHz)como de 13C (75 MHz), medidas de efeito NOE, etc. Os ângulos entre as ligações e os ângulos diedros (de torção) foram calculados com programas de modelagem molecular; vários programas e métodos diferentes foram usados, para aumentar a confiabilidade. O primeiro resultado obtido é a confirmação de que 4JHH 'diferente' 0 pode ocorrer mesmo em casos em que uma conformação W planar não é possível. Mais importante, porém, é a conclusão de que há uma relação entre os valores de 4JHH e os ângulos diedros envolvidos. O acoplamento entre H1 e H2 ocorre através das quatro ligações 'sigma' definidas pelo caminho H1-C1-C2-C3-H2 e envolve dois ângulos diedros 'teta'1 e 'teta'2. Os valores de 4JHH foram plotados contra (cos2'teta'1 x cos2'teta'2) (uma simples extensão da equação de Karplus); os pontos resultantes não se alinham com perfeição sobre uma curva contínua, mas mostram clara tendência de aumento do valor de 4JHH conforme os ângulos 'teta'1 e 'teta'2 se afastam de 90º e se aproximam de 180º. / The well known W rule, which establishes that nuclei in a planar W arrangement exhibit significant four bond coupling constants, has been a useful tool in molecular structure determination since early times of the use of nmr spectra for this purpose. Many configurations and conformations have been decided based on this rule. The continuous evolution of the nmr equipment, however, produces modifications in quality and number of available experimental data, thus forcing the chemists to frequent revisions of their points of view about the relative importance of the data that can be obtained from nmr spectra. The more recent equipment has a higher resolution and several additional features that throw some shadow over early concepts: on one hand, the high power of modern techniques such as NOE DIFF and other multi-dimensional methods reduce the importance of coupling constants; on the other hand, it is now possible to determine many more coupling constants, due mainly to the higher resolution. A natural consequence is that the chemist can now exploit the use of subtle splittings in conformational analysis. As part of our research work on the synthesis of natural products, we have prepared a number of cyclopentane derivatives. Our attention was strongly attracted to the long-range (4JHH) coupling constants that occurred in some of these compounds, as no planar W conformation seems to be possible in cyclopentanes. We have thus decided to start a more detailed study of the nmr spectra of these compounds, seeking for more clear interpretation of the data. We have first assigned all hydrogens, including the stereochemistry of each hydrogen, and measured all J values for the compounds; for this task we have used nmr spectra both of 1H (300 MHz) and 13C (75 MHz), NOE measurements, etc. Bond angles and dihedral (torsion) angles were calculated with molecular modeling programs; several different programs and methods were used to improve reliability. The first result obtained is a confirmation that a 4JHH 'different' 0 occurs even in cases where a planar W conformation is not possible. More important, however, is the conclusion that there is a correlation between the 4JHH values and the involved dihedral angles. There are two dihedral angles in the path through the bonds between two hydrogens which show 4JHH coupling. When 4JHH values are plotted against(cos2'teta'1 x cos2'teta'2) (a simple extension of Karplus equation) the points are not aligned over a continuous curve, but they show a clear tendency: 4JHH values become higher as the angles 'teta'1 and 'teta'2 vary from 90 to 180º.