As aminas heterocíclicas alifáticas, piperidina, piperazina e pirrolidina, interagem com o dióxido de enxofre, gasoso ou líquido, dando origem a uma série de compostos em diferentes estequiometrias, os quais foram investigados fundamentalmente por técnicas espectroscópicas vibracionais, infravermelho e Raman, utilizando-se como técnicas auxiliares a espectroscopia eletrônica, espectros de massas e de ressonância magnética nuclear. Os resultados obtidos caracterizam as espécies estudadas como complexos moleculares formados entre as aminas e o SO2, especialmente devido aos deslocamentos de frequências observados nos espectros Raman, para os modos vibracionais de estiramento simétrico e deformação angular do dióxido de enxofre. Os dados indicam no sentido do estabelecimento de intensas ligações de hidrogênio, as quais devem desempenhar importante papel na estabilização dos complexos. Os deslocamentos observados nos espectros Raman encontram-se de acordo com o comportamento previsto para a interação de transferência de carga, em que o LUMO do SO2 apresenta caráter antiligante em relação à ligação S-O e ligante em relação à interação O-O. / The interaction of alifatic heterocyclic amines piperidine, piperazine and pyrrolidine, with sulfur dioxide yields a variety of products of different stoichiometry. The investigation of the formed species were carried out mainly by vibrational spectroscopic techniques, infrared and Raman, and electronic spectroscopy, mass spectrometry and nuclear magnetic resonance spectra were used as auxiliary techniques. The obtained results indicate that the studied species are charge transfer molecular complexes due to the frequency shifts of the symmetric stretching and angular deformation modes of sulfur dioxide in the Raman spectra. The data are in agreement with an S-O antibonding and a O-O bonding character of the LUMO of SO2. Hydrogen bonds play an important role in the complex stabilization.

xv, 177 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / When two or more fluorescent chromophores are closely spaced in a macromolecular complex, dipolar coupling leads to delocalization of the excited states, forming excitons. The relative transition frequencies and magnitudes are sensitive to conformation, which can then be studied with optical spectroscopy. Non-invasive fluorescence spectroscopy techniques are useful tools for the study of dilute concentrations of such naturally fluorescent or fluorescently labeled biological systems. This dissertation presents two phase-selective fluorescence spectroscopy techniques for the study of dynamical processes in bio-molecular systems across a wide range of timescales. Polarization-modulated Fourier imaging correlation spectroscopy (PM-FICS) is a novel phase-selective fluorescence spectroscopy for simultaneous study of translational and conformational dynamics. We utilize modulated polarization and intensity gratings with phase-sensitive signal collection to monitor the collective fluctuations of an ensemble of fluorescent molecules. The translational and conformational dynamics can be separated and analyzed separately to generate 2D spectral densities and joint probability distributions. We present results of PM-FICS experiments on DsRed, a fluorescent protein complex. Detailed information on thermally driven dipole-coupled optical switching pathways is found, for which we propose a conformation transition mechanism. 2D phase-modulation electronic coherence spectroscopy is a third-order nonlinear spectroscopy that uses collinear pulse geometry and acousto-optic phase modulation to isolate rephasing and nonrephasing contributions to the collected fluorescence signal. We generate 2D spectra, from which we are able to determine relative dipole orientations, and therefore structural conformation, in addition to detailed coupling information. We present results of experiments on magnesium tetraphenylporphyrin dimers in lipid vesicle bilayers. The 2D spectra show clearly resolved diagonal and off-diagonal features, evidence of exciton behavior. The amplitudes of the distinct spectral features change on a femtosecond timescale, revealing information on time-dependent energy transfer dynamics. This dissertation includes co-authored and previously published material. / Committee in charge: Hailin Wang, Chairperson, Physics; Andrew Marcus, Advisor, Chemistry; Stephen Gregory, Member, Physics; Michael Raymer, Member, Physics; Marina Guenza, Outside Member, Chemistry

Three distinct aspects, disorder, polymorphism and co-crystal formation have been addressed in molecular crystals in terms of intra- and intermolecular interactions involving halogens, weak hydrogen bonds and van der Waals interactions. A basic introductory chapter highlights the importance of these three aspects followed by a foreword to the contents. Chapter 1 employs in situ cryo-crystallization techniques to study the crystal and molecular structures of compounds which are liquids at room temperature. Section 1.1 deals with the crystal structure analyses of low melting chloro- and bromo-substituted anilines which reveal both the importance of hydrogen bonds and weak interactions involving different halogens. The halogen⋅⋅⋅halogen interactions are compared with fluorine and iodine substituted compounds to bring out the relevance of both size and polarizability characteristics. Section 1.2 describes the crystal structures of benzyl derivative compounds utilizing the concept of in situ cryo-crystallization. This analysis brings out the correlation between acidity of benzyl derivative compounds with its preference of either a (sp2)C-H⋅⋅⋅π or (sp3)C-H⋅⋅⋅π interactions in the crystal packing. Chapter 2 consists of two sections dealing with the preference of halogen⋅⋅⋅halogen interactions in supramolecular chemistry. Section 2.1 discusses a statistically large number of crystal structures in halogen substituted benzanilide compounds. It reveals the importance of hetero halogen F⋅⋅⋅X (Cl, Br), homo halogen X⋅⋅⋅X (F, Cl, Br, I), C-X⋅⋅⋅π and C-H⋅⋅⋅F interactions in terms of their directionality and preferences to complement a primary N-H⋅⋅⋅O hydrogen bond in directing the three-dimensional supramolecular assembly. Section 2.2 deals with solvent induced polymorphism which highlights the role of weak interactions in two case studies. The preference and directionality of C-H⋅⋅⋅F and Cl⋅⋅⋅Cl interactions lead to dimorphic modifications in case of 3-chloro-N-(2-fluorophenyl)benzamide whereas in case of 2-iodo-N-(4-bromophenyl)benzamide the interactions are through C-H⋅⋅⋅π and I⋅⋅⋅I contacts. Further, the analysis is supported using morphological evidence, DSC (Differential scanning calorimetry) and Powder X-ray diffraction data. Chapter 3 has three sections, concentrating on disorder and its consequence in crystal structures. Section 3.1 discusses the apparent shortening of the C(sp3)–C(sp3) bond analysed via a variable temperature X-ray diffraction study in racemic 1,1′-binaphthalene-2,2′-diyl diethyl bis(carbonate). Variable temperature single crystal X-ray diffraction studies show that the shortening is entirely due to positional disorder and not due to thermal effects. A supercell formation at T≤150 K depicts the formation of a Z'= 2 structure. Section 3.2 deals with crystal structure analysis of Ethyl-4-(2-fluorophenyl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate which clarifies the discrepancy in the higher value of the residual electron density in the literature in terms of positional disorder of fluorine at ortho sites. The existence of fluorine atom at the para position on the phenyl ring of another isomeric molecule leads to disorder induced conformational polymorphism through the involvement of the ethyl group. The static disorder of ethyl group which is associated with only one molecule (Z′=2) could be resolved at 120 K. This supports the results of the previous section (3.1). Section 3.3 reports crystal structure analysis of disordered fluorine in benzanilide compounds. The preference of interactions involving fluorine in either ortho sites or meta sites could be one of the reasons for the positional disorder of both possible sites. With one of the structure showing high Z′ value due to differences in the occupancy of disordered fluorine atom. CSD (Cambridge Structural Database) analysis indicates that the percentage of disorder in halogenated crystal structures having halogen atom at either ortho site or meta site decreases from fluorine to iodine. Further, the analysis points out that the disorder in fluorine containing compounds is mostly localized at the fluorine position whereas for other halogenated disordered structures, the disorder appears at other parts of the molecule. Chapter 4 discusses co-crystal formation and analysis of intermolecular interactions. It consists of two sections. Section 4.1 discusses co-crystal formation of nicotinamide with benzoic acid and seven other derivatives by changing the functional group at different positions of benzoic acid. Hydroxyl (-OH) group at 4/3-postion of benzoic acid prefers phenol⋅⋅⋅pyridine synthon when at 2-position it prefers acid⋅⋅⋅pyridine synthon. The preference of amide anticatemer over dimer synthon is supported by additional C-H⋅⋅⋅O hydrogen bonds. In case of 3,5-dinitro-2-hydroxy benzoic acid, the disorder in hydroxyl (-OH) group at ortho site leads to salt formation. Section 4.2 describes co-crystal study of adenine and thymine (AT) as free nucleobases. This result reveals the formation of AT (2:1) complex with both Hoogsteen and “quasi-Watson-Crick” hydrogen bonds. The hydrogen bonded bases using the Hoogsteen and the “quasi-Watson-Crick” interactions generate a hexagonal supramolecular motif. Four water molecules are located inside the hexagonal void of this complex. A high temperature study on the same crystal shows that at 313K, one of the water molecules escapes from the lattice resulting in the small change in unit cell parameters. However, the space group remains the same and the hexagonal void remains unaltered. With further increase in temperature, the crystal deteriorates irreversibly which clearly brings out the importance of water molecule in the molecular recognition of adenine-thymine complex. Chapter 5 discusses crystal structure analysis of trans-atovaquone (antimalarial drug), its new polymorph form including one stereoisomer (cis) and five other derivatives with different functional groups. Based on the conformational features of these compounds and the characteristics of the nature of hydrogen bonding and other weak intra and intermolecular interactions, docking studies with cytochrome bc1 complex provide valuable insight into the atomistic details of protein-inhibitor interactions. The docking results reveal that atovaquone and its derivatives, owing to their nature of hydrogen bond and the propensity towards the formation of weaker hydrogen bonds involving the chlorine atom as well appear as good candidates for drug evaluation.

No description available.

Le travail présenté concerne la synthèse de calixarènes fonctionnalisés par des groupes sulfonates et carboxylates et l'étude détaillée des structures cristallines de leurs complexes moléculaires ou métalliques avec des métaux 3d et 4f. L'une des préoccupations majeures de ce travail concerne la compréhension des assemblages supramoléculaires dans ces systèmes. Le premier chapitre présente des éléments bibliographiques sur les calixarènes, leur histoire, les différentes conformations et les méthodes principales de fonctionnalisation puis la chimie supramoléculaire associée comprenant les complexes moléculaires et métalliques. Le deuxième chapitre est dédié à une série de complexes moléculaires de type hôte-invité formés entre le para-sulfonatocalix[4]arène (SC4) et différentes bipyridine En continuité avec ce travail nous présentons en suite la structure et les propriétés magnétiques d'un complexe métallique constitué d'un SC4 pontant deux entités dinucléaires de phenanthroline [FeIII2(μ-O)(H2O)5(phen)2] par la coordination des groupes sulfonates. Le troisième chapitre est consacré à la chimie de coordination des calixarènes sulfonatés avec les lanthanides. Nous avons mis en évidence trois types de structures cristallines qui sont toutes des polymères de coordination où les ions lanthanides jouent le rôle d'assembleur des calixarènes par la coordination des groupes sulfonates selon trois types de structure (A, B et C). Nous avons obtenu ces trois structures (A, B et C) pour l'ensemble de lanthanide (La, Pr, Nd , Eu, Gd, Tb, Dy, Ho, Yb). Le quatrième chapitre concerne la chimie de coordination des métaux de transition 3d (Co, Mn, Zn, Cu) avec des calixarènes fonctionnalisés par des groupes carboxylates sur leur partie basse. Avec le calixarène dicarboxylate nous avons obtenu une série de complexes isomorphes dans lesquels deux calixarènes sont coordinés à deux centres métalliques pour former des chaînes infinies. Le cinquième chapitre présente les résultats d'un travail exploratoire visant à synthétiser des azacalix[4]arènes, dans le but de complexer des métaux de transition. L'étude RPE des précurseurs a mis en évidence des espèces radicalaires / This work presents the synthesis of calixarenes functionalized with sulfonate and carboxylate groups and the detailed study of the crystal structures of their molecular or metal complexes with 3d and 4f metals ions. One of the major concerns of this work is the understanding of supramolecular assemblies in these systems. The first chapter gives bibliographic elements on the history, the different conformations and the main methods of functionalization of calixarenes and on their supramolecular chemistry comprising molecular and metal complexes. The second chapter is dedicated to a series of molecular complexes of the host-guest type formed between the para-sulfonatocalix[4]arene (SC4) and various bipyridine. In continuation with this work we then present the synthesis, structure and magnetic properties of a metal complex comprising a SC4 bridging by the sulfonate groups two iron(II) dinuclear entities with coordinated phenathroline [FeIII2 (μ-O)(H2O) 5(phen) 2]. The third chapter is devoted to the coordination chemistry of sulfonated calixarenes with lanthanides. We have found three types of crystal structures which are polymers wherein the lanthanide ion function as an assembler of calixarenes by the coordination of the sulfonate groups along three type of structure (A, B and C). We obtained these three structures (A, B and C) for all lanthanide (La, Pr, Nd, Eu, Gd, Tb, Dy, Ho, Yb). The fourth chapter concerns the coordination chemistry of 3d transition metals (Co, Mn, Zn) with calixarenes functionalized with carboxylate groups on lower rim. With calixarene dicarboxylate we got a series of isomorphic complexes in which two calixarenes are coordinated to two metal centers to form infinite chains. The fifth chapter presents the results of an exploratory work to synthesize azacalix[4]arene with the aim to complex transition metals ions. The EPR study of the precursors has evidenced free radical species

The knowledge of geometry of molecular complexes formed via molecular association in solution through weak interactions is always important to understand the origin of stability and function of an array of molecules, supramolecular assemblies, and macromolecular networks. Simple 1:1 molecular complexes are very useful in this regard as they provide a model to understand both the nature of these interactions and their structural implications. Several weak noncovalent forces from long range (van der Waal’s, electrostatic, induction, dispersion) to short range (charge transfer) govern the geometry, that is, relative orientation of the two molecules in such a complex. On one hand, we find 1:1 electron donor acceptor (EDA) complexes such as naphthalene-tetracyanobenzene, hexamethylbenzene-chloranil etc. which stack parallel or in slipped parallel geometry in their crystals. On the other, benzene dimer has been found to stabilize in T shaped geometry in all its three physical states. In this thesis, I focus on 1:1 EDA complexes in solution. A good volume of literature is available which deals with the optical studies on the formation of such complexes. It has been suggested that the nature of the intermolecular interactions stabilizing these complexes in the gas phase or in their crystals is modified by the presence of solvent-solute interactions in solution thus bringing in difference in the solution geometry. However, the existing experimental techniques, both optical and magnetic, are unable to determine the exact geometries of 1:1 EDA complexes in solution. This opens an opportunity to probe their geometry in solution. The quadratic nonlinearity or first hyperpolarizability (β) of a molecule is a measure of the change in dipole moment (or polarization) in the second order of the applied electrical field and thus has a purely electronic origin. It is a tensorial property and can be resolved in components along the three dimensions. The number of β components and the nonlinear optical anisotropies in a typical donor-acceptor type dipolar molecule, defined as (equation) (where1, 2, 3 axes define the molecular frame, 1 being the direction along the principal axis of symmetry and pointing from the acceptor toward the donor), are determined by the symmetry /structure of the molecule. It has been shown theoretically that the 1:1 EDA complexes possess large hyperpolarizabilities. In the case of pNA dimers calculation revealed that the geometry of the dimer and its symmetry is important for obtaining the correct estimate of β from its tensorial components. Therefore, it should be possible to use the values of tensorial β components to construct the unknown geometry of such complexes. Experimentally macroscopic depolarization ratios (D and D′) in the laboratory fixed frame (XYZ, X being the direction of polarization and Z the direction of propagation of the incident light), are measured from the polarization resolved intensities of second harmonic scattering from molecules in solution using the hyper-Rayleigh scattering technique. The depolarization ratios are correlated to the anisotropy parameters, u and v through a co-ordinate transformation. In this thesis I, have first, characterized the quadratic nonlinear optical property of a variety of 1:1 electron donor acceptor complexes and used the values of u and v obtained from depolarized hyper-Rayleigh scattering to deduce their geometry in solution. Chapter 1 provides an introduction to the 1:1 electron donor acceptor complexes, their relevance to chemistry and biology. It also contains an introduction to nonlinear optical processes in molecules. The objective of the present work and scope of the investigation carried out in this thesis is presented in this chapter. Chapter 2 describes the details of the experimental polarization resolved HRS technique. The geometrical model adopted for the analysis of the HRS data has also been introduced and the method of analysis has been described in detail in this chapter. Chapter 3 presents the measurement of β values of two series of 1:1 EDA complexes of variously substituted methylbenzenes donors with tetrachloro-p-benzoquinone (CHL) and dicyanodichloro-p-benzoquinone (DDQ) acceptors at 1064 nm. In agreement with recent theoretical results we find large first hyperpolarizabilities for these complexes. The β values are greater than that of the typical push-pull molecule p-nitroaniline (pNA). We also find that in general β decreases with decrease in the donor strength. Chapter 4 presents the β values for the two series of EDA complexes of CHL and DDQ acceptors at 1907 nm. The values of β are less in magnitude at 1907 nm than that at 1064 nm which is due to the dispersion effect in β. In Chapter 5 and 6, it is described how depolarized hyper-Rayleigh scattering can be utilized to probe geometries of 1:1 complexes in solution. Chapter 5 concentrates mainly on 1:1 EDA complexes of CHL and DDQ and TCNB (tetracyanobenzene), while chapter 6 contains examples of other 1:1 molecular complexes where the noncovalent interactions are much weaker, such as in benzene-naphthalene, benzene-methoxybenzene, benzene-hexafluorobenzene and benzene-chlorobenzene pairs. We find the geometry of 1:1 EDA complexes in solution in terms of tilt angle (θ) and twist angle (ϕ) between the donor and acceptor pairs. The angle θ varies from 29°-47° for different pairs of EDA complexes, while ϕ varies within 34° and 38°. We find that the geometry of 1:1 EDA complexes in solution is different (twisted and tilted cofacial and twisted ‘V’) from those in the crystalline or gaseous states (cofacial), if known. We find that both benzene-naphthalene and benzene-chlorobenzene pairs assume twisted ‘T’ shape geometry with θ = 82° and 85°, respectively, and φ = 38°, while benzene-hexafluorobenzene assumes a twisted ‘V’ shape. A strong solvent effect is seen in the geometry of the benzene- methoxybenzene complex. The tilt angle is 55° when chloroform is used as a solvent and it is 82° without chloroform. Chapter 7 is the concluding chapter where the main work done in this thesis is summarized and future directions are presented.

No description available.