Collagen is one of the major protein constituents in mammals and is present in all tissues and organs with the exceptions of keratin tissues such as hair and nails. Collagen monomers self-aggregate into a number of structures. In order to understand the physical bases for the structural polymorphism observed in collagen, a good starting point is one of the simplest collagen aggregates, segmental long spacing (SLS) collagen. Although SLS collagen formation induced by the presence of adenosine 5’-triphosphate is widely known, effects of other triphosphates, on the other hand, are much less studied. By varying the pH, it is discovered that all the nucleoside 5’-triphophsates, as well as inorganic triphosphate, are able to induce SLS formation over certain pH ranges. Adenosine 5’-diphosphate and para-nitrophenylphosphate cannot induce SLS formation at any pH. Based on the pH ranges at which SLS collagen can be formed, it is concluded the triphosphate functionality, with one negative charge per phosphate group, is primarily responsible for the formation of SLS collagen. Since inorganic triphosphate is able to induce SLS collagen formation, the presence of the nucleoside is optional for the assembly process; however if present, the assembly process prefers the nucleosides carrying acidic protons. Using electron spectroscopic imaging (ESI) technique, it is found phosphorus, present only in nucleotides but not in polypeptides, is localized in certain regions of SLS collagen, forming a unique banding pattern transverse the long axis of the SLS collagen. Nitrogen mapping indicates the localization of phosphorus is not due to accumulation of materials. The phosphorus banding pattern demonstrates an excellent consistency across SLS collagen assembled from both bovine and recombinant human collagen monomers. Results from molecular simulation are consistent with the experimental results. All threephosphate groups seem to be involved in the assembly process to some degree. In the last chapter of the thesis, a reliable protocol to synthesis native type collagen fibers is introduced.

Collagen is one of the major protein constituents in mammals and is present in all tissues and organs with the exceptions of keratin tissues such as hair and nails. Collagen monomers self-aggregate into a number of structures. In order to understand the physical bases for the structural polymorphism observed in collagen, a good starting point is one of the simplest collagen aggregates, segmental long spacing (SLS) collagen. Although SLS collagen formation induced by the presence of adenosine 5’-triphosphate is widely known, effects of other triphosphates, on the other hand, are much less studied. By varying the pH, it is discovered that all the nucleoside 5’-triphophsates, as well as inorganic triphosphate, are able to induce SLS formation over certain pH ranges. Adenosine 5’-diphosphate and para-nitrophenylphosphate cannot induce SLS formation at any pH. Based on the pH ranges at which SLS collagen can be formed, it is concluded the triphosphate functionality, with one negative charge per phosphate group, is primarily responsible for the formation of SLS collagen. Since inorganic triphosphate is able to induce SLS collagen formation, the presence of the nucleoside is optional for the assembly process; however if present, the assembly process prefers the nucleosides carrying acidic protons. Using electron spectroscopic imaging (ESI) technique, it is found phosphorus, present only in nucleotides but not in polypeptides, is localized in certain regions of SLS collagen, forming a unique banding pattern transverse the long axis of the SLS collagen. Nitrogen mapping indicates the localization of phosphorus is not due to accumulation of materials. The phosphorus banding pattern demonstrates an excellent consistency across SLS collagen assembled from both bovine and recombinant human collagen monomers. Results from molecular simulation are consistent with the experimental results. All threephosphate groups seem to be involved in the assembly process to some degree. In the last chapter of the thesis, a reliable protocol to synthesis native type collagen fibers is introduced.

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / Kirkwood Buff (KB) theory is one of the most important theories of solutions. The theory can relate integrals over radial (pair) distribution functions (rdfs) in the grand canonical ensemble to common thermodynamic properties. An inversion of the KB theory has been proposed by Ben-Naim and this has led to the wide spread popularity of KB theory. The idea of the KB inversion procedure is to calculate KB integrals from available thermodynamic properties. The KB theory can be used to validate the force field (ff) parameters used in molecular dynamics simulations. We have tested a series of small molecule ff parameters using KB theory that consists of both atom centered partial atomic charges and extra charge sites. The results indicate that using extra charge sites, derived from QM calculations, does not necessarily provide a more accurate representation of condensed phase properties. A further study aimed at an ongoing project of deriving new biomolecular ff parameters based on KB theory, has developed ff parameters for esters in order to represent the ester conjugation of the phospholipid molecule. The models were further tested against experimental properties. Preferential solvation (PS) is an important concept of solution mixtures that can be described using KB theory. The difference between local composition and bulk composition in solution mixtures leads to the concept of PS. A generalized explanation based on local mole fractions was derived by Ben-Naim using KB theory. However, the original expressions have been modified over years. Here, we propose a new approach based on local volume fractions to explore PS in binary and ternary solution mixtures. Experimental and simulation data were used to examine different approaches to PS. A relationship between the rdf and the triplet distribution function can be obtained using the Kirkwood Superposition Approximation (KSA). A combination of Fluctuation Solution Theory and experimental rdfs are used to examine the KSA at a series of state points for pure water. The accuracy of several other approximate relationships between the pair and triplet correlation functions was also investigated and are in good agreement for regions of the phase diagram where the compressibility is small.

AgÃncia Nacional do PetrÃleo / Tanto o gÃs natural quanto o biogÃs possuem em sua composiÃÃo metano, diÃxido de carbono, nitrogÃnio, hidrogÃnio, compostos sulfurados (incluindo o sulfeto de hidrogÃnio), etc. O diÃxido de carbono (CO2) e o Ãcido sulfÃdrico, ou sulfeto de hidrogÃnio (H2S) sÃo gases altamente indesejÃveis. O CO2 diminui o poder de combustÃo do gÃs natural e o H2S à um gÃs extremamente tÃxico. AlÃm disso, na presenÃa de umidade, ambos geram Ãcidos que corroem tubulaÃÃes e equipamentos. A absorÃÃo em soluÃÃo de aminas à o processo convencional de remoÃÃo destes gases. Entretanto, este processo despendem muito gasto energÃtico com a regeneraÃÃo das aminas, alÃm de formar subprodutos corrosivos devido à degradaÃÃo destas. Desta maneira, a adsorÃÃo fÃsica em zeolitas à uma alternativa promissora para a remoÃÃo destes gases. Assim, este trabalho tem por objetivo estudar a adsorÃÃo de gases Ãcidos, CO2 e H2S, em faujasitas puras, NaY e NaX, e modificadas, AgX, CaX e USY (zeolita dealuminizada ou ultraestabilizada) atravÃs de metodologias experimentais e de simulaÃÃo molecular. As zeolitas AgX e CaX foram obtidas atravÃs da modificaÃÃo da zeolita NaX. Todos os adsorventes foram caracterizados, quanto à estrutura cristalina, composiÃÃo quÃmica e caracterÃsticas texturais, e foram obtidas isotermas experimentais a 25 ÂC de CO2 em todos os adsorventes estudados. Foi utilizado o mÃtodo de Monte Carlo no ensemble Grande CanÃnico (GCMC) para obter as isotermas simuladas e os parÃmetros do campo de forÃa capazes de reproduzir dados experimentais de CO2 e H2S em faujasitas. / Natural gas and biogas have in their composition methane, carbon dioxide, nitrogen, hydrogen, sulfur compounds (including hydrogen sulfide), etc. The carbon dioxide (CO2) and hydrogen sulfide (H2S) are highly undesirable. CO2 decreases the combustion power of the natural gas and H2S is an extremely toxic gas. Moreover, in the presence of moisture, they generate acids that corrode pipes and equipment. The absorption in amines solution is the conventional process to removal these gases. However, this process spends a lot of energy with the regeneration of the amines, besides forming corrosive by-products due to degradation of these. Thus, the physical adsorption using zeolites is a promising alternative for remove these gases. The aim of this study is to evaluate the adsorption of acid gases, CO2 and H2S, in pure, NaY and NaX, and modified, AgX, CaX and USY (dealuminated zeolite), faujasites through experimental methods and molecular simulation. The AgX and CaX zeolites were obtained by modifying the NaX zeolite. All absorbents were obtained and characterized. Experimental adsorption isotherms were obtained of CO2 on all studied adsorbents at 25 ÂC. The force field parameters were obtained by fitting to our own experimental data, CO2 in faujasites, and validated with available data taken from the literature, H2S in faujasites, by simulated isotherms using the Grand Canonical Monte Carlo (GCMC) method.

nÃo hà / Os altos nÃveis de emissÃo de CO2 neste Ãltimo sÃculo tÃm gerado alerta e preocupaÃÃo Ãs autoridades a nÃvel mundial. Incentivos para desenvolver tecnologias de captura e armazenamento de CO2 ganham destaque nesse cenÃrio. Dentre as alternativas viÃveis para captura do referido gÃs està o processo de adsorÃÃo. A literatura à vasta nos estudos experimentais de adsorÃÃo de CO2 em diversos materiais impregnados, entretanto poucos trabalhos se dedicam ao entendimento dos fenÃmenos em nÃvel atÃmico. O presente estudo objetiva investigar a adsorÃÃo de CO2 em faujasitas do tipo X e carbonos ativados impregnados com monoetanolamina (MEA), mediante o uso de simulaÃÃo molecular. Para isso, modelos de MEA, CO2, faujasita e carbono ativado foram elaborados. Para a faujasita, construiu-se a estrutura com base nos dados cristalogrÃficos reportados na literatura. No carbono ativado, os poros foram representados pelo modelo de placas paralelas de grafeno e realizou-se o estudo em trÃs tamanhos caracterÃsticos (8,9, 18,5, 30,9 Ã) de modo a representar distintas regiÃes de adsorÃÃo e tambÃm permitir correlacionar dados com o carvÃo comercial WV-1050. A molÃcula de CO2 foi construÃda com os modelos de 3 centros (ensaios em faujasitas) e de 1 centro (ensaios em carbonos ativados). Os adsorventes foram carregados com quantidades crescentes de MEA e o impacto desta adiÃÃo foi avaliado atravÃs do levantamento de novas isotermas de CO2 utilizando-se o mÃtodo de Monte Carlo no ensemble Grande CanÃnico (GCMC). Com o modelo proposto faujasita/MEA/CO2, foi possÃvel reproduzir a tendÃncia experimental de reduÃÃo de adsorÃÃo de CO2 com aumento da concentraÃÃo de MEA, em concordÃncia com resultados experimentais apresentados na literatura. Em carbonos ativados, observou-se que os valores de CO2 adsorvidos a alta pressÃo (acima de 4 bar) sempre decaÃam com o carregamento de MEA para ambos os poros, como foi evidenciado experimentalmente em carbonos reais. No entanto, a simulaÃÃo revelou que as quantidades adsorvidas a baixa pressÃo (abaixo de 1 bar) sÃo maiores quando se adiciona monoetanolamina ao material carbonoso. Os resultados, com base nas tÃcnicas aplicadas nesse estudo, indicam que os sistemas NaX e carbono ativado modificados com MEA sÃo pouco viÃveis para captura de CO2 no que diz respeito ao critÃrio isolado de capacidade de adsorÃÃo / The high levels of CO2 emissions over the last century have generated concern and alert worldwide. Incentives to promote technologies for CO2 capture and storage are highlighted in this situation. Among the viable alternatives to capture that gas is the adsorption process. The literature contains many experimental studies of CO2 adsorption in various impregnated materials, despite that, few papers are devoted to the understanding of such phenomena at the atomic level. This study investigates the CO2 adsorption in X-faujasites and activated carbons impregnated with monoethanolamine (MEA) using molecular simulation. Thus, models of MEA, CO2, faujasite and activated carbon were proposed. For faujasite, the structure was modeled based on the crystallographic data reported in the literature. For activated carbon, the pores were represented by the slit pores model of graphene and the study was conducted in three pore sizes (8.9, 18.5, 30.9 Ã) to represent different regions of the adsorption and also allow for data correlation with the commercial activated carbon WV-1050. The CO2 molecule was modeled in the three-centers (faujasites tests) and one-center (carbons tests) models. The adsorbents were loaded with increasing amounts of monoethanolamine and the impact of this addition was evaluated through a set of simulated CO2 isotherms using the Grand Canonical Monte Carlo (GCMC) method. With the model faujasite/MEA/CO2, it was possible to reproduce the decreasing experimental CO2 adsorption with increased MEA concentration. In carbons, it was observed that the values of adsorbed CO2 at high pressure (above 4 bar) always decrease with MEA increasing loadings for both pores, as verified experimentally in real carbons. However, the simulation has shown that the amount adsorbed at low pressures (below 1 bar) is enhanced with monoethanolamine concentration in carbonaceous material. These results, considering the techniques used in this study, indicate that the activated carbon and NaX systems modified with monoethanolamine are unfeasible for capturing CO2 if adsorption capacity is the only criterion to take into account

AgÃncia Nacional do PetrÃleo / Activated carbons are amorphous materials represented by a pore size distribution (PSD) which usually reproduce the experimental isotherm of N2 at 77 K. Presently, we obtain this distribution using the activated carbon slit-pore model and isotherms calculated by molecular simulation. In this study, we have evaluated the extent to which the use of more realistic activated carbon models influences on the characterization, as well as the possibility of representing the activated carbon by a minimum three-pore PSD. Adsorption isotherms were calculated using the Grand Canonical ensemble within the Monte Carlo method, and compared with experimental isotherms of commercial activated carbons. The deconvolution method with non negative least squares was used to determine the PSDs. We observed that the models containing heterogeneity factors were more accurate than the simplified models, and that activated carbons could be well represented by a minimum three-pore distribution without significant loss of precision. Furthermore, we demonstrated that the minimum PSD could be applied to formulate virtual porous carbon models that are useful in the heterogeneity study. Finally, we propose the use of the minimum PSD to replace the classical calculations of average pore size. / Carbonos ativados sÃo materiais amorfos representados por uma distribuiÃÃo de tamanho de poros (PSD) que usualmente reproduz a isoterma experimental de N2 a 77 K. Presentemente esta distribuiÃÃo à obtida com o uso do modelo de carbono ativado de placas paralelas de grafeno e isotermas calculadas por simulaÃÃo molecular. Neste estudo avaliou-se a influÃncia do uso de modelos de poros de carbono ativado mais realistas sobre a caracterizaÃÃo, bem como a possibilidade de representar o carbono ativado por uma PSD mÃnima constituÃda de apenas trÃs poros. Isotermas de adsorÃÃo foram calculadas utilizando-se o algoritmo de Monte Carlo no ensemble grande canÃnico e comparadas com as isotermas experimentais de carbonos ativados comerciais. O mÃtodo de deconvoluÃÃo com mÃnimos quadrados nÃo negativos foi utilizado para determinaÃÃo das PSDs. Observou-se que modelos contendo fatores de heterogeneidade mostraram-se mais precisos que os modelos simplificados. Notou-se ainda que efetivamente o carbono ativado pode ser representado por uma PSD mÃnima de trÃs poros sem perda significativa de precisÃo. AlÃm disso, demonstrou-se que a distribuiÃÃo mÃnima pode ser usada para elaborar modelos virtuais de carbono que sÃo Ãteis no estudo de heterogeneidades. Finalmente propomos o uso da PSD mÃnima em substituiÃÃo ao cÃlculo clÃssico de tamanho mÃdio de poros.

A captura, estocagem e separaÃÃo de gases em processos de combustÃo à considerado um passo importante no desenvolvimento e consolidaÃÃo de novas tecnologias, devido as necessidades ambientais e ao grande interesse econÃmico envolvido. A separaÃÃo de gases Ãcidos (CO2 e H2S) à uma etapa de fundamental importÃncia para reduzir impactos ambientais e atender as especificaÃÃes de seguranÃa e mercado. A adsorÃÃo em faujasitas se apresenta como uma alternativa economicamente atraente em processos industriais, mas o elevado nÃmero de processos e condiÃÃes de temperatura e pressÃo onde pode ser utilizada, torna um estudo experimental impraticÃvel. Outro fator relevante sÃo as condiÃÃes de seguranÃa impostas durante o manuseio do Ãcido sulfÃdrico, necessitando de maior investimento em equipamentos, manutenÃÃo e sistemas de seguranÃa. Diante disse a simulaÃÃo molecular pode ser utilizada para obter propriedades imprescindÃveis para o dimensionamento e implantaÃÃo de PSAs. A base da utilizaÃÃo da simulaÃÃo molecular à a determinaÃÃo do campo de forÃa. Nesse trabalho um conjunto de parÃmetros de campo forÃa, baseados em campos de forÃa clÃssicos (UFF), foi proposto para CO2 em faujasitas sÃdicas. Em seguida a mesma metodologia de parametrizaÃÃo foi utilizada para H2S, N2, O2 e CH4. Os resultados obtidos a baixa pressÃo foram comparados com estudos experimentais e outros modelos propostos pela literatura, obtendo excelente concordÃncia em diferentes temperaturas e razÃes Si/Al, permitindo determinar o posicionamento dos sÃtios e do calor de adsorÃÃo. Outros cÃtions de compensaÃÃo foram testados para predizer a adsorÃÃo de nitrogÃnio em faujasitas. As isotermas para os cÃtions monovalentes obtiveram elevada precisÃo, para bivalentes os resultados representaram o padrÃo de adsorÃÃo experimental, embora com isotermas de menor precisÃo. Por fim, a adsorÃÃo da mistura N2/CO2 foi estudada apresentado boa concordÃncia com dados experimentais, demonstrando a eficiÃncia do mÃtodo como uma alternativa para determinaÃÃo de propriedades de misturas industriais. / The environmental needs and the great economic interest involved. The capture, storage and separation of gases in combustion processes is considered an important step in the development and consolidation of new technology, The separation of acidic gases (CO2 and H2S) is an important step to reduce environmental impacts and meet safety specifications and market. The adsorption on faujasitas presents itself as an economically attractive alternative in industrial processes, but the high number of processes and temperature and pressure conditions where it can be used, makes an experimental study impractical. Another relevant factor are security conditions imposed during the handling of hydrogen sulphide, necessitating greater investment in equipment, maintenance and safety systems. On said the molecular simulation can be used to obtain indispensable properties for the design and deployment of PSAs. The molecular simulation basis is the force field determination. In this work a set of force field parameters, based on classical force fields (UFF), has been proposed for CO2 in sodium faujasitas. The same methodology was used for H2S, N2, O2 and CH4 parameterization. The results obtained at low pressure were compared with experimental studies and other models proposed by literature, obtaining excellent concordance in different temperatures and Si/Al ratios, allowing determining the placement of adsorption sites and the heat. Other balancing cations were tested to predict nitrogen adsorption. The isotherms for the monovalent cations obtained high precision, to the bivalent results represented the standard experimental adsorption isotherms, albeit with less precision. Finally, the adsorption of mixture N2/CO2 was studied presented good agreement with experimental data, demonstrating the efficiency of the method as an alternative for determination of industrial properties of mixtures.

Deoxyribonucleic acid (DNA) is arguably the most studied and most important biological molecule. Recently, it has also been established as a potential candidate for nanoconstruction. Self-assembly of DNA molecules has emerged as a simple yet elegant technique to organize matter with sub-nanometer precision. The unique base-pairing properties which helps DNA to carry genetic information, also makes it a suitable building block for creating stable and robust nanostructures. Recent decades have witnessed a major revolution in the synthesis of different topological structures made of DNA molecules at nanoscale like, two dimensional arrays, nanotubes, polyhedra, smiley faces, three dimensional crystals etc. Due to their easier design, high fidelity and automated chemistry, DNA nanostructures have proposed applications in diverse fields of bio-nanotechnology and synthetic biology. The field of structural DNA nanotechnology is just entering in adulthood and offer paramount challenge towards the journey of DNA-based nanostructures from the laboratory to their practical implementation in the real world. The aim of my dissertation is to develop a de novo computational framework to investigate the nanoscale structure and properties of DNA-based nanostructures. This will help to understand the molecular origin of interaction governing the structure and stability of DNA nanostructures. In this thesis, we have studied the in-solution behavior of self-assembled DNA nanostructures. The state of art all atom molecular dynamics (MD) simulation has been extensively implemented to understand the various thermodynamic properties of these self-assembled soft matter systems. We expect that the results presented here will lead to better design of self-assembled DNA nanostructures to address the real world challenges. In particular, we have developed algorithms to build very accurate atomistic models of various DNA nanostructures like crossover DNA molecules, DNA nanotubes (DNTs) and DNA icosahedron (IDNA). Further, we discuss a computational framework to understand the in situ structure and dynamics of these DNA nanostructures using state-of-art MD simulation. We carried out several hundred nanosecond long MD simulations on these systems which sometimes contains close to one million atoms. Following the trajectories of nanostructures in physiological conditions, we predicted numerous properties like equilibrium solution structure behavior and elastic properties which are difficult to measure in experiments. DNTs are self-assembled tubular templates where the circular double helical domains, kept at the vertices of a polygon, are connected at crossovers junctions. Ned Seeman and co-workers at New York University have synthesized different kind of DNTs using tile-based self-assembly of oligonucleotides. To investigate their microscopic structure, stability and mechanical properties, we have come up with 3d atomistic models of various DNTs which will facilitate further studies of these nanotubes towards their proposed nanotechnological and biological applications. In chapter 3 of this thesis, we discuss the analysis of several nanoseconds long all-atom MD simulation trajectories of various DNTS in the presence of explicit salt solution. We conclude that 6-helix DNT (6HB) structures are most stable and well behaved due to the better crossover designs and geometry. There has been considerable interest to investigate and enhance the mechanical strengths of DNTs to create rigid motifs. One simple way to increase the rigidity is to add further helices to the 6HB, which is known to be the most stable design of DNT, with the same tile-based crossover method. In chapter 4, we report atomistic models of 6HB flanked symmetrically with two double helical DNA pillars (6HB+2) and 6HB flanked symmetrically by three double helical DNA pillars (6HB+3). From the fluctuation analysis of the equilibrium MD simulation trajectories, we calculated the stretch modulus and persistence length of these DNTs. The measured persistence lengths of these nanotubes are ∼10 μm, which is 2 orders of magnitude larger than that of dsDNA. We also find a gradual increase of persistence length with an increasing number of pillars, in quantitative agreement with previous experimental findings. We also carried out non-equilibrium Steered-Molecular-Dynamics (SMD) to measure the stretch modulus from the force-extension behavior of these pillared DNTs. The values of the stretch modulus calculated using contour length distribution of equilibrium MD simulations are similar to those obtained from non-equilibrium SMD simulations. The addition of pillars makes these DNTs very rigid. Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long standing challenge in biotechnology. Recently, a new class of DNA nanopores through the lipid bilayer membranes has been characterized using advanced imaging techniques and transmembrane ionic current recordings. In chapter 5 of the thesis, we present a MD simulation study of 6HB embedded in POPC lipid bilayer membranes. The analyses of 0.2 µs long equilibrium MD simulation trajectories demonstrate that structure is stable and well behaved. We observe that the head groups of the lipid molecules close to DNT cooperatively tilt towards the hydrophilic sugar-phosphate backbone of DNA to form a toroidal structure around the patch of DNT protruding in the membrane. Based on this observation, we propose a new mechanism, which has been largely overlooked so far, to explain the stability to this DNA-lipid molecular self-assembly. We further explore the effect of monovalent ionic concentrations to the in-solution structure and stability of the nanocomposite. Transmembrane ionic current measurements during the constant electric field simulation provide the I-V characteristics of the water filled DNT lumen in lipid membrane. The conductivity of the DNT lumen turns out to be several nS and increases with ionic concentration. Recently, Krishnan’s research group at NCBS Bangalore and Chicago University have characterized DNA icosahedra (IDNA) using advance imaging techniques and validated it for biological targeting and bioimaging in vivo. A high resolution structural model of such polyhedra would be critical to widening their applications in both materials and biology. In chapter 6 of this thesis, we discuss an atomistic model of this well-characterized IDNA to study the in-solution behavior using MD simulation. We provide quantitative estimate of the surface and volume of the equilibrium structure which is essential to estimate its maximal cargo carrying capacity. Importantly, our simulation of gold nanoparticles (AuNP) encapsulated within DNA icosahedra (IAuNP) revealed enhanced stability of the AuNP loaded structure as compared to the empty icosahedra. This is consistent with experimental results that show high yields of cargo-encapsulated DNA icosahedra that have led to its diverse applications for precision targeting. These studies reveal that the stabilizing interactions between the cargo and the DNA scaffold powerfully positions DNA polyhedra as targetable nanocapsules for payload delivery. The insights from our study can be further exploited for precise molecular display for diverse biological applications. Finally, in chapter 7, we give a summary of the main results presented in this dissertation. We also briefly discuss the ongoing research work and the bright future of this emerging field of DNA nanotechnology. We believe that this thesis deepens the microscopic understanding of the recent experimental observation and provides impetus in the real world application of DNA nanostructures in vitro and well as in vivo.

Carbon capture and sequestration are considered to be a temporary fix to the climate change global crisis. Following the noble gas tracers injection field experiment at Salt Creek in the state of Wyoming, USA, these tracers may be used to characterise the reservoir as a potential geological sequestration site for carbon dioxide. This study aims to investigate various thermodynamics properties of the five noble gases (Xe, Kr, Ar, Ne, and He) in n-decane at reservoir conditions (340 K – 460 K and 10 MPa – 200 MPa). The study utilises the SKS force field to describe n-decane and both Gibbs Ensemble Monte Carlo and molecular dynamics simulations were used to investigate the solubility, diffusivity, and vapour-liquid equilibrium of the five binary mixtures. The size of the noble gases was found to be important in these nonpolar mixtures where typical interactions are weak and short-ranged. The enthalpies of solvation were calculated and found to be directly correlated to the size of the solute where the energy required for the formation of a cavity to accommodate the solute is compensated by the nature of the intermolecular interaction between solvent and solute. The mixture of Ar + n-decane is of interest particularly because the sigma value for Ar is very similar to that of the CH3 group, resulting in the overall non-mononicity of several thermodynamics properties. Additionally, maxima in enthalpies of solvation were observed in Xe and Kr in n-decane solution at 200 MPa. While these maxima were observed in two different species at similar conditions, they are accommodated by unusually high uncertainties - further investigation is required before definitive conclusions can be drawn. The results from the vapour-liquid equilibrium study of the five noble gas + n-decane binary mixtures were in good agreement with the Peng-Robinson equation of state predictions. What is more, the diffusion coefficient ratios amongst the five noble gases in n-decane were investigated in light of Stoke-Einstein’s relation and Enskog’s hard-sphere relation. Three different radii of solute-solvent interaction were investigated and the best fit was observed when R =radius of solute + radius of gyration of n-decane. Additionally, the diffusion coefficients were utilised in the reservoir simulation to investigate the role of diffusion within the reservoir.

L'interprétation des expériences de relaxométrie RMN nécessite une modélisation précise des interactions entre le noyau étudié et son environnement. Pour un noyau quadrupolaire, l'interaction entre le gradient du champ électrique (EFG) émis par l'environnement avec le quadruple électrostatique du noyau est prépondérante. Notre travail a porté sur le développement du calcul des temps de relaxation RMN pour ces noyaux par simulation moléculaire. Nous nous sommes intéressés à la relaxation d'ions mono-atomiques en phase condensée à travers deux systèmes simples et réalistes : des solutions aqueuses d'électrolytes et des verres de silicate de sodium. L'EFG dé aux électrons de l'ion est obtenu en calculant la réponse du nuage électronique grâce à des calculs quantiques combinés à une récente méthode pour reconstruire la contribution des électrons de cœur. L'EFG dû à l'environnement est obtenu à partir d'une simulation moléculaire où les interactions sont décrites par un champ de force polarisable nouvellement développé. Les temps de relaxation obtenus en combinant ces deux contributions reproduisent correctement les résultats expérimentaux. Les simulations moléculaires nous permettent aussi d'extraire les mécanismes microscopiques. Pour les ions dans l'eau à dilution infinie, nous avons étudié les propriétés statistiques et dynamiques des fluctuations de l'EFG. Nous avons montré en particulier le rôle fondamental des fluctuations de densité de l'eau dans la première sphère de solvatation de l'ion. Cette thèse ouvre la voie à une meilleur compréhension des processus de relaxation RMN des ions mono-atomiques quadrupolaires dans des systèmes simples ou complexes. / Interpreting NMR relaxometry experiments requires an accurate modeling of interactions between the nucleus under study and its environment. For a quadrupolar nucleus, the interaction between the electric field gradient (EFG) arising from the environment and the electrostatic quadrupole of the nucleus is preponderant. The present work deals with a new method to compute NMR relaxation times for such nuclei with molecular simulations. We consider the relaxation of monoatomic ions in condensed matter through two simple and realistic systems: aqueous electrolytes and sodosilicate glasses. The EFG due to electrons around the ion is obtained by computing the electronic response with quantum calculation combined with a new method to obtain the contribution of core electrons. The EFG due to the environment is obtained from a molecular simulation where interactions are described using a recently developed polarisable force field. NMR relaxation times obtained by combining both these contributions compare well with experimental data. Molecular simulations allow us to highlight the microscopic mechanisms. For ions in water at infinite dilution, we studied the statistical and dynamical properties of EFG fluctuations. We notably demonstrated the primary role of water density fluctuations in the first solvation shell around the ion. This thesis opens the way for a better understanding of the mechanism behind the NMR relaxation of monoatomic and quadrupolar ions in simple and complex systems.