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Efficient sampling is the key to success of molecular simulation of complex physical systems. Still, a unique recipe for achieving this goal is unavailable. Hybrid Monte Carlo (HMC) is a promising sampling tool offering a smart, free of discretization errors, propagation in phase space, rigorous temperature control, and flexibility. However, its inability to provide dynamical information and its weakness in simulations of reasonably large systems do not allow HMC to become a sampler of choice in molecular simulation of complex systems. In this thesis, we show that performance of HMC can be dramatically improved by introducing in the method the splitting numerical integrators and importance sampling. We propose a novel splitting integration scheme called Adaptive Integration Approach or AIA, which leads to very promising improvements in accuracy and sampling in HMC simulations. Given a simulation problem and a time step, AIA automatically chooses the optimal scheme out of the family of two-stage splitting integrators. A system-specific integrator identified by our approach is optimal in the sense that it provides the best conservation of energy for harmonic forces. The role of importance sampling on the performance of HMC is studied through the modified Hamiltonian Monte Carlo (MHMC) methods, sampling with respect to a modified or shadow Hamiltonian. The particular attention is paid to Generalized Shadow Hybrid Monte Carlo (GSHMC), introduced by Akhmatskaya and Reich in 2008. To improve the performance of MHMC in general and GSHMC in particular, we develop and test the new multi-stage splitting integrators, specially formulated for sampling with respect to modified Hamiltonians. The novel adaptive two-stage integration approach or MAIA, specifically derived for MHMC is presented. We also discuss in detail the adaptation of GSHMC to the NPT ensemble and provide the thorough analysis of its performance. Moreover, for the first time, we formulate GSHMC in the grand canonical ensemble. A general framework, useful for an extension of other Hybrid Monte Carlo methods to the grand canonical ensemble, is also provided. The software development is another fundamental part of the present work. The algorithms presented in this thesis are implemented in MultiHMC-GROMACS, an in-house version of the popular software package GROMACS. We explain the details of such implementation and give useful recommendations and hints for implementation of the new algorithms in other software packages. In summary, in this thesis, we propose the new numerical algorithms that are capable of improving the accuracy and sampling efficiency of molecular simulations with Hybrid Monte Carlo methods. We show that equipping the Hybrid Monte Carlo algorithm with extra features makes it even a “smarter” sampler and, no doubts, a strong competitor to the well-established molecular simulation techniques such as molecular dynamics (MD) and Monte Carlo. The up to 60 times increase in sampling efficiency of GSHMC over MD, due to the new algorithms in simulations of selected systems, supports such a belief., MTM2013-46553-C3-1-P

Broadly speaking, molecular simulations are used for two different purposes. First, zooming out, it allows for high-throughput screening of a much larger chemical space than is feasible by experimental work. Second, zooming in, it serves as a tool similar to a microscope, allowing scientists to understand atomic-level phenomena that underlie chemical properties. These two uses serve a variety of applications, from drug discovery to catalyst development to semiconductor processing. In this work, we illustrate the steps necessary to apply molecular simulations for its two purposes, using nanoporous materials as the example application.First, we consider the selection of the molecular simulation method itself. Common methods are Monte Carlo and molecular dynamics (MD) simulations. Though the fundamentals of these methods have existed for well over half a century, techniques are still being developed to overcome the small system sizes and timescales to which we are limited. Thermostats are one such technique, frequently used in MD simulations to allow sampling of the canonical ensemble without requiring the large computational expense of simulating a heat bath. Many thermostats have been proposed, and several are in common use. The computational chemist’s choice and parameterization of thermostat is not trivial. We have shown that some of the most common thermostats in use today do not sample their intended ensembles, and that this can bring about large errors in a simulation. Fortunately, we have also found that alternative thermostats exist which do not exhibit these errors, and we advise molecular simulation practitioners to use them.Having selected the molecular simulation technique, a computational chemist that seeks to perform a high-throughput screening must also find a library of materials on which the technique can be performed. Some databases of synthesized nanoporous materials exist, such as the International Zeolite Association (IZA) database and the Computation-Ready Experimental Metal-Organic Framework database, and multiple databases of hypothetical materials are also available. However, if a novel material class is desirable for exploration, the library must be developed. We became interested in zeolite-templated carbons (ZTCs), a material class in which two-dimensional graphene sheets are assembled in a three-dimensional scaffold, but we found no computational library of ZTCs existed. We developed a Monte Carlo technique which generates a ZTC for a given zeolite template, and we performed this in silico synthetic procedure using zeolites taken from the IZA database and the hypothetical zeolite databases. We then found that we could use the mathematical concept of minimal surfaces to describe the ZTCs, and in so doing, we established a link between experimentally-known ZTCs and schwarzites, which had so far been purely hypothetical materials. Schwarzites are negatively-curved carbons, and with their establishment as experimentally-known materials, the triumvirate of two-dimensional nanocarbons (along with positively-curved fullerenes and nanotubes and flat graphene sheets) is completed.With the simulation method and material library at hand, the computational chemist is ready to perform the high-throughput screening. One important application of nanoporous materials is for adsorptive separations, which can be more energy efficient than distillation. When designing adsorbents for particular separations, understanding how the molecular structure affects gas adsorption is important. We screened tens of thousands of hypothetical zeolites to fill in the gaps that remain in our understanding of the natural gas purification process. Through this screening, we were able to find which adsorbent properties were most correlated with the adsorbent’s separation performance. Furthermore, we were able to test the validity of the commonly-used Ideal Adsorbed Solution Theory (IAST) to predict mixture isotherms from pure-component data.Finally, we examine a particular material in-depth, illustrating the second broad purpose of molecular simulations. Continuing with the theme of using nanoporous materials for separations, we studied the behavior of benzene and xylenes adsorbed in MOF-5, a prototypical metal-organic framework (MOF). We found that the adsorbates separated into liquid and vapor phases that extended over multiple unit cells of MOF-5. This result was surprising because condensation is not generally found in materials with pore size below 2 nm, as the confinement decreases the number of neighbors an adsorbate can interact with, suppressing the energetic benefit of the liquid phase over the more entropically-favorable vapor phase. However, the limiting pore size that had been found in prior studies assumed a one-dimensional capillary-like pore structure, whereas MOF-5 has a three-dimensional pore structure that less restricts the number of neighboring adsorbate molecules. Using NMR, our collaborators were able to find experimental evidence that further attested to our phase separation hypothesis.

Free energy evaluation in molecular simulations of both classical and quantum systems is computationally intensive and requires sophisticated algorithms. This is because free energy depends on the volume of accessible phase space, a quantity that is inextricably linked to the integration measure in a coordinate representation of a many-body problem. In contrast, the same problem expressed as a field theory (auxiliary field or coherent states) isolates the particle number as a simple parameter in the Hamiltonian or action functional and enables the identification of a chemical potential field operator. We show that this feature leads a “direct” method of free energy evaluation, in which a particle model is converted to a field theory and appropriate field operators are averaged using a field-theoretic simulation conducted with complex Langevin sampling. These averages provide an immediate estimate of the Helmholtz free energy in the canonical ensemble and the entropy in the microcanonical ensemble. The method is illustrated for a classical polymer solution, a block copolymer melt exhibiting liquid crystalline and solid mesophases, and a quantum fluid of interacting bosons.

Orientador: Luís Fernando Mercier Franco Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Química Resumo: O cálculo de propriedades termodinâmicas configura uma etapa importante na modelagem e no projeto de operações unitárias industriais. Esse cálculo pode ser feito a partir de equações de estado que buscam descrever o comportamento molecular de um sistema em níveis microscópicos. Teorias de perturbação termodinâmica (TPT) têm auxiliado enormemente no desenvolvimento de novas equações de estado baseadas em Mecânica Estatística. Embora teorias de perturbação de primeira e de segunda ordem sejam bastante comuns, elas requerem aproximações para serem compreendidas em uma forma analítica. Recentemente, uma nova equação de estado estatística baseada em uma TPT de segunda ordem foi proposta na qual o fluido de referência é retratado como um corpo convexo rígido (elipsoide de revolução, esfero-cilindro ou cilindro) e o potencial de perturbação é definido como um poço quadrado simetricamente esférico. Este novo modelo termodinâmico emprega duas aproximações que recaem sobre os funcionais de energia livre da Teoria do Segundo Coeficiente do Virial de Onsager: a primeira aproximação restringe o uso da equação de estado a sistemas com distribuição orientacional isotrópica (desordenada), enquanto a segunda aproximação desvincula os graus de liberdade translacionais dos rotacionais, sendo válida apenas em baixas densidades. Usando simulações de Monte Carlo no conjunto canônico (NVT), investigamos a validade de tais aproximações, calculando os dois primeiros coeficientes de perturbação de uma expansão em série de potências a altas temperaturas (ESAT) da energia livre de Helmholtz perturbada e determinando o parâmetro de ordem nemática uniaxial dos sistemas avaliados. Os resultados encontrados indicam que essas aproximações soam bastante razoáveis para uma determinada faixa de densidades reduzidas e anisotropias geométricas. Ademais, apresentamos ainda o cálculo da energia livre de Helmholtz total do sistema perturbado a partir de simulações de Monte Carlo no conjunto NVT. Esse cálculo pode, por exemplo, ser empregado na determinação dos termos de perturbação de alta ordem da ESAT, visando correlacioná-los às variáveis do sistema, como os parâmetros de anisotropia e do potencial atrativo, derivando-se assim um termo de correção que poderia, a princípio, ser utilizado para melhorar a capacidade preditiva da nova equação de estado Abstract: The calculation of thermodynamic properties is an important step in the modeling and in the design of unit operations in chemical industries. Such a calculation may be carried out through equations of state that aim at describing the molecular behavior of chemical systems at microscopic levels. Thermodynamic perturbation theories (TPT) have been the center of the development of the new generation of equations of state. Although first- and second-order perturbation theories are very common, they require approximations for obtaining an analytical form. Recently, a new equation of state has been proposed in which the reference fluid is constituted of hard convex bodies (ellipsoids of revolution, spherocylinders or cylinders), and the perturbation potential is defined as a spherically symmetric square well. This new thermodynamic model applies two approximations to the free-energy functionals of Onsager's Second Virial Theory: the first approximation restrains the equation of state to systems with an isotropic (disordered) orientation distribution, while the second approximation decouples the translational degrees of freedom from the rotational ones, being valid only at low densities. Using Monte Carlo simulations in the canonical ensemble (NVT), we investigated the validity of such approximations by calculating the first- and second-order perturbation coefficients of the high-temperature series expansion (HTSE) of the Helmholtz free energy and by determining the uniaxial nematic order parameter of the evaluated systems. With our findings, these approximations seem to be quite reasonable for a certain range of reduced densities and anisotropies. We also presented a calculation of the full Helmholtz free energy of the perturbed system using NVT-Monte Carlo simulations. The calculation can be used for determining higher order perturbation terms that can be then correlated to variables of the system, such as anisotropy and potential parameters, thus deriving a correction function that could in principle be used to improve the predictive capacity of the new equation of state Mestrado Engenharia Química Mestre em Engenharia Química CNPQ 130496/2020-0

CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico A adsorção de hidrocarbonetos tem sido sistematicamente investigada por causa das suas diversas aplicações nos processos de separação na indústria petroquímica e em processos catalíticos . A determinação experimental de isotermas de adsorção, tanto de componentes puros quanto de suas misturas, em geral demanda bastante tempo e recursos financeiros. Assim, a simulação molecular aparece como uma ferramenta atrativa para estimar as propriedades de adsorção e avaliar novos materiais adsorventes. No entanto, não há uma maneira sistemática de se obter os parâmetros do campo de força entre átomos diferentes. Em geral, esses parâmetros são ajustados para melhor descrever as propriedades de adsorção, como a capacidade de adsorção, o calor isostérico de adsorção e os coeficientes de Henry. Essa abordagem limita a capacidade preditiva da simulação molecular. Neste trabalho foi proposto uma nova regra de combinação para o potencial de Lennard-Jones (LJ) com o objetivo de melhorar a capacidade preditiva de simulação molecular que será baseada apenas no campo de força para as espécies puras (adsorvente e adsorvato). Foram realizados estudos de adsorção de alcanos lineares, na faixa de átomos de carbono de 1-6 usando simulações de Monte Carlo (GCMC) para três temperaturas diferentes em zeólita do tipo MFI. Os alcanos foram descritos de acordo com o campo de força TraPPE que apresenta uma boa representação para o comportamento de alcanos, em fase fluida. O conjunto Grande Canônico (GCMC), implementado no código aberto Cassandra V2.2 foi utilizado para simular a adsorção. A nova regra de combinação e a regra clássica de Lorentz-Berthelot foram testadas. Os resultados foram comparados com dados experimentais e resultados de simulação molecular anteriores reportadas na literatura. Os resultados indicaram que o uso de regras de combinação descreve satisfatoriamente a maioria dos sistemas investigados, sendo, por vezes, superior às simulações usando parâmetros ajustados, confirmando assim a possibilidade de usar essa ferramenta na forma preditiva para avaliação da adsorção em zeólitas. Para reforçar esta avaliação, foram realizadas novas simulações envolvendo misturas de metano-etano em zeólita tipo 5A e 2-metil-pentano e n-hexano em silicalita. Os novos resultados reforçam a conclusão anterior. The adsorption of hydrocarbons has been systematically investigated because of its diversity applications in separation processes in the petrochemical industry and in catalytic processes. The experimental determination of adsorption isotherms for both pure components and their mixtures, usually requires a lot of time and financial resources. Thus, molecular simulation appears as an attractive tool to estimate the properties of adsorption and evaluate new materials. However, there is no systematic way of obtaining the force field parameters between different atoms. In general, these parameters are adjusted to better describe the adsorption properties, such as adsorption capacity, isosteric heat and Henry coefficients. This approach limits the predictive capacity of molecular simulation. In this work, was proposed a new combination rule for the Lennard-Jones (LJ) potential with the objective of improving the predictive capacity of molecular simulation that will be based only on the force field for pure species (adsorbent and adsorbate). Linear alkanes adsorption studies were performed in the 1-6 carbon atoms range using Monte Carlo simulations (GCMC) for three different temperatures in MFI type zeolite. The alkanes were described according to the TraPPE force field which shows a good representation for the alkanes behavior in the fluid phase. The Grand Canonical ensemble (GCMC), implemented in the open source Cassandra V2.2 was used to simulate the adsorption. The new combination rule and the classic Lorentz-Berthelot rule were tested. The results were compared with previous experimental data and molecular simulation results reported in the literature. The results indicated that the use of combination rules satisfactorily describes most of the systems investigated, being sometimes superior to the simulations using adjusted parameters, thus confirming the possibility of using this tool in the predictive form to evaluate the adsorption in zeolites. In order to reinforce this evaluation, new simulations involving mixtures of methane-ethane in zeolite type 5A and 2-methyl-pentane and n-hexane in silicalite were carried out. The new results reinforce the previous conclusion. Dissertação (Mestrado)

An increase in demand for energy efficient processes for the separation of saturated and unsaturated light hydrocarbons mixtures drives the need of noncryogenic processes. The adsorptive separation using Metal‐Organic Frameworks with coordinatively unsaturated metal sites may provide a cost‐effective alternative due to the strong binding of the metal cation with the unsaturated hydrocarbons. Since experiments on adsorption equilibrium of gas mixtures are challenging, we propose classical force field based simulations to analyse the ability of MOF‐74 with different metal substitutions for the separation of C2 and C3 olefin/paraffin binary mixtures. We parametrized the force field by fitting to available experimental single‐component adsorption isotherms of ethane, ethene, propane, and propene in M–MOF‐74 (M=Co, Fe, Mn, and Ni). The force field was validated for a variety of temperatures ranged from 273 K to 353 K. We then conducted Monte Carlo simulations in the Grand‐Canonical ensemble to elucidate the adsorption mechanisms of the saturated/unsaturated hydrocarbon mixtures, at 318 K and 353 K. We computed the adsorption isotherms, and from these the adsorption selectivity, and addressed the variations of MOF properties with different metal cations. Fe‐based MOF‐74 appears the best option for both ethane/ethene and propane/propene separation applications. This finding partly agrees with previous work based on the Ideal Adsorbed Solution Theory.

The Kirkwood-Buff (KB) theory provides a rigorous framework to predict thermodynamic properties of isotropic liquids from the microscopic structure. Several thermodynamic quantities relate to KB integrals, such as partial molar volumes. KB integrals are expressed as integrals of RDFs over volume but can also be obtained from density fluctuations in the grand-canonical ensemble. Various methods have been proposed to estimate KB integrals from molecular simulation. In this work, we review the available methods to compute KB integrals from molecular simulations of finite systems, and particular attention is paid to finite-size effects. We also review various applications of KB integrals computed from simulations. These applications demonstrate the importance of computing KB integrals for relating findings of molecular simulation to macroscopic thermodynamic properties of isotropic liquids.

Many endeavors have been undertaken in the attempt to develop new adsorbent materials employed in the removal of CO2 in exhaust gas streams. Concurrently, computational techniques have progressively contributed to this subject matter. Therefore, this study aims to investigate, through molecular simulation, the selective adsorption of CO2 in operational conditions similar to a post-combustion capture scenario. Thus, we developed molecular models of the adsorbents NaX, MCM-41, Cu-BTC, IRMOF-1 and UiO-66, besides hybrid solids created through impregnation with primary, secondary and tertiary amines in faujasite and mesoporous silica. The force fields used were able to predict accurately single and multicomponent adsorbent behavior of different gases, namely: CO2, N2, O2, NO2 and H2O. To that end, the grand canonical ensemble was used coupled with the Monte Carlo method (GCMC) to calculate isotherms of 0-100 °C in a broad pressure range. The results with NaX and its hybrids pointed to a preferential adsorption of CO2 when compared to N2. Evaluating CO2 selectivity in relation to N2 (SCO2/N2), it was observed that, in low temperatures, the hybrids produced similar values to unmodified NaX. In high temperature, a higher sensitivity was observed for that parameter, with the hybrid NaX-DEA as the best adsorbent. In the study with a humid stream, it was observed that the presence of water vapor, even in small amounts (1%v/v), is enough to saturate the adsorbents and promote a drastic decline in CO2 adsorption, possibly due to the strong competition between the CO2 and H2O molecules for the solid’s site III. The model developed for MCM-41 was able to replicate the experimental tendency of the adsorption of CO2, N2 and the CO2/N2 system. Furthermore, it was possible to identify the preferential location of the CO2 and N2 molecules in the silica. The SCO2/N2 was investigated evaluating the influence of temperature, pressure, stream composition, pore size and impregnation of amine groups. The results showed that a higher SCO2/N2 is achieved at low temperature and pressure, pore size between 12-17.5 Å, and with DEA immobilized with, approximately, 21% in mass. In the study with the MOFs, results showed that Cu-BTC was able to adsorb more CO2 than IRMOF-1 and UiO-66 in the investigated temperature range. It was estimated that at 100 °C the CO2 adsorption capacity in Cu-BTC was 2.8 times higher than in IRMOF-1 and 1.5 times higher than in UiO-66. On the other hand, evaluating the CO2/N2, CO2/O2 and CO2/NO2 selectivity, it was observed that zirconium MOF had better performance than the others, especially in high temperatures. The study of multicomponent adsorption with MOFs also revealed the strong competition between the CO2 e NO2 molecules, confirmed by energy histograms and adsorption instantaneous. Muitos esforços foram empreendidos na tentativa de desenvolver novos materiais adsorventes aplicados à remoção de CO2 em correntes de exaustão de gases. Paralelamente a isso, técnicas computacionais têm contribuído progressivamente com a temática. Dessa forma, este trabalho se propõe a investigar, por meio de simulação molecular, a adsorção seletiva de CO2 em condições de operação similares ao cenário de captura pós-combustão. Assim, foram desenvolvidos modelos moleculares dos adsorventes NaX, MCM-41, Cu-BTC, IRMOF-1 e UiO-66, além de sólidos híbridos criados por meio da impregnação com aminas primárias, secundárias e terciárias na faujasita e sílica mesoporosa. Os campos de força utilizados foram capazes de prever com acurácia o comportamento adsortivo mono e multicomponentes de diferentes gases, a citar: CO2, N2, O2, NO2 e H2O. Para isso, utilizou-se o ensemble grande canônico acoplado ao método de Monte Carlo (GCMC) para levantar isotermas de 0-100 °C em uma ampla faixa de pressão. Os resultados com a NaX e seus híbridos apontaram uma adsorção preferencial do CO2 em relação ao N2. Avaliando-se a seletividade do CO2 em relação ao N2 (SCO2/N2), observou-se que, à baixa temperatura, os híbridos apresentaram valores similares à NaX não modificada. Em alta temperatura, observou-se uma maior sensibilidade para esse parâmetro, tendo o híbrido NaX-DEA como o melhor adsorvente. No estudo com corrente úmida, observou-se que a presença de vapor d’água, mesmo que em pequenas quantidades (1%v/v), é suficiente para saturar os adsorventes e promover um drástico decaimento de adsorção de CO2, possivelmente pela forte competição entre as moléculas de CO2 e H2O ao sítio III do sólido. O modelo desenvolvido para a MCM-41 foi capaz de reproduzir a tendência experimental da adsorção de CO2, N2 e do sistema CO2/N2. Além disso, pôde-se identificar a localização preferencial das moléculas de CO2 e N2 no interior da sílica. A SCO2/N2 foi investigada avaliando-se a influência de temperatura, pressão, composição da corrente, tamanho do poro e impregnação de grupos aminados. Os resultados mostraram que uma maior SCO2/N2 é alcançada à baixa temperatura e pressão, poro com tamanho entre 12-17,5 Å e com DEA imobilizado com, aproximadamente, 21% em massa. No estudo com as MOFs, os resultados mostraram que a Cu-BTC foi capaz de adsorver mais CO2 que a IRMOF-1 e UiO-66 em toda a faixa de temperatura investigada. Estimou-se que a 100 °C a capacidade de adsorção de CO2 na Cu-BTC foi 2,8 vezes maior que na IRMOF-1 e 1,5 vezes maior que na UiO-66. Por outro lado, ao avaliar-se a seletividade CO2/N2, CO2/O2 e CO2/NO2, notou-se que a MOF de zircônio apresentou melhor desempenho que as demais, principalmente em temperaturas elevadas. O estudo de adsorção multicomponente com as MOFs também revelou a forte competição existente entre as moléculas de CO2 e NO2, comprovadas por histogramas de energia e instantâneos de adsorção.

The separation performance of the metal−organic framework MIL-47 for xylene isomers was studied by Monte Carlo simulations in the grand-canonical ensemble. The experimental adsorption isotherms of xylene isomers in MIL-47 between 343 and 423 K were reproduced by using force fields available in the literature. Mixture isotherms were computed and compared with the mixture isotherms predicted by using pure component adsorption data and the ideal adsorption solution theory. This theory accurately predicts mixture isotherms of xylene isomers in MIL-47. the ideal adsorption sorption theory was further employed to calculate the separation factors of xylene isomers in MIL-47. The order of preferential adsorption was found to be ortho > para > meta. The adsorption selectivity was found to increase with pressure, and the results showed a good agreement with the experimental data available. Henry coefficients and low coverage heats of adsorption and adsorption entropies were computed at 543 K showing an excellent ag...

We present canonical-ensemble molecular-dynamics (MD) simulations of disjoining-pressure isotherms for symmetric, free aqueous thin films. For such symmetric films, the disjoining pressure is purely attractive. Lifshitz's theory, based on continuum dispersion forces, predicts that the disjoining pressure varies as an inverse cube of film thickness, with a constant of proportionality that can be calculated within the framework of this theory. Our MD results indicate that Lifshitz theory, which assumes a slab geometry for the water density profile and neglects the fluid structure, underpredicts the disjoining pressure by about 50 times for films ranging from about 1 to 2 nm at 479 K. To investigate more closely actual experimental conditions, we also perform simulations of water films surrounded by inert gas molecules. The additional gas component adds an extra thermodynamic degree of freedom to the system, allowing for the chemical potential of the water in the external liquid reservoir to be maintained co...

Here is studied the variation in cohesion of cement main phase (C-S-H) as a result of cationic polyelectrolytes addition (quaternary amines spermine and norspermidine). Cohesion study was carried out by molecular simulation techniques (Monte Carlo) using a primitive model in a canonical ensemble (NVT). The proposed model takes into account the influence of ionic size of each particle and the addition of polyelectrolytes with different charge number and separation. The results obtained show that electrostatic interactions are responsible for the cohesion of the hardened cement. It was found that in absence of cationic polyelectrolytes, cohesion is lost when the C-S-H lamellae are at separations larger than 1 nm. Adding cationic polyelectrolytes generates a distribution of hydroxide ions around the polyelectrolyte charges, facilitates the distribution of calcium and sodium ions in the entire space between C-S-H surfaces; this allows the cohesive forces exist at greater distances of separation between the surfaces.

This work is divided into two distinct parts. The first part consists of the study of the metal organic framework UiO-66Zr, where the aim was to determine the force field that best describes the adsorption equilibrium properties of two different gases, methane and carbon dioxide. The other part of the work focuses on the study of the single wall carbon nanotube topology for ethane adsorption; the aim was to simplify as much as possible the solid-fluid force field model to increase the computational efficiency of the Monte Carlo simulations. The choice of both adsorbents relies on their potential use in adsorption processes, such as the capture and storage of carbon dioxide, natural gas storage, separation of components of biogas, and olefin/paraffin separations. The adsorption studies on the two porous materials were performed by molecular simulation using the grand canonical Monte Carlo (μ,V,T) method, over the temperature range of 298-343 K and pressure range 0.06-70 bar. The calibration curves of pressure and density as a function of chemical potential and temperature for the three adsorbates under study, were obtained Monte Carlo simulation in the canonical ensemble (N,V,T); polynomial fit and interpolation of the obtained data allowed to determine the pressure and gas density at any chemical potential. The adsorption equilibria of methane and carbon dioxide in UiO-66Zr were simulated and compared with the experimental data obtained by Jasmina H. Cavka et al. The results show that the best force field for both gases is a chargeless united-atom force field based on the TraPPE model. Using this validated force field it was possible to estimate the isosteric heats of adsorption and the Henry constants. In the Grand-Canonical Monte Carlo simulations of carbon nanotubes, we conclude that the fastest type of run is obtained with a force field that approximates the nanotube as a smooth cylinder; this approximation gives execution times that are 1.6 times faster than the typical atomistic runs.

Thermostatting methods are discussed in the context of canonical sampling in the presence of driving stochastic forces. Generalisations of the Nosé-Hoover method and Langevin dynamics are introduced which are able to dissipate excess heat introduced by steady Brownian perturbation (without a priori knowledge of its strength) while preserving ergodicity. Implementation and parameter selection are considered. It is demonstrated using numerical experiments that the methods derived can adaptively control the target canonical ensemble in the presence of nonlinear driving perturbations.

Durante la última década y paralelamente al incremento de la velocidad de computación, las técnicas de simulación molecular se han erigido como una importante herramienta para la predicción de propiedades físicas de sistemas de interés industrial. Estas propiedades resultan esenciales en las industrias química y petroquímica a la hora de diseñar, optimizar, simular o controlar procesos. El actual coste moderado de computadoras potentes hace que la simulación molecular se convierta en una excelente opción para proporcionar predicciones de dichas propiedades. En particular, la capacidad predictiva de estas técnicas resulta muy importante cuando en los sistemas de interés toman parte compuestos tóxicos o condiciones extremas de temperatura o presión debido a la dificultad que entraña la experimentación a dichas condiciones. La simulación molecular proporciona una alternativa a los modelos termofísicos utilizados habitualmente en la industria como es el caso de las ecuaciones de estado, modelos de coeficientes de actividad o teorías de estados correspondientes, que resultan inadecuados al intentar reproducir propiedades complejas de fluidos como es el caso de las de fluidos que presentan enlaces de hidrógeno, polímeros, etc. En particular, los métodos de Monte Carlo (MC) constituyen, junto a la dinámica molecular, una de las técnicas de simulación molecular más adecuadas para el cálculo de propiedades termofísicas. Aunque, por contra del caso de la dinámica molecular, los métodos de Monte Carlo no proporcionan información acerca del proceso molecular o las trayectorias moleculares, éstos se centran en el estudio de propiedades de equilibrio y constituyen una herramienta, en general, más eficiente para el cálculo del equilibrio de fases o la consideración de sistemas que presenten elevados tiempos de relajación debido a su bajos coeficientes de difusión y altas viscosidades. Los objetivos de esta tesis se centran en el desarrollo y la mejora tanto de algoritmos de simulación como de potenciales intermoleculares, factor considerado clave para el desarrollo de las técnicas de simulación de Monte Carlo. En particular, en cuanto a los algoritmos de simulación, la localización de puntos críticos de una manera precisa ha constituido un problema para los métodos habitualmente utilizados en el cálculo de equlibrio de fases, como es el método del colectivo de GIBBS. La aparición de fuertes fluctuaciones de densidad en la región crítica hace imposible obtener datos de simulación en dicha región, debido al hecho de que las simulaciones son llevadas a cabo en una caja de simulación de longitud finita que es superada por la longitud de correlación. Con el fin de proporcionar una ruta adecuada para la localización de puntos críticos tanto de componentes puros como mezclas binarias, la primera parte de esta tesis está dedicada al desarrollo y aplicación de métodos adecuados que permitan superar las dificultades encontradas en el caso de los métodos convencionales. Con este fin se combinan estudios de escalado del tamaño de sitema con técnicas de "Histogram Reweighting" (HR). La aplicación de estos métodos se ha mostrado recientemente como mucho mejor fundamentada y precisa para el cálculo de puntos críticos de sistemas sencillos como es el caso del fluido de LennardJones (LJ). En esta tesis, estas técnicas han sido combinadas con el objetivo de extender su aplicación a mezclas reales de interés industrial. Previamente a su aplicación a dichas mezclas reales, el fluido de LennardJones, capaz de reproducir el comportamiento de fluidos sencillos como es el caso de argón o metano, ha sido tomado como referencia en un paso preliminar. A partir de simulaciones realizadas en el colectivo gran canónico y recombinadas mediante la mencionada técnica de "Histogram Reweighting" se han obtenido los diagramas de fases tanto de fluidos puros como de mezclas binarias. A su vez se han localizado con una gran precisión los puntos críticos de dichos sistemas mediante las técnicas de escalado del tamaño de sistema. Con el fin de extender la aplicación de dichas técnicas a sistemas multicomponente, se han introducido modificaciones a los métodos de HR evitando la construcción de histogramas y el consecuente uso de recursos de memoria. Además, se ha introducido una metodología alternativa, conocida como el cálculo del cumulante de cuarto orden o parámetro de Binder, con el fin de hacer más directa la localización del punto crítico. En particular, se proponen dos posibilidades, en primer lugar la intersección del parámetro de Binder para dos tamaños de sistema diferentes, o la intersección del parámetro de Binder con el valor conocido de la correspondiente clase de universalidad combinado con estudios de escalado. Por otro lado, y en un segundo frente, la segunda parte de esta tesis está dedicada al desarrollo de potenciales intermoleculares capaces de describir las energías inter e intramoleculares de las moléculas involucradas en las simulaciones. En la última década se han desarrolldo diferentes modelos de potenciales para una gran variedad de compuestos. Uno de los más comunmente utilizados para representar hidrocarburos y otras moléculas flexibles es el de átomos unidos, donde cada grupo químico es representado por un potencial del tipo de LennardJones. El uso de este tipo de potencial resulta en una significativa disminución del tiempo de cálculo cuando se compara con modelos que consideran la presencia explícita de la totalidad de los átomos. En particular, el trabajo realizado en esta tesis se centra en el desarrollo de potenciales de átomos unidos anisotrópicos (AUA), que se caracterizan por la inclusión de un desplazamiento de los centros de LennardJones en dirección a los hidrógenos de cada grupo, de manera que esta distancia se convierte en un tercer parámetro ajustable junto a los dos del potencial de LennardJones.En la segunda parte de esta tesis se han desarrollado potenciales del tipo AUA4 para diferentes familias de compuesto que resultan de interés industrial como son los tiofenos, alcanoles y éteres. En el caso de los tiofenos este interés es debido a las cada vez más exigentes restricciones medioambientales que obligan a eliminar los compuestos con presencia de azufre. De aquí la creciente de necesidad de propiedades termodinámicas para esta familia de compuestos para la cual solo existe una cantidad de datos termodinámicos experimentales limitada. Con el fin de hacer posible la obtención de dichos datos a través de la simulación molecular hemos extendido el potencial intermolecular AUA4 a esta familia de compuestos. En segundo lugar, el uso de los compuestos oxigenados en el campo de los biocombustibles ha despertado un importante interés en la industria petroquímica por estos compuestos. En particular, los alcoholes más utilizados en la elaboración de los biocombustibles son el metanol y el etanol. Como en el caso de los tiofenos, hemos extendido el potencial AUA4 a esta familia de compuestos mediante la parametrización del grupo hidroxil y la inclusión de un grupo de cargas electrostáticas optimizadas de manera que reproduzcan de la mejor manera posible el potencial electrostático creado por una molecula de referencia en el vacío. Finalmente, y de manera análoga al caso de los alcanoles, el último capítulo de esta tesis la atención se centra en el desarrollo de un potencial AUA4 capaz de reproducir cuantitativamente las propiedades de coexistencia de la familia de los éteres, compuestos que son ampliamente utilizados como solventes., Parallel with the increase of computer speed, in the last decade, molecular simulation techniques have emerged as important tools to predict physical properties of systems of industrial interest. These properties are essential in the chemical and petrochemical industries in order to perform process design, optimization, simulation and process control. The actual moderate cost of powerful computers converts molecular simulation into an excellent tool to provide predictions of such properties. In particular, the predictive capability of molecular simulation techniques becomes very important when dealing with extreme conditions of temperature and pressure as well as when toxic compounds are involved in the systems to be studied due to the fact that experimentation at such extreme conditions is difficult and expensive.Consequently, alternative processes must be considered in order to obtain the required properties. Chemical and petrochemical industries have made intensive use of thermophysical models including equations of state, activity coefficients models and corresponding state theories. These predictions present the advantage of providing good approximations with minimal computational needs. However, these models are often inadequate when only a limited amount of information is available to determine the necesary parameters, or when trying to reproduce complex fluid properties such as that of molecules which exhibit hydrogen bonding, polymers, etc. In addition, there is no way for dynamical properties to be estimated in a consistent manner.In this thesis, the HR and FSS techniques are combined with the main goal of extending the application of these methodologies to the calculation of the vaporliquid equilibrium and critical point of real mixtures. Before applying the methodologies to the real mixtures of industrial interest, the LennardJones fluid has been taken as a reference model and as a preliminary step. In this case, the predictions are affected only by the omnipresent statistical errors, but not by the accuracy of the model chosen to reproduce the behavior of the real molecules or the interatomic potential used to calculate the configurational energy of the system.The simulations have been performed in the grand canonical ensemble (GCMC)using the GIBBS code. Liquidvapor coexistences curves have been obtained from HR techniques for pure fluids and binary mixtures, while critical parameters were obtained from FSS in order to close the phase envelope of the phase diagrams. In order to extend the calculations to multicomponent systems modifications to the conventional HR techniques have been introduced in order to avoid the construction of histograms and the consequent need for large memory resources. In addition an alternative methodology known as the fourth order cumulant calculation, also known as the Binder parameter, has been implemented to make the location of the critical point more straightforward. In particular, we propose the use of the fourth order cumulant calculation considering two different possibilities: either the intersection of the Binder parameter for two different system sizes or the intersection of the Binder parameter with the known value for the system universality class combined with a FSS study. The development of transferable potential models able to describe the inter and intramolecular energies of the molecules involved in the simulations constitutes an important field in the improvement of Monte Carlo techniques. In the last decade, potential models, also referred to as force fields, have been developed for a wide range of compounds. One of the most common approaches for modeling hydrocarbons and other flexible molecules is the use of the unitedatoms model, where each chemical group is represented by one LennardJones center. This scheme results in a significant reduction of the computational time as compared to allatoms models since the number of pair interactions goes as the square of the number of sites. Improvements on the standard unitedatoms model, where typically a 612 LennardJones center of force is placed on top of the most significant atom, have been proposed. For instance, the AUA model consists of a displacement of the LennardJones centers of force towards the hydrogen atoms, converting the distance of displacement into a third adjustable parameter. In this thesis we have developed AUA 4 intermolecular potentials for three different families of compounds. The family of ethers is of great importance due to their applications as solvents. The other two families, thiophenes and alkanols, play an important roles in the oil and gas industry. Thiophene due to current and future environmental restrictions and alkanols due ever higher importance and presence of biofuels in this industry.