This thesis reports a comprehensive study of the electrostatic solvation energy computation for macromolecules. In the molecular dynamics (MD) simulations it is important to be able to compute the free energy of the system accurately and efficiently. The solvation energy which is dominated by the electrostatics plays a significant role in the dynamics of macromolecules in solution. The standard way of computing the electrostatic solvation energy is to solve the Poisson-Boltzmann (PB) equations. However, due to the large size of the system, the computation cost of solving the PB equation becomes a bottleneck even for the continuum implicit solvent. The alternative method is the newly developed generalized Born (GB) method which gives a good approximation to the PB calculation if the Born radii are properly computed. The computation of the Born radii is the core computation in the GB method and is laborious. In this thesis we present a novel error-bounded fast surface GB approach which significantly improves the traditional surface GB approaches. An analytic algebraic spline model is built for the geometric model of the molecular surfaces which allows one to do the accurate computation on a coarse mesh. Based on the surface GB theory, we develop an algorithm that computes the Born radii by using the fast summation algorithm at a complexity nearly linear in terms of the number of atoms of the molecule and the number of elements on the mesh of the molecular surface. The algorithm is also extended to the electrostatic forces calculations. Finally we propose a hierarchical coarse grained (CG) model aiming at reducing the number of atoms in a macromolecule while still being able to reproduce the geometry as well as the electrostatic interactions of the atomic model. / text

Calculating the solvation energies of surfactants is a way to predict the cmc. The solvation energies were determined for a homologous series of betaines, (CH₃)₃N+(CH₂)nCOO- where n = 1 to 6. Their structure is composed of only the hydrophilic head group of a surfactant. The solvation energies were determined from both the gas phase energy and free energy of solution. Conformational analysis was performed on each molecule to locate the lowest energy structures and determine the Boltzmann population of each conformation for each molecule. The final solvation energies for each molecule are expectation values based on their energies and Boltzmann populations. The plotted solvation energies versus n form a parabolic curve that is similar to the literature cmc data where the betaine has a long hydrocarbon tail. However, the solvation energies peak at n = 3 and the cmc data peaks at n = 4. The dipole moments were also examined. The gas phase dipole moments were graphed and have a maximum at n = 3, similar to the solvation energy. The solution dipole moments have a linear graph, not comparable to the solvation energies. Therefore, the stability of the gas phase structures contributes more to the final solvation energy than the stability of the molecule in water. The correlation between the plots of log cmc vs n and solvation energy vs n indicates that it is possible to computationally predict the cmc with this method. The hydrophobic contribution can be accounted for based on a known correlation between chain length and the cmc, and the hydrophilic contribution can be examined with this method. Therefore, it is possible to design a new surfactant molecule that has a cmc within the range of the biological activity to be sent for synthesis. / Master of Science

<div>The widely accepted Non-equilibrium Greens functions (NEGF) method and the Self-Consistent Born Approximation, to include scattering, is employed. Due to the large matrix sizes typically needed when solving Greens functions, an efficient recursive algorithm is typically utilized. However, the current state of the art of this so-called recursive Greens function algorithm only allows the inclusion of local scattering or non-locality within a limited range. Most scattering mechanisms are Coulombic and are therefore non-local. Recently, we have developed an addition to the recursive Greens function algorithm that can handle arbitrary non-locality. Validation and performance will be assessed for nanowires.</div><div><br></div><div>The second half of this work discusses the modeling of an active ingredient in a liquid environment. The state of the art is outlined with options for different modeling approaches - mainly the implicit and the explicit solvation model. Extensions of the explicit model to include an open, quantum environment is the main work of the second half. First results for an extension of the commonly used molecular dynamics with thermodynamic integration are also presented.</div>

The Abraham solvation model (ABSM) is an experimentally derived predictive model used to help predict various solute properties. This work covers various uses for the ABSM including predicting molar enthalpies of vaporization, predicting solvent coefficients for two new solvents (2,2,5,5-tetramethyloxolane and diethyl carbonate), predicting values for multiple new ionic liquids (ILs). This work also introduces a novel method for updating IL ABSM parameters by updating cation- and anion-specific values using linear algebra and binary matrices.

No presente trabalho descrevemos nossos resultados relativos à investigação da dinâmica de solvatação mecânica por meio de simulações por dinâmica molecular, respeitando o regime da resposta linear, em sistemas-modelo de argônio líquido com um soluto monoatômico ou diatômico dissolvido. Estudamos sistematicamente a influência dos parâmetros moleculares dos solutos (tamanho, polarizabilidade) e da densidade frente a vários modelos de solvatação. Funções de Correlação Temporal da Energia de Solvatação foram calculadas com relação à correlações de n-corpos (n = 2; 3) distinguindo interações repulsivas e atrativas para ambos os sistemas líquidos. Também obtivemos segundas derivadas temporais dessas funções referindo-se à parcelas translacionais, rotacionais e roto-translacionais na solução do diatômico. Encontramos que funções de correlação temporal coletivas podem ser razoavelmente bem aproximadas por correlações binárias a densidades baixas e, a densidades altas, correlações ternárias tornam-se mais importantes produzindo um descorrelacionamento mais rápido das funções coletivas devido a efeitos de cancelamento parciais. As funções de correlação para interações repulsivas e atrativas exibem comportamentos dinâmicos independentes do modelo de solvatação devido a fatores de escalonamento linear que afetam apenas as amplitudes das dessas funções de correlação temporal. Em geral, os sistemas com grau de liberdade rotacional apresentam tempos de correlação mais curtos para a dinâmica coletiva e tempos de correlação mais longos para as funções binárias e ternárias. Finalmente, esse estudo mostra que os sistemas contendo o diatômico relaxam-se predominantemente por mecanismos translacionais binários em modelos de solvatação envolvendo alterações apenas na polarizabilidade do soluto, e por mecanismos rotacionais atrativos binários em modelos envolvendo alterações no comprimento de ligação. / In the present work, we describe our results concerning our molecular dynamics investigation of the mechanical solvation dynamics within the linear response regime in model systems composed by liquid argon with a monoatomic or diatomic solute. The effect of molecular parameters (size, polarizability) and density has been elucidated for various solvation models. Time Correlation Functions for the solvation energy were calculated and separated into n-body (n = 2; 3) contributions distinguishing repulsive and attractive interactions in both liquid systems. In addition, we computed second time derivatives of these functions in order to describe translational, rotational, and roto-translational portions in the solutions containing the diatomics. We found that collective time correlation functions are well described by binary correlations at low liquid densities and, at high densities, ternary correlations become more important producing faster decaying collective time correlation functions due to partial cancellation effects. The repulsive and attractive time correlation functions exhibit a dynamic behavior that is independent on the solvation model due to linear scaling factors that only affect the absolute amplitudes of these functions. In general, the systems involving a rotational degree of freedom furnish smaller correlation times for the collective solvation dynamics, but stronger correlated two-body and three-body terms. Finally, this study shows that the solvation dynamics for the solution containing the diatomics relaxes predominatly by binary translational mechanisms when solvation models involving changes only in the polarizability parameter are considered. Binary attractive rotational mechanism become important in models with changes in the bond length.

No presente trabalho descrevemos nossos resultados relativos à investigação da dinâmica de solvatação mecânica por meio de simulações por dinâmica molecular, respeitando o regime da resposta linear, em sistemas-modelo de argônio líquido com um soluto monoatômico ou diatômico dissolvido. Estudamos sistematicamente a influência dos parâmetros moleculares dos solutos (tamanho, polarizabilidade) e da densidade frente a vários modelos de solvatação. Funções de Correlação Temporal da Energia de Solvatação foram calculadas com relação à correlações de n-corpos (n = 2; 3) distinguindo interações repulsivas e atrativas para ambos os sistemas líquidos. Também obtivemos segundas derivadas temporais dessas funções referindo-se à parcelas translacionais, rotacionais e roto-translacionais na solução do diatômico. Encontramos que funções de correlação temporal coletivas podem ser razoavelmente bem aproximadas por correlações binárias a densidades baixas e, a densidades altas, correlações ternárias tornam-se mais importantes produzindo um descorrelacionamento mais rápido das funções coletivas devido a efeitos de cancelamento parciais. As funções de correlação para interações repulsivas e atrativas exibem comportamentos dinâmicos independentes do modelo de solvatação devido a fatores de escalonamento linear que afetam apenas as amplitudes das dessas funções de correlação temporal. Em geral, os sistemas com grau de liberdade rotacional apresentam tempos de correlação mais curtos para a dinâmica coletiva e tempos de correlação mais longos para as funções binárias e ternárias. Finalmente, esse estudo mostra que os sistemas contendo o diatômico relaxam-se predominantemente por mecanismos translacionais binários em modelos de solvatação envolvendo alterações apenas na polarizabilidade do soluto, e por mecanismos rotacionais atrativos binários em modelos envolvendo alterações no comprimento de ligação. / In the present work, we describe our results concerning our molecular dynamics investigation of the mechanical solvation dynamics within the linear response regime in model systems composed by liquid argon with a monoatomic or diatomic solute. The effect of molecular parameters (size, polarizability) and density has been elucidated for various solvation models. Time Correlation Functions for the solvation energy were calculated and separated into n-body (n = 2; 3) contributions distinguishing repulsive and attractive interactions in both liquid systems. In addition, we computed second time derivatives of these functions in order to describe translational, rotational, and roto-translational portions in the solutions containing the diatomics. We found that collective time correlation functions are well described by binary correlations at low liquid densities and, at high densities, ternary correlations become more important producing faster decaying collective time correlation functions due to partial cancellation effects. The repulsive and attractive time correlation functions exhibit a dynamic behavior that is independent on the solvation model due to linear scaling factors that only affect the absolute amplitudes of these functions. In general, the systems involving a rotational degree of freedom furnish smaller correlation times for the collective solvation dynamics, but stronger correlated two-body and three-body terms. Finally, this study shows that the solvation dynamics for the solution containing the diatomics relaxes predominatly by binary translational mechanisms when solvation models involving changes only in the polarizability parameter are considered. Binary attractive rotational mechanism become important in models with changes in the bond length.

No presente trabalho descrevemos nossos resultados relativos à investigação da dinâmica de solvatação mecânica por meio de simulações por dinâmica molecular, respeitando o regime da resposta linear, em sistemas-modelo de argônio líquido com um soluto monoatômico ou diatômico dissolvido. Estudamos sistematicamente a influência dos parâmetros moleculares dos solutos (tamanho, polarizabilidade) e da densidade frente a vários modelos de solvatação. Funções de Correlação Temporal da Energia de Solvatação foram calculadas com relação à correlações de n-corpos (n = 2; 3) distinguindo interações repulsivas e atrativas para ambos os sistemas líquidos. Também obtivemos segundas derivadas temporais dessas funções referindo-se à parcelas translacionais, rotacionais e roto-translacionais na solução do diatômico. Encontramos que funções de correlação temporal coletivas podem ser razoavelmente bem aproximadas por correlações binárias a densidades baixas e, a densidades altas, correlações ternárias tornam-se mais importantes produzindo um descorrelacionamento mais rápido das funções coletivas devido a efeitos de cancelamento parciais. As funções de correlação para interações repulsivas e atrativas exibem comportamentos dinâmicos independentes do modelo de solvatação devido a fatores de escalonamento linear que afetam apenas as amplitudes das dessas funções de correlação temporal. Em geral, os sistemas com grau de liberdade rotacional apresentam tempos de correlação mais curtos para a dinâmica coletiva e tempos de correlação mais longos para as funções binárias e ternárias. Finalmente, esse estudo mostra que os sistemas contendo o diatômico relaxam-se predominantemente por mecanismos translacionais binários em modelos de solvatação envolvendo alterações apenas na polarizabilidade do soluto, e por mecanismos rotacionais atrativos binários em modelos envolvendo alterações no comprimento de ligação. / In the present work, we describe our results concerning our molecular dynamics investigation of the mechanical solvation dynamics within the linear response regime in model systems composed by liquid argon with a monoatomic or diatomic solute. The effect of molecular parameters (size, polarizability) and density has been elucidated for various solvation models. Time Correlation Functions for the solvation energy were calculated and separated into n-body (n = 2; 3) contributions distinguishing repulsive and attractive interactions in both liquid systems. In addition, we computed second time derivatives of these functions in order to describe translational, rotational, and roto-translational portions in the solutions containing the diatomics. We found that collective time correlation functions are well described by binary correlations at low liquid densities and, at high densities, ternary correlations become more important producing faster decaying collective time correlation functions due to partial cancellation effects. The repulsive and attractive time correlation functions exhibit a dynamic behavior that is independent on the solvation model due to linear scaling factors that only affect the absolute amplitudes of these functions. In general, the systems involving a rotational degree of freedom furnish smaller correlation times for the collective solvation dynamics, but stronger correlated two-body and three-body terms. Finally, this study shows that the solvation dynamics for the solution containing the diatomics relaxes predominatly by binary translational mechanisms when solvation models involving changes only in the polarizability parameter are considered. Binary attractive rotational mechanism become important in models with changes in the bond length.

(EN) The solvation model based on LSER was applied to study the retention behaviour of analytes in liquid and gas chromatography. In a first chapter, a retention description of 21 solutes was investigated by using the solvation model in a wide range of mobile phase composition methanol-water and acetonitrile-water. Generally, the retention of aromatic compounds was better described by the solvation model, compared to aliphatic compounds. Effect of the particular analytes used to formulate the LSER model on ability of retention description was studied. Different results of a retention estimation was achieved by using the regression set of compounds including aromatic solutes only or by contrast aliphatic solutes only. The solvation model developed on the basis of oxygen derivatives provided distinct results in comparison to model formulated with nitrogen derivatives only. The second chapter of this work, focused on gas chromatography, dealt with a description of retention of 152 isomers C5-C8 alkenes by the LSER model. The solvation descriptor L was obtained by using two estimation methods Havelec-Ševčík (HS) and Platts-Butina (PB), the descriptor E was calculated according to its definition. Two models for retention description of alkenes were constructed, the HS model and the PB model, derived...

(EN) This dissertation thesis is focused on physicochemical and chromatographic characterization of polyaniline-coated stationary phases. In the first part, surfaces of bare silica and octadecyl silica sorbents were modified by in-situ chemical polymerization of aniline hydrochloride and their subsequent systematic characterization was performed by using the linear solvation energy relationship approach in the HILIC mode of capillary LC. In addition, several common physicochemical techniques were used to characterize properties of these altered materials. The modified sorbents were then packed into capillary columns. The retention interactions taking place between solute and the separation system were evaluated on the basis of retention data of a number of various solutes. The results showed that polyaniline coating had a significant effect on the retention promoting interactions of both polyaniline-coated stationary phases. The assumed mixed-mode retention mechanism was proven for both the stationary phases. The second part dealt with investigation of the separation potential of polyaniline- coated silica stationary phase in different chromatographic modes. The retention factor curves of structurally similar solutes were constructed as a function of organic modifier portion in the mobile phase....

A series of para-substituted acetophenones bearing a furanyl or a thiophenyl moiety show a large Stokes-shift, which is a function of various solvent properties. Photophysical properties such as emission lifetime of the compounds have been determined using time-correlated-single photon counting to secure the intrinsic fluorescence behaviour. The solvent dependent position of the UV/Vis emission band [small nu, Greek, tilde]max,em of the compounds has been measured in 26 various solvents. The influence of the solvent on [small nu, Greek, tilde]max,em is of very complex nature and mathematically analysed by multiple square linear solvation energy (LSE)-correlation analysis using Catalán's four-solvent parameter set. Solvent acidity has a strong influence on the bathochromic shift of 2,5-disubstituted furan derivatives compared to the non-5-substituted furan and thiophene derivatives, which show a contrary behaviour. Therefore, the 5-cyanofuranyl-substituted acetophenone derivative is useful as a probe for measuring environmental properties by fluorescence spectroscopy. / Dieser Beitrag ist aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.