Predicting and quantifying solvent effects on non-covalent interactions is often very challenging, as they are influenced and modulated by multiple factors. In this thesis, a series of molecular torsion balances is used as a tool to tackle the complexities of noncovalent interactions in solution. Chapter 1 presents an up-to-date literature review on solvent effects on non-covalent interactions, with a particular focus on solvent effects on conformational equilibria and molecular torsion balances. Chapter 2 demonstrates the use of molecular torsion balances and a simple explicit solvation computational model to show that the electrostatic potential of the substituted aromatic rings is largely dependent on the explicit solvation of the substituent. The contribution of both bond polarisation and through-space field effects is also covered. Chapter 3 provides a literature review on the deuterium isotope effects on non-covalent interactions, presenting a range of contradictory findings. Molecular torsion balances are used here as a probe of H/D isotope effects on the conformational equilibria, solvent isotope effects and the solvophobic effect in aqueous mixtures. The balances are studied from thermodynamic and kinetic viewpoints, through which both intra- and intermolecular interactions are examined. It is shown here that H/D isotope effects on the presented system are either non-existent or negligibly small. Chapter 4 presents the use of molecular torsion balances to investigate carbonylcarbonyl interactions, taking into account steric and solvent effects. This is compared experimentally and computationally against two existing theories rationalising these interactions. In Chapter 5, a background of metal-ligand interactions is outlined, along the most widely utilised theories rationalising them. The electronic effects of Pt complexation by a pyridyl-substituted molecular torsion balance is analysed both experimentally and computationally, and the arising discrepancies are addressed. The applicability limits of the previously presented simple solvation models are determined using systems displaying extreme electronic effects.

Solvent effects on the chemical exchange of a push pull Ethylenes <p> Chemical exchange rates provide a sensitive probe of solvent effects in solution. The push-pull ethylene methyl 3-dimethylamino-2-cyanocrotonate (MDACC) has three exchange processes E-Z (the same as E' -Z'), E-E', and Z-Z', and we have measured these rates in acetone-d6, chloroform-d, tetrahydrofuran-d8, toluene-d8, methanol-d4, acetonitrile-d3, and methylene chloride-d2 through 1D 1 H.NMR at different temperatures. From this we obtain ΔG+, ΔHt+, ΔS+ of activation for each solvent by employing an Eyring plot. As the solvent changes, ΔH+ is approximately constant whereas ΔS+ follows the solvent polarity. </p> <p> Since the equilibrium constant is less than one, we would expect it to increase with temperature, but it decreases. This is seen in the Van't Hoff plot where the slope is positive indicating that the process of going from the major site to the minor site is exothermic, so not only is the rate governed by entropy effects, but also the equilibrium constant between E and Z. </p> <p> The rotation between the C-N and the C=C bond occurs through a non-concerted mechanism. Two reasons why this occurred was apparent through EXSY, since the intensity of the off diagonal peak varies with different mixing time and second, the rates from C=C rotation (E-Z) and C-N rotations (E-E' and Z-Z') are different at the same temperature </p> / Thesis / Master of Science (MSc)

No description available.

Nesta tese estudamos o espectro de absorção da Merocianina de Brooker (MB) e três derivados em solventes com diferentes polaridades. O interesse no estudo desses sistemas se dá pela presença de algumas propriedades particulares das merocianinas, por exemplo, apresentam um grande deslocamento solvatocrômico devido à mudança na polaridade do meio. Nós apresentamos os resultados teóricos obtidos para o espectro de absorção das moléculas considerando diferentes estruturas para o estado fundamental: formas trans, cis, zwiteriônica (zw), protonada (MBH+) e dímero(MB2). O efeito do solvente foi considerado utilizando diferentes modelos de solvatação: (i) modelo contínuo polarizável (PCM), (ii) através de uma configuração eletrostática média do solvente (ASEC), (iii) incluindo algumas moléculas explícitas do solvente juntamente com um ambiente eletrostático gerado pelas demais moléculas do solvente. Como uma investigação adicional, apresentamos nossos resultados de medidas experimentais para o espectro de absorção da MB em vários solventes variando acidez e concentração. Vimos, através de cálculos quânticos, que as formas cis/trans apresentam a excitação eletrônica na mesma região, e que a deformação estrutural gerada pela forma zw provoca um deslocamento para o vermelho na excitação eletrônica. Os nossos resultados teóricos e experimentais mostram que a forma MBH+ apresenta um solvatocromismo pequeno, com deslocamento de 20 nm provocado pela mudança água-clorofórmio. Realizando medidas experimentais através da titulação espectroscópica nós obtivemos o pKa associado ao processo de desprotonação/protonação da MB em água e metanol. Em água obtivemos um valor de 8.7, em boa concordância com valores da literatura. Apresentamos um valor inédito do pKap da MB em metanol, 9.9. Conseguimos uma boa descrição teórica para a excitação eletrônica da MB em solventes com alta polaridade, na região entre 430-500 nm, utilizando o método quântico TD-DFT com funcionais B3LYP e CAM-B3LYP e conjunto de funções base 6-311+G**, porém a excitação em solventes de baixa polaridade, que ocorre na região entre 550-650 nm, não é corretamente descrita considerando a MB nos solventes. Nós vimos, através de estudos experimentais, que a sonda MB pode agregar em solventes de baixa polaridade. Os cáculos teóricos para dímeros em solução mostraram a existência de uma excitação eletrônica de baixa intensidade nesta região. Adicionalmente, os espectros experimentais em solventes de baixa polaridade mostraram 2 bandas, onde a segunda se assemelha com a banda observada para a forma MBH+. Para explicar essas 2 bandas experimentais para a MB, apresentamos uma proposta teórica onde ocorre uma transferência de prótons (H+) entre os monômeros do dímero formado, gerando uma estrutura desprotonada (MBH-) e uma protonada (MBH+). Cálculos teóricos para a forma MBH- mostram que essa forma apresenta uma excitação eletrônica de intensidade moderada na região entre 550-650 nm. Com essa hipótese nós conseguimos descrever, através de cálculos teóricos, o solvatocromismo anômalo observado experimentalmente para o espectro eletrônico de absorção da MB nas duas regiões de polaridade dos solventes: alta polaridade, sendo descrita pela forma MB, e baixa polaridade, descrita pela forma MBH-. / In this thesis we studied the absorption spectrum of merocyanine Brooker (MB) and three derivatives in solvents with different polarities.The interest in this system is given by the presence of some particular properties of this molecule, for example, it presents a large solvatochromic shift due to the change in the polarity of the medium. We present the results for the absorption spectrum of the molecules considering different structures to the ground state: forms trans, cis, zwitterionic (zw), protonated MBH+ and dimer (MB2). The solvent effect was treaty by different ways: (i) continuous model using the PCM polarizable, (ii) by an average electrostatic configuration of solvent, ASEC, (iii) including some explicit solvent molecules with an electrostatic environment generated by other solvent molecules. As an additional investigation, we present results of experimental measurements in the thesis. We have seen, through quantum calculations, that the forms cis/trans have the electronic excitation in the same region and the structural deformation generated in the zw form causes a red shift. Our theoretical and experimental results show that the MBH+ form has a small solvatochromism, with displacement of 20 nm caused by water-chloroform change. Performing spectroscopic titration we got the pKa associated with the process of deprotonation/protonation of MB in water and methanol. In water we obtained a value of 8.7, in good agreement with the values reported in the literature. We present a unpublished pKap for the MB in methanol, 9.9. We got a good theoretical description for electronic excitation of MB in solvents with high polarity, in the region between 430-500 nm, using a method quantum TD-DFT B3LYP and CAM-B3LYP functional whit basic functions set 6-311+G** but the excitation in low polarity solvents, which occurs in the region between 550-650 nm, is not properly described considering the MB form in the solvents. We have seen, through experimental studies that the MB probe can aggregate in low polarity solvents. Theoretical calculations for dimer in solution showed the existence of a low intensity electron excitation in this region. Additionally, the experimental spectra in low polarity solvents showed 2 bands, where in the second band is similar to the observed to MBH+ form. To explain these two experimental bands for MB, we present a theoretical proposal where there is a proton transfer (H+) between the monomers of the dimer, generating a deprotonated structure (MBH-) and a protonated (MBH+). Theoretical calculations for the MBH- show that this form presents an electronic excitation of moderate intensity in the region between 550-650 nm. With this assumption we can describe, through theoretical calculations, the anomalous solvatochromism for the electronic absorption spectrum of MB in the two polarity regions of solvents: high polarity is described by the MB form, and low polarity, described by the MBH- form.

Non-covalent interactions in solution are subject to modulation by surrounding solvent molecules. This thesis presents two experimental molecular balances that have been used to quantify solvent effects on non-covalent interactions, including electrostatic and dispersion interactions. The first chapter introduces literature where non-covalent interactions have been studied in a range of solvents, particularly those where the effects of aqueous or fluorous solvents have been investigated. These solvents are of particular interest as they both invoke solvophobic effects on organic molecules, but have differing chemical and physical properties. The second chapter describes the adaptation of the Wilcox molecular torsion balance to study interactions between organic and fluorinated carbon chains in a range of solvents. Solvent cohesion was found to be the principle force driving both the alkyl and fluorous chains together in aqueous solvents, where no contribution to the interaction energy arising from dispersion forces could be detected. In fluorous and polar organic solvents evidence was found for weak favourable dispersion interactions between the alkyl chains. In contrast dispersion forces between the chains were found to be disrupted by competitive van der Waals interactions with surrounding solvent molecules in apolar organic solvents. Association of the fluorous chains was found to be solely driven by solvent cohesion. The final chapter describes the design and synthesis of a novel synthetic molecular-balance framework and describes its application to simultaneously measure solvent and substituent effects on the position of conformational equilibria. Despite the simplicity of the model system, surprisingly complicated behaviour emerged from the interplay of conformational, intramolecular and solvent effects. Nonetheless, a large data set of experimental equilibrium constants was analysed using a simple solvent model, which was able to account for both the intuitive and more unusual patterns observed. A means of dissecting electrostatic and solvent effects to reveal pseudo gas-phase behaviour has resulted from the analysis of experimental data obtained in many solvents.

No description available.

Inter-molecular interactions have significant influences on linear and nonlinear optical properties of molecules including one- and two-photon absorptions, emissions, and various high order nonlinear polarizations. The related investigation has become an active and challenging research area. The theoretical structure-to-property relationship obtained from quantum chemical calculations of single organic conjugated molecules often can not be directly applied to real materials in condensed phases. One has to consider the effect of environment, that is, inter-molecular interactions, where the model systems experience in real experiments or applications. The change of molecular conformations under all kinds of interactions and its effects on linear and nonlinear optical properties are the central issue of this thesis. Special attentions have been paid to symmetrical diamino substituted distyrylbenzene chromophores with different torsional angles, two dipolar merocyanine dyes of various orientations, two isomers of a V-shaped 2-hydroxypyrimidine derivative and their various dimers, and the structural fluctuations of interacting polar chromophores in solutions. Quantum chemical methods in combination with molecular dynamics simulations have been employed to study molecular conformations and optical properties in solutions, in particular the solvent and aggregation effects on one- and two-photon absorption. More specifically, time-dependent density functional theory has been used for all electronic calculations, while the polarizable continuum model and supermolecule approach have also been employed to take into account solvent effects. Moreover, the propagation of an ultrashort laser pulse through a one-dimensional asymmetric organic molecular medium which possesses large permanent dipole moments has been simulated by solving full Maxwell-Bloch equations using predictor-corrector finite-difference time-domain method. We have focused on the supercontinuum generation of spectra and the formation of attosecond pulses. / QC20100630

No description available.

Cyclophilin A (CypA) is the well-studied member of a group of ubiquitous and evolutionarily conserved families of enzymes called peptidyl–prolyl isomerases (PPIases). These enzymes catalyze the cis-trans isomerization of peptidyl-prolyl bond in many proteins. The distinctive functional path triggered by each isomeric state of peptidyl-prolyl bond renders PPIase-catalyzed isomerization a molecular switching mechanism to be used on physiological demand. PPIase activity has been implicated in protein folding, signal transduction, and ion channel gating as well as pathological condition such as cancer, Alzheimer’s, and microbial infections. The more than five order of magnitude speed-up in the rate of peptidyl–prolyl cis–trans isomerization by CypA has been the target of intense research. Normal and accelerated molecular dynamic simulations were carried out to understand the catalytic mechanism of CypA in atomistic details. The results reaffirm transition state stabilization as the main factor in the astonishing enhancement in isomerization rate by enzyme. The ensuing intramolecular polarization, as a result of the loss of pseudo double bond character of the peptide bond at the transition state, was shown to contribute only about −1.0 kcal/mol to stabilizing the transition state. This relatively small contribution demonstrates that routinely used fixed charge classical force fields can reasonably describe these types of biological systems. The computational studies also revealed that the undemanding exchange of the free substrate between β- and α-helical regions is lost in the active site of the enzyme, where it is mainly in the β-region. The resultant relative change in conformational entropy favorably contributes to the free energy of stabilizing the transition state by CypA. The isomerization kinetics is strongly coupled to the enzyme motions while the chemical step and enzyme–substrate dynamics are in turn buckled to solvent fluctuations. The chemical step in the active site of the enzyme is therefore not separated from the fluctuations in the solvent. Of special interest is the nature of catalysis in a more realistic crowded environment, for example, the cell. Enzyme motions in such complicated medium are subjected to different viscosities and hydrodynamic properties, which could have implications for allosteric regulation and function.

Radicals are core reactive species that occur in almost every subfield of chemistry. In particular, solution phase radicals find their way into biochemistry (e.g. vitamin B12), and in polymer chemistry (e.g. radical polymerizations) just to name a few. Yet, given the proliferation of radical chemistry, there are still fundamental aspects of it that are poorly understood. This dissertation probed factors that influence the solvent cage effect. The solvent cage effect is where two radicals are held in close proximity to one another and prevented from easily escaping (to form free radicals) by a cage of solvent molecules. A convenient metric of the solvent cage effect is the radical recombination efficiency (FcP). Typically, FcP correlates with the bulk viscosity of the solution, however, this parameter only produces qualitative assessments. This dissertation outlines a method to quantitatively predict FcP using the microviscosity. This microviscosity dependence holds for non polar, aromatic, polar, and hydrogen-bonding solvents, along with solutions that contain polymers. Microviscosity is a great metric because it addresses an underlying reason for the solvent cage effect, the strength of the cage. Not only does the strength of the solvent cage around the radical pair affect FcP, but so does the identity of the radicals themselves. That is, the strength of the solvent cage is one piece to forming a total predictive model. FcP for the Cp'2Mo2(CO)6 dimer also varies with the wavelength of irradiation. Identifying the mechanism by which this wavelength dependence occurs may also provide another factor to include in an overall model of the solvent cage effect. Also, an attempt at synthesizing an asymmetric molybdenum dimer was performed. This asymmetric dimer would allow the study of solvent caged radical pairs that are different from each other. Predicting the photochemical cage pair recombination efficiency (FcP) is the major topic of this dissertation. However, there is also the collisional cage recombination efficiency (Fcʹ). This is where free radicals come together in what is called a collisional solvent cage pair. A method and values of Fcʹ are detailed later in this dissertation. This dissertation contains previously published and unpublished co-authored material.