One of the essential requirements of biomolecular modeling is an accurate description of water as a solvent. The challenge is to make this description computationally facile -- reasonably fast, simple, robust and easy to incorporate into existing software packages, yet accurate. The most rigorous procedure to model the effect of aqueous solvent is to explicitly model every water molecule in the system. For many practical applications, this approach is computationally too intense, as the number of required water atoms is on an average at least one order of magnitude larger than the number of atoms of the molecule of interest. Implicit solvent models, in which solvent molecules are replaced by a continuous dielectric, have become a popular alternative to explicit solvent methods. However, implicit solvation models often lack various microscopic details which are crucial for accuracy. One such missing effect that is currently missing from popular implicit models is the so called effect of charge hydration asymmetry (CHA). The missing effect of charge hydration asymmetry -- the asymmetric response of water upon the sign of solute charge -- manifests a characteristic, strong dependence of solvation free energies on the sign of solute charge. Here, we incorporate this missing effect into the continuum solvation framework via the conceptually simplest Born equation and also in the generalized Born model. We identify the key electric multipole moments of model water molecules critical for the various degrees of CHA effect observed in studies based on molecular dynamics simulations using different rigid water models. We then use this gained insight to incorporate CHA first into the Born model, and then into the generalized Born model. The proposed framework significantly improves accuracy of the hydration free energy estimates tested on a comprehensive set of varied molecular solutes -- monovalent and divalent ions, small drug-like molecules, charged and uncharged amino acid dipeptides, and small proteins. We finally develop a methodology to resolve the issue with unacceptably large uncertainty that stems from a variety of fundamental and technical difficulties in experimental quantification of CHA from charged solutes. Using the proposed corrections in the continuum framework, we untangle the charge-asymmetric response of water from its symmetric response, and further circumvent the difficulties by extracting accurate estimate propensity of water to cause CHA from accurate experimental hydration free energies of neutral polar molecules. We show that the asymmetry in water's response is strong, about 50% of the symmetric response. / Ph. D.

No description available.

<p>Accurate calculations of free energies for molecular association and solvation are important for the understanding of biochemical processes, and are useful in many pharmaceutical applications. In this thesis, molecular dynamics (MD) simulations are used to calculate thermodynamic properties for solvation and ligand binding.</p><p>The thermodynamic integration technique is used to calculate p<i>K</i>_a values for three aspartic acid residues in two different proteins. MD simulations are carried out in explicit and Generalized-Born continuum solvent. The calculated p<i>K</i>_a values are in qualitative agreement with experiment in both cases. A combination of MD simulations and a continuum electrostatics method is applied to examine p<i>K</i>_a shifts in wild-type and mutant epoxide hydrolase. The calculated p<i>K</i>_a values support a model that can explain some of the pH dependent properties of this enzyme.</p><p> Development of the linear interaction energy (LIE) method for calculating solvation and binding free energies is presented. A new model for estimating the electrostatic term in the LIE method is derived and is shown to reproduce experimental free energies of hydration. An LIE method based on a continuum solvent representation is also developed and it is shown to reproduce binding free energies for inhibitors of a malaria enzyme. The possibility of using a combination of docking, MD and the LIE method to predict binding affinities for large datasets of ligands is also investigated. Good agreement with experiment is found for a set of non-nucleoside inhibitors of HIV-1 reverse transcriptase.</p><p>Approaches for decomposing solvation and binding free energies into enthalpic and entropic components are also examined. Methods for calculating the translational and rotational binding entropies for a ligand are presented. The possibility to calculate ion hydration free energies and entropies for alkali metal ions by using rigorous free energy techniques is also investigated and the results agree well with experimental data.</p>

Accurate calculations of free energies for molecular association and solvation are important for the understanding of biochemical processes, and are useful in many pharmaceutical applications. In this thesis, molecular dynamics (MD) simulations are used to calculate thermodynamic properties for solvation and ligand binding. The thermodynamic integration technique is used to calculate pKa values for three aspartic acid residues in two different proteins. MD simulations are carried out in explicit and Generalized-Born continuum solvent. The calculated pKa values are in qualitative agreement with experiment in both cases. A combination of MD simulations and a continuum electrostatics method is applied to examine pKa shifts in wild-type and mutant epoxide hydrolase. The calculated pKa values support a model that can explain some of the pH dependent properties of this enzyme. Development of the linear interaction energy (LIE) method for calculating solvation and binding free energies is presented. A new model for estimating the electrostatic term in the LIE method is derived and is shown to reproduce experimental free energies of hydration. An LIE method based on a continuum solvent representation is also developed and it is shown to reproduce binding free energies for inhibitors of a malaria enzyme. The possibility of using a combination of docking, MD and the LIE method to predict binding affinities for large datasets of ligands is also investigated. Good agreement with experiment is found for a set of non-nucleoside inhibitors of HIV-1 reverse transcriptase. Approaches for decomposing solvation and binding free energies into enthalpic and entropic components are also examined. Methods for calculating the translational and rotational binding entropies for a ligand are presented. The possibility to calculate ion hydration free energies and entropies for alkali metal ions by using rigorous free energy techniques is also investigated and the results agree well with experimental data.

Abstract Electrostatic interactions are very important in biomolecular systems. Electrostatic forces have received a great deal of attention due to their long-range nature and the trade-off between desolvation and interaction effects. It remains a challenging task to study and to predict the effects of electrostatic interactions in biomolecular systems. Computer simulation techniques that account for such interactions are an important tool for the study of biomolecular electrostatics. This study is largely concerned with the role of electrostatic interactions in biomolecular systems and with developing novel models to estimate the strength of such interactions. First, a novel formulation based upon continuum electrostatics to compute the electrostatic potential in and around two biomolecules in a solvent with ionic strength is presented. Many, if not all, current methods rely on the (non)linear Poisson-Boltzmann equation to include ionic strength. The present formulation, however, describes ionic strength through the inclusion of explicit ions, which considerably extends its applicability and validity range. The method relies on the boundary element method (BEM) and results in two very similar coupled integral equations valid on the dielectric boundaries of two molecules, respectively. This method can be employed to estimate the total electrostatic energy of two protein molecules at a given distance and orientation in an electrolyte solution with zero to moderately high ionic strength. Secondly, to be able to study interactions between biomolecules and membranes, an alternative model partly based upon the analytical continuum electrostatics (ACE) method has been also formulated. It is desirable to develop a method for calculating the total solvation free energy that includes both electrostatic and non-polar energies. The difference between this model and other continuum methods is that instead of determining the electrostatic potential, the total electrostatic energy of the system is calculated by integrating the energy density of the electrostatic field. This novel approach is employed for the calculation of the total solvation free energy of a system consisting of two solutes, one of which could be an infinite slab representing a membrane surface.

Este trabalho visou compreensão da solvatação em solventes puros e misturas binárias, e aplicar as informações obtidas para analisar o efeito de solventes na síntese de líquido iônico, e na dependência das propriedades de filmes de acetatos de celulose, AC, sobre o grau de substituição do éster. Para a compreensão da solvatação utilizou-se compostos (sondas solvatocrômicas) cujos espectros Uv-Vis são sensíveis às propriedades do meio. Juntamente com tais sondas, foram usadas outras duas ferramentas: (i) Modelo de solvatação preferencial; proposto por nosso grupo e que descreve a composição da camada de solvatação da sonda, considerando a existência de um \"agregado\" água - solvente orgânico. (ii)Correlações multi-paramêtricas de energia livre de solvatação; que correlacionam uma propriedade dependente do meio com as propriedades dos solventes e suas misturas. Primeiramente, estudamos a solvatação de pares de sondas que possuíam pKas semelhantes e lipofilicidades diferentes em solventes próticos. Concluiu-se que a acidez e a dipolaridade/polarizabilidade dos solventes são as propriedades mais importantes. As conclusões foram corroboradas por cálculos teóricos, que mostraram a relação entre as características estruturais da sonda e suas susceptibilidades às propriedades do meio. O mesmo conjunto de sondas foi usado no estudo de misturas água-solventes próticos. Neste, aplicou-se com sucesso o modelo de solvatação acima mencionado e, de forma inédita, conseguimos racionalizar as constantes de equilíbrio para a troca das espécies presentes (água, solvente e água-solvente) na camada de solvatação com as propriedades dos solventes puros e/ou das misturas binárias. Os resultados revelaram que a composição da camada de solvatação é regida pelas propriedades de solventes, em particular a lipofilicidade e basicidade. As sondas RB e WB foram estudadas em misturas de água com alcoóis e com solventes apróticos. O intuito era ampliar a aplicabilidade do modelo de solvatação, para o qual precisávamos conhecer o volume molar do agregado, VSolv-A, e a constante de dissociação, Kdissoc, do agregado água-solvente. Estas duas grandezas eram obtidas de forma simultânea, através de dados de densidade. Desta vez, fizemos uso de cálculos teóricos para obter, de forma independente, o volume molar e depois utilizá-lo, como parâmetro constante (não ajustável) na cálculo de Kdissoc. A comparação dos resultados mostrou que, por ambas as abordagens, o desvio entre os valores de Kdissoc era mínimo. Por outro lado, em nenhum caso a ordem de Kdissoc se alterava. Esta observação deve-se ao fato de que o cálculo simultâneo de Kdissoc e VSolv-A foi sempre baseado em número grande de dados de densidade (18) de forma que os ajustes por interação não convergissem para um falso mínimo; o nível de teoria usado nos cálculos teóricos foi adequado. Quanto às aplicações, ficou evidente como a escolha do solvente afeta a velocidade da síntese do líquido iônico. Em relação aos filmes de AC, tentamos reproduzir as propriedades dos mesmos, através de uso de dois modelos etanol-acetato de etila e celulose-triacetato de celulose. Os dados da mistura líquida mostraram solvatação preferencial; foram tratados com sucesso pelo mesmo modelo aplicado para misturas binárias aquosas. O modelo sólido reproduziu os dados da AC qualitativamente. / This work is aimed at understanding solvation in pure solvents and binary mixtures and, the application of the information obtained in order to analyze the solvents effects on the synthesis of an ionic liquid, and on the dependence of the properties of cellulose acetate films, CA, on the degree of substitution of the ester. To understand salvation, was have used compounds (solvatchromic probes), whose UV-vis spectra are susceptible to the environment properties. In addition to these probes, were used more two tools: (i) Preferential solvation model; it was proposed by our research group and describes the composition of the probe solvation shell, considering the existence of an aggregate between water and organic solvent. (ii) Multi-parameter solvation free energy equations that correlate the solvent dependent properties with solvents properties and their mixtures. At first, we have studied pairs of probes that have similar pKa values and different lipophilicity in protic solvents. We have concluded that solvent acidity and dipolarity/polarizability are the most important properties. These conclusions are supported by theoretical calculations, that have shown the relationship between structural features of the probe and its susceptibility to environment properties. The same set of probes was used in order to study water - protic solvents mixtures. In this, we have applied the above cited solvation model successfully and rationalized the equilibrium constants of the exchange of species present (water, solvent and water -solvent) in the solvation shell with the properties of pure solvents and / or binary mixtures. These results revealed that the composition of solvation shell is controlled by the properties of solvents, in special, lipophilicity and basicity. The probes RB and WB were studied in mixtures of water with alcohols and with aprotic solvents. The intention was to broaden the applicability of the solvation model, for which, we needed to know the molar volume of the aggregate VSolv-W, and the dissociation constant, Kdissoc, of the same. Previously, these two quantities were obtained, simultaneously, by iteration of density data. We have used theoretical calculations in order to obtain VSolv-W and then use it as constant parameter (not adjustable one) in the calculation of Kdissoc. Comparison of the results showed that, in both approaches, the differences between Kdissoc values were minimal. Moreover, the order of Kdissoc has not changed. This observation is due to the fact that the simultaneous calculation of Kdissoc and VSolv-W was always based on a large number of density data (18) so that the interation did not converge to a false minimum; the level of theory used in the theoretic calculations was appropriate. Regarding applications, our results showed the importance of the choice of solvent to the synthesis of an ionic liquid. We have attempted to reproduce the properties of CA by the use of two models, ethanol-ethyl acetate and cellulose triacetate-cellulose. The data of the liquid mixture showed preferential solvation; were successfully treated by the same model applied to aqueous binary mixtures. The solid model reproduces the CA data qualitatively.

<p>The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented.</p><p>For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions.</p><p>A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands.</p><p>A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding.</p><p>The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.</p>

The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented. For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions. A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands. A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding. The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.

Este trabalho visou compreensão da solvatação em solventes puros e misturas binárias, e aplicar as informações obtidas para analisar o efeito de solventes na síntese de líquido iônico, e na dependência das propriedades de filmes de acetatos de celulose, AC, sobre o grau de substituição do éster. Para a compreensão da solvatação utilizou-se compostos (sondas solvatocrômicas) cujos espectros Uv-Vis são sensíveis às propriedades do meio. Juntamente com tais sondas, foram usadas outras duas ferramentas: (i) Modelo de solvatação preferencial; proposto por nosso grupo e que descreve a composição da camada de solvatação da sonda, considerando a existência de um \"agregado\" água - solvente orgânico. (ii)Correlações multi-paramêtricas de energia livre de solvatação; que correlacionam uma propriedade dependente do meio com as propriedades dos solventes e suas misturas. Primeiramente, estudamos a solvatação de pares de sondas que possuíam pKas semelhantes e lipofilicidades diferentes em solventes próticos. Concluiu-se que a acidez e a dipolaridade/polarizabilidade dos solventes são as propriedades mais importantes. As conclusões foram corroboradas por cálculos teóricos, que mostraram a relação entre as características estruturais da sonda e suas susceptibilidades às propriedades do meio. O mesmo conjunto de sondas foi usado no estudo de misturas água-solventes próticos. Neste, aplicou-se com sucesso o modelo de solvatação acima mencionado e, de forma inédita, conseguimos racionalizar as constantes de equilíbrio para a troca das espécies presentes (água, solvente e água-solvente) na camada de solvatação com as propriedades dos solventes puros e/ou das misturas binárias. Os resultados revelaram que a composição da camada de solvatação é regida pelas propriedades de solventes, em particular a lipofilicidade e basicidade. As sondas RB e WB foram estudadas em misturas de água com alcoóis e com solventes apróticos. O intuito era ampliar a aplicabilidade do modelo de solvatação, para o qual precisávamos conhecer o volume molar do agregado, VSolv-A, e a constante de dissociação, Kdissoc, do agregado água-solvente. Estas duas grandezas eram obtidas de forma simultânea, através de dados de densidade. Desta vez, fizemos uso de cálculos teóricos para obter, de forma independente, o volume molar e depois utilizá-lo, como parâmetro constante (não ajustável) na cálculo de Kdissoc. A comparação dos resultados mostrou que, por ambas as abordagens, o desvio entre os valores de Kdissoc era mínimo. Por outro lado, em nenhum caso a ordem de Kdissoc se alterava. Esta observação deve-se ao fato de que o cálculo simultâneo de Kdissoc e VSolv-A foi sempre baseado em número grande de dados de densidade (18) de forma que os ajustes por interação não convergissem para um falso mínimo; o nível de teoria usado nos cálculos teóricos foi adequado. Quanto às aplicações, ficou evidente como a escolha do solvente afeta a velocidade da síntese do líquido iônico. Em relação aos filmes de AC, tentamos reproduzir as propriedades dos mesmos, através de uso de dois modelos etanol-acetato de etila e celulose-triacetato de celulose. Os dados da mistura líquida mostraram solvatação preferencial; foram tratados com sucesso pelo mesmo modelo aplicado para misturas binárias aquosas. O modelo sólido reproduziu os dados da AC qualitativamente. / This work is aimed at understanding solvation in pure solvents and binary mixtures and, the application of the information obtained in order to analyze the solvents effects on the synthesis of an ionic liquid, and on the dependence of the properties of cellulose acetate films, CA, on the degree of substitution of the ester. To understand salvation, was have used compounds (solvatchromic probes), whose UV-vis spectra are susceptible to the environment properties. In addition to these probes, were used more two tools: (i) Preferential solvation model; it was proposed by our research group and describes the composition of the probe solvation shell, considering the existence of an aggregate between water and organic solvent. (ii) Multi-parameter solvation free energy equations that correlate the solvent dependent properties with solvents properties and their mixtures. At first, we have studied pairs of probes that have similar pKa values and different lipophilicity in protic solvents. We have concluded that solvent acidity and dipolarity/polarizability are the most important properties. These conclusions are supported by theoretical calculations, that have shown the relationship between structural features of the probe and its susceptibility to environment properties. The same set of probes was used in order to study water - protic solvents mixtures. In this, we have applied the above cited solvation model successfully and rationalized the equilibrium constants of the exchange of species present (water, solvent and water -solvent) in the solvation shell with the properties of pure solvents and / or binary mixtures. These results revealed that the composition of solvation shell is controlled by the properties of solvents, in special, lipophilicity and basicity. The probes RB and WB were studied in mixtures of water with alcohols and with aprotic solvents. The intention was to broaden the applicability of the solvation model, for which, we needed to know the molar volume of the aggregate VSolv-W, and the dissociation constant, Kdissoc, of the same. Previously, these two quantities were obtained, simultaneously, by iteration of density data. We have used theoretical calculations in order to obtain VSolv-W and then use it as constant parameter (not adjustable one) in the calculation of Kdissoc. Comparison of the results showed that, in both approaches, the differences between Kdissoc values were minimal. Moreover, the order of Kdissoc has not changed. This observation is due to the fact that the simultaneous calculation of Kdissoc and VSolv-W was always based on a large number of density data (18) so that the interation did not converge to a false minimum; the level of theory used in the theoretic calculations was appropriate. Regarding applications, our results showed the importance of the choice of solvent to the synthesis of an ionic liquid. We have attempted to reproduce the properties of CA by the use of two models, ethanol-ethyl acetate and cellulose triacetate-cellulose. The data of the liquid mixture showed preferential solvation; were successfully treated by the same model applied to aqueous binary mixtures. The solid model reproduces the CA data qualitatively.