Orientador: Roberto Rittner Neto / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-19T09:46:54Z (GMT). No. of bitstreams: 1 Cormanich_RodrigoAntonio_M.pdf: 17962045 bytes, checksum: e9b512f22b0c39e10dfff2d962a24647 (MD5) Previous issue date: 2011 / Resumo: São reportadas na presente dissertação as análises conformacionais dos aminoácidos da glicina, L-alanina, sarcosina e N,N-dimetilglicina e dos ésteres metílicos da L-valina, L-fenilalanina e L-tirosina, utilizando cálculos teóricos e espectroscopias de RMN de H e infravermelho. Todos os cálculos foram executados em nível B3LYP/aug-cc-pVDZ e comparados com os dados obtidos experimentalmente, para o caso dos ésteres metílicos da L-valina, L-fenilalanina e L-tirosina utilizando as espectroscopias de RMN de H e de infravermelho. Os valores de JHH em vários solventes forneceram informações importantes a respeito das variações populacionais com a mudança do meio para estes três sistemas moleculares. As populações relativas dos confôrmeros, obtidas em solventes com diferentes valores de constante dielétrica, foram também determinadas pela deconvolução da banda referente ao estiramento da ligação C=O dos espectros de infravermelho. Os resultados experimentais obtidos em cada solvente estão em boa concordância quando comparados com as estruturas obtidas utilizando cálculos teóricos de solvatação implícita IEFPCM (Integral Equation Formalism Polarized Continuum Model) e, portanto, validam estes últimos. Assim, em divergência aos dados da literatura, este trabalho sugere, baseado nas análises de orbitais naturais de ligação (NBO) e de teoria quântica de átomos em moléculas (QTAIM), que as preferências conformacionais destes importantes compostos são governados por efeitos estéricos e hiperconjugativos e não devido à possível formação de ligações de hidrogênio intramoleculares / Abstract: The conformational analysis of glycine, L-alanine, sarcosine and N,N-dimetilglycine aminoacids and L-valine, L-phenylalanine and L-tyrosine methyl esters, using theoretical calculations and H NMR and infrared spectroscopies, are reported in the present dissertation. All calculations were carried out at the B3LYP/aug-cc-pVDZ level of theory and compared with experimental data obtained for the L-valine, L-phenylanaline and L-tyrosine, using the H NMR and infrared spectroscopies. The JHH values in various solvents provided important informations about the populational variation with the environment changing to these three molecular systems. Conformer relative populations, obtained in solvents of different dieletric constant values, were also measured by the infrared spectra C=O stretching band deconvolution. The experimental results obtained in each solvent are in good agreement in comparison to the obtained structures using the implicit solvent model IEFPCM (Integral Equation Formalism Polarized Continuum Model) theoretical calculations and, therefore, validate the last ones. Indeed, in divergence with literature data, this work suggests, within the framework of natural bond orbital (NBO) and the quantum theory of atoms in molecules (QTAIM) analysis, that these important compounds conformational preferences are ruled by steric and hyperconjugative effects and not as due to possible intramolecular hydrogen bonding formation / Mestrado / Quimica Organica / Mestre em Química

Soluble guanylyl cyclase (sGC) is the receptor for nitric oxide and a highly sought-after therapeutic target for the management of cardiovascular diseases. New compounds that stimulate sGC show clinical promise, but where these stimulator compounds bind and how they function remains unknown. Here, using a photolyzable diazirine derivative of a novel stimulator compound, IWP-051, and MS analysis, we localized drug binding to the 1 heme domain of sGC proteins from the hawkmoth Manduca sexta and from human. Covalent attachments to the stimulator were also identified in bacterial homologs of the sGC heme domain, referred to as H-NOX domains, including those from Nostoc sp. PCC 7120, Shewanella oneidensis, Shewanella woodyi, and Clostridium botulinum, indicating that the binding site is highly conserved. The identification of photoaffinity-labeled peptides was aided by a signature MS fragmentation pattern of general applicability for unequivocal identification of covalently attached compounds. Using NMR, we also examined stimulator binding to sGC from M. sexta and bacterial H-NOX homologs. These data indicated that stimulators bind to a conserved cleft between two subdomains in the sGC heme domain. L12W/T48W substitutions within the binding pocket resulted in a 9-fold decrease in drug response, suggesting that the bulkier tryptophan residues directly block stimulator binding. The localization of stimulator binding to the sGC heme domain reported here resolves the longstanding question of where stimulators bind and provides a path forward for drug discovery.

Incident ¹H⁺ and ⁴He⁺ ions at 0.3-2.6 MeV and ¹⁹F^q⁺ ions at 25, 27 and 35 MeV were used to study the M-shell x-ray production cross sections of Au, Pb, Bi and U. For the incident fluorine ions, projectile charge state dependence of the cross sections were extracted from measurements made with varying target thicknesses ( ~1 to ~300 μg/cm²). The efficiency of the Si(Li) detector was determined by measuring the K-shell x-ray production of various low Z elements and comparing these values to the prediction of the CPSS theory. The experimental results are compared to the prediction of first Born approximation for direct ionization to the continuum and to the OBK of Nikolaev for the electron capture to the K-, L-, M-...shells of the incident ion. Comparison is also made with the ECPSSR theory that accounts for the energy loss, Coulomb deflection, and relativistic effects in the perturbed stationary state theory.

Ces dernières décennies, les xénolites de péridotites provenant des kimberlites et des basaltes ont contribué de manière déterminante à la compréhension de l’état physico-chimique du manteau supérieur de la Terre dont dépend la modélisation directe de déformation telle que le rebond post-glaciaire. Une telle approche requiert a priori la détermination des conditions physiques P, T et σ dont témoignent la chimie minérale et la texture de ces roches. Un protocole original d’inversion thermodynamique de données expérimentales pour des pyroxènes en équilibre mutuel, a d’abord été développé dans le but d’obtenir un géothermobaromètre fiable. D’autre part, l’étude menée par spectroscopie IRTF de pyroxènes montre que ces minéraux nominalement anhydres (NAMs) contiennent en fait de l’eau sous forme dissoute, de 38 à 450 ppm pour les cpx, et de 19 à 184 ppm pour les opx.Par son rôle perturbateur du réseau cristallin, cette eau affecte directement les propriétés physico-chimiques du manteau terrestre (viscosité, diagrammes de phase, conductivité électrique). La dissolution de cette eau est correlée à fO2, P et T, et seulement indirectement à la chimie des minéraux. Des analyses 1H, 27Al et 29Si MAS RMN sur ces phases contenant des teneurs non négligeables en fer, ainsi que sur des mélanges kaolinite+magnétite, permettent, entre autres, d’authentifier les signatures spectrales de ces pyroxènes naturels mais aussi de quantifier les espèces Al en termes de sites d’occupation. La complémentarité de ces outils, appliqués ici avec succès, ouvre de nouvelles perspectives de compréhension et modélisation des processus profonds. / Over the last decades, peridotite xenoliths brought up by kimberlites and basalts have largely and critically contributed to the understanding of the physical and chemical state of the Earth’s upper-mantle, a prerequisite for direct modelling of deep deformations such as those at work in post-glacial rebound. Such an approach first requires quantification of the physical conditions (P, T, σ) in control of mineral chemistry and rock textures. An original protocol for thermodynamic inversion of experimental data on mutually-equilibrated pyroxenes, was first developed to obtain a reliable geothermobarometer. Moreover, FTIR spectroscopic studies of pyroxenes show that these nominally anhydrous minerals (NAMs) actually contain dissolved water, from 38 to 450 ppm for cpx’s and from 19 to 184 ppm for opx’s. According to its disruptive action onto the crystalline network, such water directly affects the physical and chemical properties of the Earth’s mantle (viscosity, phase diagrams, electrical conductivity). Dissolution of this water component is correlated to fO2, P and T, but only indirectly to mineral composition. Last, 1H, 27Al and 29Si MAS NMR analyses on the same pyroxenes (as iron-bearing minerals), as well as on kaolinite+magnetite mixes, have authenticated NMR spectra for natural pyroxenes, but have also yielded constraining data on site occupancies, specially for Al. These complementary tools applied here with some success, open new prospects for the understanding and modelling of deep processes.

Le nombre de cibles potentielles pour la conception de nouvelles molécules à activité thérapeutique ne cesse de croître. Pour chaque cible, il est nécessaire d’identifier des molécules actives et de les optimiser afin d’atteindre l’affinité et la sélectivité recherchées. Ces nouveaux défis accentuent la nécessité d’améliorer notre compréhension des facteurs qui mènent à la reconnaissance moléculaire entre une drogue potentielle et une macromolécule biologique, et particulièrement des facteurs énergétiques à la base de la stabilisation d’un complexe d’interaction. Dans le cadre de ce travail, nous nous sommes intéressés à l’effet que pouvaient avoir les équilibres de protonation/déprotonation des résidus ionisables d’une protéine sur les paramètres thermodynamiques caractérisant la complexation d’un ligand. Dasns ce but, nous avons étudié l’interaction entre l’α-chymotrypsine et un de ses inhibiteurs compétitifs, la proflavine. Cette protéine est représentative d’un nombre important d’enzymes présentant le même mécanisme catalytique. La compréhension des facteurs qui régissent les équilibres de protonation/déprotonation des résidus ionisables présents dans son site actif ainsi que de l’effet sur ceux-ci de l’interaction avec des ligands est d’une importance primordiale pour le développement d’inhibiteurs plus sélectifs de ces protéases.<p>Cette étude s’est essentiellement composée de trois volets. (i) La réalisation d’un modèle du complexe d’interaction afin de confronter des données structurales aux données expérimentales recueillies. (ii) L’étude de l’interaction entre l’α-chymotrypsine et la proflavine par spectroscopie de Résonance Magnétique Nucléaire (RMN) afin de mettre en évidence les résidus ionisables dont les équilibres de protonation/déprotonation sont influencés par la complexation du ligand. (iii) L’étude de la thermodynamique de l’interaction par Calorimétrie à Titrage Isotherme (ITC) et spectroscopie d’absorption en fonction de l’état d’ionisation des résidus identifiés par l’étude RMN.<p>Le modèle du complexe d’interaction entre l’α-chymotrypsine et la proflavine a été réalisé sur base de la structure cristallographique du complexe entre cet inhibiteur et une protéase apparentée à la chymotrypsine, la thrombine. Il ressort de l’analyse du modèle obtenu que la proflavine est profondément enfouie dans le subsite S1 de l’enzyme et présente une très grande complémentarité de surface avec cette poche hydrophobe. Nous avons également pu constater la présence de plusieurs molécules d’eau immobilisées au sein du complexe, et d’une molécule en particulier faisant office de relais de liens-H.<p>L’étude de l’interaction entre l’α-chymotrypsine et la proflavine par RMN du 1H a été précédée par une étude de l’effet du degré de maturité de l’enzyme sur les interactions liant les différents résidus composant la triade catalytique (Asp102, His57 et Ser195). Lors de l’activation du précurseur inactif de l’enzyme, le chymotrypsinogène, vers la forme mature, l’α-chymotrypsine, il semble en effet que le lien-H entre le NH&949;2 de l’His57 et le Oγ de la Ser195 soit affaibli, contrairement à celui qui relie le NHδ1 de cette même histidine au Oδ1 de l’Asp102. Nous rapportons pour la première fois l’observation de l’influence de la protonation de l’Asp102 sur les déplacements chimiques des protons NHδ1 et NH&949;2 de l’His57. L’étude de l’interaction entre l’α-chymotrypsine et la proflavine par RMN, nous a permis de mettre en évidence l’effet de la complexation du ligand sur l’état d’ionisation des résidus His57 et Asp102 de la triade catalytique, les pKa de ces résidus dans l’enzyme libre valant respectivement 7 et approximativement 4.<p>Les paramètres thermodynamiques de l’interaction α-chymotrypsine - proflavine et des différents équilibres de protonation/déprotonation qui y sont liés ont été obtenus par spectroscopie d’absorption et ITC. Cette dernière technique constitue un outil précieux pour l’étude d’interactions moléculaires car il s’agit de la seule technique expérimentale permettant la mesure directe de l’enthalpie d’interaction. Lorsque des équilibres de protonation/déprotonation sont thermodynamiquement liés à l’interaction, il s’agit également de la seule technique permettant la quantification de ces effets. En mesurant la constante d’affinité et l’enthalpie d’interaction observées à différents pH et dans différents tampons, nous avons pu, sur base du modèle obtenu par RMN, déterminer les paramètres thermodynamiques intrinsèques des différents équilibres.<p>La corrélation entre les données thermodynamiques obtenues par ITC et spectroscopie d’absorption et les données structurales obtenues par RMN et sur base de l’analyse du modèle du complexe d’interaction, nous a permis de rationaliser les facteurs à la base de l’interaction préférentielle de l’inhibiteur avec une des formes de l’enzyme. L’interaction entre l’α-chymotrypsine et la proflavine est la plus favorable lorsqu’à la fois l’His57 et l’Asp102 sont déprotonnés. Cette interaction est caractérisée par un terme enthalpique favorable et un terme entropique légèrement défavorable. Ce dernier terme s’expliquerait en partie par l’immobilisation dans le site d’interaction de plusieurs molécules d’eau. L’affinité entre l’α-chymotrypsine et la proflavine diminue lorsque l’His57 se protonne. La répulsion électrostatique entre les charges positives de la proflavine et de l’His57 est vraisemblablement un des facteurs permettant d’expliquer cette diminution de la constante d’affinité. Nous n’avons pu mettre en évidence d’interaction entre ces deux molécules dès lors que l’Asp102 est protonné, malgré que ce résidu soit situé relativement loin de la proflavine dans le complexe. Il s’agit donc d’un effet indirect, probablement relayé par l’His57. Tant que l’Asp102 est déprotonné, sa charge négative compenserait la charge positive de l’His57 et réduirait la répulsion électrostatique avec la proflavine, ce qui n’est plus le cas lorsque l’aspartate se protonne. / Doctorat en sciences appliquées / info:eu-repo/semantics/nonPublished

Abstract The subject of this thesis is the characterization of chemical reactions and adsorption by means of remote detection (RD) method of nuclear magnetic resonance (NMR). The thesis consists of three related topics: In the first one, novel RD NMR based methods for characterizing chemical reactions were presented. In the second topic RD NMR methods were used to study the performance of new kind of microfluidic reactors. The third project concentrated on the development of a novel way to quantify the adsorption of flowing gas mixtures in porous materials. Even though all the topics cover quite different areas of research, they have few common nominators: remote detection NMR, microfluidics and method development. Microfluidic devices are of interest for many areas of science (such as molecular biology, disease diagnosis, chemistry) as they offer great promises for future technologies. Small dimensions enable, among many other things, the benefits of small sample volumes, large surface to volume ratio, efficient heat exchange and precise control of flow features and chemical reactions. The efficient evolution of microfluidic processes requires also the development of new innovative ways to characterize the performance of microfluidic devices. In this work, remote detection NMR is utilized for the purpose. RD is a method where the encoding and detection of information are separated physically. In many cases, the encoding and detection are performed with two separate RF coils while a fluid is passing through the studied system. In the first part of the thesis work, we introduced the concept of remote detection exchange (RD-EXSY) NMR spectroscopy. We demonstrated that the RD-EXSY method can provide unique chemical information. Furthermore, the time-of-flight (TOF) information, which is a natural side product of the experimental setup used, can be converted into indirect spatial information, showing the active reaction regions in a microfluidic device. Additionally, we demonstrated that by applying the principles of Hadamard spectroscopy in the encoding of the indirect spectral dimension we were able to produce with high efficiency RD-EXSY TOF images with direct spatial information. This allows even more accurate characterization of the active regions. The second topic concentrates on the development of microfluidc hydrogenation reactors. In the project atomic layer depositon (ALD) method was used for the first time to deposit both catalyst nanoparticles and support material on the surface of wall-coated microreactors. As a model reaction continuous flow propene hydrogenation into propane was studied by means of remote detection NMR. Reaction yield, mass transport phenomena and the activity of the catalyst surface were determined from the RD NMR data. Thirdly we presented a novel method for gas adsorption measurements in porous materials using RD TOF NMR. Traditional adsorption measurements are carried out at static conditions for a single gas component, as multi-component adsorption measurements are challenging and time-consuming. We investigated adsorption of continuously flowing propane and propene gases as well as their mixture in packed beds of mesoporous materials. The unique time-of-flight information obtained using the RD NMR method was utilized in the determination of flow velocity, which was then converted into amount of adsorbed gas.

The interaction of a diverse set of opioid alkaloids and peptides with various opioid receptors has been examined using biochemical and pharmacological techniques. Structural information on the compounds was obtained from single crystal X-ray diffraction and nuclear magnetic resonance studies, and modelled by computational methods. The introduction of a dithiocarbazate moiety into the 7a-position of a bridged thebaine was shown to afford a degree of μ selectivity in this class of nonselective compounds. X-ray diffraction analysis of this compound and comparison with the structure of [Met5]enkephalin showed the importance of the sulphydryl moiety. The conformation of [Leu5]enkephalin, in which the amino acid methionine is replaced by leucine, at the same receptor is unlikely to be similar. A series of morphinan derivatives which had been developed as μ-antagonists were evaluated. Substitution patterns of the morphinan ring nucleus and their effect upon activity were examined. X-ray analysis of several key compounds was performed. Unexpectedly a 3-hydroxymorphinan-6-one analogue showed an ability to differentiate apparently similar opioid Kreceptors. The implications in terms of K-receptor subtypes are discussed. The opioid receptor binding characteristics of structurally diverse K-receptor ligands were examined in two different buffer systems. Electrostatic modelling of the K-ligands, based upon crystal structure coordinates, was performed. From electrostatic potential maps a requirement for ligands acting at Kreceptors is postulated. Solution conformations of the endogenous K-ligand, dynorphin A(1-8), were determined by nuclear magnetic resonance studies and compared with the wo preferring [Leu5]enkephalin. Models were proposed based upon dihedral angles determined from HCtl-NH coupling constants, amide proton-deuteron exchange and amide proton temperature coefficient data. Candidate conformations were shown to be stable under dynamic simulation conditions. Electrostatic modelling of a chosen dynorphin An-8) conformation gave results comparable with the observed electrostatic model of the K-ligands. The proposed model is discussed in terms of its suitability as a retro-model for the active site ofthe K-opioid receptor.

Abstract This thesis presents computational first-principles investigations of nuclear magnetic resonance (NMR) parameters in metal-containing nanosystems. Special attention is paid to the relativistic effects observed in the vicinity of heavy elements. Small transition metal complexes are used to assess the feasibility of a quasirelativistic density functional theory (DFT) approach for calculating nuclear magnetic shielding tensors of increasingly heavy metal nuclei, followed by applications of the concept to larger systems. Nuclear magnetic shielding constants, shielding anisotropies, and chemical shifts with respect to metal ions are calculated in dimethyl and water complexes of the group-12 transition metals 67Zn, 111/113Cd, and 199/201Hg, using Hartree–Fock and DFT methods with relativistic corrections from the Breit–Pauli Perturbation Theory (BPPT). Four-component relativistic Dirac–Hartree–Fock and correlated, nonrelativistic ab initio calculations are used to benchmark the BPPT and DFT methods, respectively. The DFT/BPPT approach, combined with Monte Carlo simulations at finite temperatures, is subsequently used to calculate the chemical shift of a guest 129Xe inside a tetrahedral, iron-based cage. Complementing experiments, the encapsulation of xenon is verified, and empirically elusive details are revealed about the guest dynamics. Finally, the full shielding tensors of 31P and 195Pt and the indirect spin–spin coupling constants between the two nuclei are studied in five crystalline platinum(II) dialkyldithiophosphato complexes, concentrating on the solid-state chemical shift anisotropy and asymmetry parameters of phosphorus and platinum. The NMR parameters are calculated using DFT and the two-component zerothorder regular approximation (ZORA) for relativistic effects, combining molecular and solid-state models to incorporate indispensable contributions due to spin–orbit and crystal lattice corrections for the shielding tensors. Four-component matrix-Dirac–Kohn–Sham shielding calculations are used to benchmark the ZORA method. Qualitative, in cases nearly quantitative agreement is obtained with experiments, allowing the validation of the X-ray structures of the complexes, as well as a deeper analysis of the differences between them, including the major contributions to the NMR parameters. The results presented here demonstrate that computational NMR, a branch of relativistic quantum chemistry, is applicable and useful in studying nanoscale systems containing heavy elements, such as transition metals. Approximations are necessary to enable the treatment of large and complex targets, but sufficient accuracy is achieved for supplementing experiments with reliable and useful data that provides additional insight and analysis possibilities.

Abstract This thesis presents computational studies of both the static and dynamic parameters of the nuclear magnetic resonance (NMR) spectroscopy of gaseous xenon. First, state-of-the-art static magnetic resonance parameters are computed in small xenon clusters by using methods of quantum chemistry, and second, time-dependent relaxation phenomena are investigated via molecular dynamics simulations at different experimental conditions. Based on the underlying quantum and classical mechanics concepts, computational methods represent a procedure complementary to experiments for investigating the properties of atoms, molecules, clusters and solids. Static NMR spectral parameters, chemical shift, shielding anisotropy and asymmetry parameter, nuclear quadrupole coupling, and spin-rotation coupling, are calculated using different electronic structure methods ranging from the uncorrelated Hartree-Fock method to correlated second-order Møller-Plesset many-body perturbation, complete/restricted active space multiconfiguration self-consistent field, and to coupled-cluster approaches. The bond length dependence of these properties is investigated in the xenon dimer (Xe2). A well-characterized property in experimental NMR, the second virial coefficient of nuclear shielding, is theoretically calculated by a variety of methods and convincingly verified against experimental findings. Here, it is mandatory to include effects from special relativity as well as electron correlation. As a side result, a purely theoretical potential energy curve for Xe2, comparable to best experimental ones, is calculated. A pairwise additive scheme is established to approximate the NMR properties in differently coordinated sites of xenon clusters Xen (n = 2 - 12). Especially the pairwise additive chemical shift values are found to be in close agreement with quantum-chemical results and only a small scaling factor close to unity is needed for the correct behavior. Finally, a dynamical magnetic resonance property, the experimental nuclear spin-lattice relaxation rate R1 of monoatomic Xe gas due to the chemical shift anisotropy (CSA) mechanism is validated from first principles. This approach is based on molecular dynamics simulations over a large range of temperatures and densities, combined with the pairwise additive approximation for the shielding tensor. Therein, the shielding time correlation function is seen to reflect the characteristic time scales related to both interatomic collisions and cluster formation. For the first time, the physics of gaseous xenon is detailed in full in the context of CSA relaxation.

This study has focused on the synthesis of truncated analogues of the hydroxyethylene dipeptide isosteres, such as Ritonavir®, currently in clinical use as HIV-1 protease inhibitors. The reactions of pyridine-2- and quinoline-2-carbaldehydes with methyl acrylate, in the presence of 1,4-diazabicyclo[2.2.2]octane (DABCO) or 3- hydroxyquinuclidine (3-HQ) as nucleophilic catalysts, have afforded a series of Baylis- Hillman adducts, acetylation and cyclisation of which have provided access to a series of indolizine-2-carboxylate esters. The carboxylic acids, obtained by base-catalyzed hydrolysis of these esters, have been coupled with various protected (and unprotected) amino compounds using the peptide coupling agent, 1,1’-carbonyldiimidazole (CDI), to afford a series of indolizine-2-carboxamides as indolizine-based truncated Ritonavir® analogues in quantitative yield. Aza-Michael reactions of pyridine-3-carbaldehydederived Baylis-Hillman adducts with various amino compounds have provided access to a range of pyridine-based products as mixtures of diastereomeric aza-Michael products. The assignment of the relative stereochemistry of the aza-Michael products has been established using 1-D and 2-NOESY experiments and computer modelling techniques. Computer modelling studies have also been conducted on selected aza-Michael products using ACCELRYS Cerius2 software, followed by interactive docking into the HIV-1 protease receptor site, using AUTODOCK 4.0. The docking studies have revealed hydrogen-bonding interactions between the enzyme and the synthetic ligands. Saturation Transfer Difference (STD) NMR experiments have also indicated binding of some of the aza-Michael products to the HIV-1 protease subtype C enzyme, thus indicating their binding and possible inhibitory potential.