Tesi sul tema "Ionic-Molecular systems"

Protic ionic liquids (PILs) are a vast class of compounds that are expected to play an increasing role as fuel cell electrolytes. A crucial aspect of these systems is represented by the reversible proton transfer reaction between a Bronsted acid and a Bronsted base giving rise to the ionic phase out of a molecular neutral state. Thermodynamic, structural and chemical properties of a prototypical PIL, ethylammonium nitrate (EAN), have been investigated by a combination of different computational approaches, ranging from ab initio to classical simulations based on a reactive Monte Carlo algorithm. Ab initio methods have been applied to map the potential energy surface and reaction energies of EAN-related molecules and small clusters. Crystal structures and vibrational properties of small clusters have also been investigated at the ab initio level. The ab initio data have been used to parametrise a reactive force field, able to reproduce the acid-base equilibrium of EAN, and which has subsequently been used to carry out a detailed investigation of the hydrogen bond network in liquid EAN, using the size of the hydrogen atom as a free parameter to explore a wide variety of conditions ranging from weak to strong hydrogen bonding. Equilibrium properties such as the crystal and liquid density are well reproduced by the model which provides only a rather crude description of fluidity and cohesive energy. In addition, Monte Carlo simulations have been carried out to investigate the properties of small EAN clusters in equilibrium with their vapour. The results show a complex pattern I of ionic and neutral molecular phases as a function of cluster size and thermodynamic conditions. As a side investigation, a simulation study of electrowetting and liquid-vapour nucleation for the restricted primitive model was carried out in order to clarify crucial aspects of Coulomb systems.

Protic ionic liquids (PILs) are a class of solvents prepared from the mixing of equimolar quantities of a Brønsted acid and base resulting in both neutral and ionic species in equilibrium with one another. Their evolving application as solvents for innovative processes requires further understanding of their properties and how they originate at the molecular level. Three topics remain widely debated concerning PILs: 1) the effects of low concentrations of water as an impurity, 2) the structure–property relations in PILs and 3) the connection between PILs and their precursor components in terms of both molecular interactions and bulk properties. In this work, these three topics are studied using a variety of experimental techniques and fundamental theory for selected representative PIL systems. To clarify the effect of water at low concentrations, the statistical thermodynamic theory of solutions has been applied to quantify the interactions between species solely from thermodynamic data. Results showed both a strong composition dependence of the effect of water on the liquid structure in aprotic and protic ILs, but also that water did not significantly weaken ion–ion interactions at low concentrations. After clarifying the effects of water at low concentration on PIL behaviour, it has been shown that incorporating hydrogen bond donor functionality to the cation can increase the ionic nature of acetate PILs. This increase in ionic nature provides an excellent rationalization for the effect of cation structure on the thermodynamic and solvatochromic properties of three PILs. By studying the effect of varying composition of precursor acid and base, a deeper insight into the molecular origin of trends in bulk properties and solvation behaviour can be found. Furthermore, it has been shown that the solvation environment is highly composition dependent, offering insight into a new strategy in the application of PILs and their precursor materials as tuneable solvation media.

Changes in the ionic and dipolar molecular mobility in a polymer system are the basis for the changes in the dielectric mechanical properties of polymer materials. Frequency Dependent Dielectric Measurements (FDEMS) and Ion Time-of-Flight (ITOF) are two important techniques to investigate ionic and dipolar molecular mobility in polymer systems. The results can be related to the macro- and molecular dielectric, electrical and dynamic properties of polymeric materials. The combination of these two methods provides a full view of electric, dielectric and dynamic behavior for the systems as they undergo chemical and/or physical changes during polymerization crystallization, vitrification, and/or phase separation.;The research on microscopic mass mobility in polymer systems was done on three aspects: (1) ion mobility in an epoxy-amine reaction system; (2) dipolar mobility and relaxation during dimethacrylate resin cure and (3) dye molecule migration and diffusion in polymer films.;In the ion mobility study, we separately monitor the changes in the ion mobility and the number of charge carriers during the epoxy-amine polymerization with FDEMS and ITOF measurements. The isolation of the number of carriers and their mobility allows significant improvement in monitoring changes in the state and structure of a material as it cures.;For the dipolar mobility and relaxation study, FDEMS measurements were used to detect structural evolution and spatial heterogeneity formation during the polymerization process of dimethacrylate resins. The dielectric spectra, glass transition (Tg) profiles and dynamic mechanical measurements were used to investigate the existence of two cooperative regions of sufficient size to create two alpha-relaxation processes representing oligomer rich and polymer microgel regions during the polymerization.;For the dye migration research, we tried to develop a visually color changing paper (VCP) due to dye molecule migration in polymer films. The mobility of dye molecules in polyvinyl films was controlled by the acidity of the environment. Ionamine derivatives of dyes were stable when mixed with acid. their diffusion in polymer films can be quickly triggered as the result of an acid/base neutralization reaction. The effect of the type of base, acid and the compatibility of polymer films on the diffusion rate is discussed.

Mestrado em Biotecnologia - Biotecnologia Molecular
Aiming at finding more biocompatible and environmentally-benign separation processes, aqueous biphasic systems composed of ionic liquids can be envisaged as an alternative and advantageous approach for the extraction and purification of the most diverse biomolecules. In this work, the main goal consisted on the study of the ability of polysaccharides, as a benign alternative over inorganic salts typically used, to form aqueous biphasic systems with ionic liquids. To this aim, the phase diagrams and respective compositions of the two phases in equilibrium for ternary systems consisting of several ionic liquids, water, and polysaccharides were determined at 298 K. By the combination of different families of ionic liquids, achieved by a representative variety of cations and anions, with dextrans and maltodextrins, it was possible to infer on the effect of the IL structural characteristics, as well as on the polysaccharides molecular weight through the formation ability of aqueous two-phase systems. Finally, and to ascertain on the potential application of these new systems such as extraction techniques, some of them were also used and evaluated regarding their aptitude to extract amino acids. The use of polysaccharides, namely dextran and maltodextrin, as salting-out molecules to form aqueous biphasic systems with ionic liquids was the main focus of this work. It was demonstrated here, for the first time, that a new class of aqueous biphasic systems composed of ionic liquids and polysaccharides can be formed while contributing to the development of more efficient and sustainable separation and purification techniques. These systems can be also seen as promising routes in the improvement of biotechnological processes which increasingly tend to be decisive in industry.
No âmbito da procura de processos de separação mais biocompatíveis e amigos do ambiente, os sistemas aquosos bifásicos com líquidos iónicos constituem uma abordagem alternativa e vantajosa para a extração e purificação das mais diversas biomoléculas. Neste trabalho pretendeu-se estudar especificamente a capacidade de polissacarídeos, como uma alternativa mais benigna face aos sais normalmente utilizados, para formar sistemas aquosos bifásicos com líquidos iónicos. Para tal, determinaram-se os diagramas de fase e composições das duas fases em equilíbrio para diversos sistemas ternários formados por líquidos iónicos, água e polissacarídeos a 298 K. O estudo destes novos sistemas, combinando diferentes famílias de líquidos iónicos representados por uma variedade alargada de catiões e aniões, com dextranas e maltodextrinas, permitiu avaliar o efeito das características estruturais dos líquidos iónicos, bem como da massa molecular dos polissacarídeos, na capacidade de formação de sistemas de duas fases aquosas. Por fim, e para suportar a sua aplicação como novas técnicas de extração, alguns destes sistemas foram também avaliados no que respeita à sua capacidade para extrair aminoácidos. A utilização de polissacarídeos, nomeadamente de dextrano e maltodextrina, enquanto moléculas indutoras de salting-out para formar sistemas aquosos bifásicos com líquidos iónicos, constituiu o foco principal deste trabalho. Pela primeira vez foi mostrado que existe uma nova classe de sistemas aquosos bifásicos constituídos por líquidos iónicos e polissacarídeos contribuindo assim para o desenvolvimento de técnicas de separação e purificação de uma forma mais eficiente, sustentável e ecológica. Estes sistemas poderão ainda ser vistos como vias promissoras no melhoramento de processos biotecnológicos que tendem a ser cada vez mais decisivos na indústria.

Adsorption is a ubiquitous phenomenon that plays key roles in numerous applications including molecule separation, energy storage, catalysis, and lubrications. Since adsorption is sensitive to molecular details of adsorbate molecule and adsorbent materials, it is often difficult to describe theoretically. Molecular modeling capable of resolving physical processes at atomistic scales is an effective method for studying adsorption. In this dissertation, the adsorption of small molecules in three emerging materials systems: porous liquids, room-temperature ionic liquids, and atomically sharp electrodes immersed in aqueous electrolytes, are investigated to understand the physics of adsorption as well as to help design and optimize these materials systems. Thermodynamics and kinetics of gas storage in the recently synthesized porous liquids (crown-ether-substituted cage molecules dispersed in an organic solvent) were studied. Gas molecules were found to store differently in cage molecules with gas storage capacity per cage in the following order: CO2>CH4>N2. The cage molecules show selectivity of CO2 over CH4/N2 and demonstrate capability in gas separation. These studies suggest that porous liquids can be useful for CO2 capture from power plants and CH4 separation from shale gas. The effect of adsorbed water on the three-dimensional structure of ionic liquids [BMIM][Tf2N] near mica surfaces was investigated. It was shown that water, as a dielectric solvent and a molecular liquid, can alter layering and ordering of ions near mica surfaces. A three-way coupling between the self-organization of ions, the adsorption of interfacial water, and the electrification of the solid surfaces was suggested to govern the structure of ionic liquid near solid surfaces. The effects of electrode charge and surface curvature on adsorption of N2 molecules near electrodes immersed in water were studied. N2 molecules are enriched near neutral electrodes. Their enrichment is enhanced as the electrode becomes moderately charged but is reduced when the electrode becomes highly charged. Near highly charged electrodes, the amount of N2 molecules available for electrochemical reduction is an order of magnitude higher near spherical electrodes with radius ~1nm than near planar electrodes. The underlying molecular mechanisms are elucidated and their implications for development of electrodes for electrochemical reduction of N2 are discussed.
Doctor of Philosophy
Adsorption is a ubiquitous phenomenon that plays key roles in numerous applications including molecule separation, energy storage, catalysis, and lubrications. Since adsorption is sensitive to molecular details of adsorbate molecule and adsorbent materials, it is often difficult to describe theoretically. Molecular modeling capable of resolving physical processes at atomistic scales is an effective method for studying adsorption. In this dissertation, the adsorption of small molecules in three emerging materials systems: porous liquids, room-temperature ionic liquids, and atomically sharp electrodes immersed in aqueous electrolytes, are investigated to understand the physics of adsorption as well as to help design and optimize these materials systems. Thermodynamics and kinetics of gas storage in the recently synthesized porous liquids (crown-ether-substituted cage molecules dispersed in an organic solvent) were studied. Gas molecules were found to store differently in cage molecules with gas storage capacity per cage in the following order: CO2>CH4>N2. The cage molecules show selectivity of CO2 over CH4/N2 and demonstrate capability in gas separation. These studies suggest that porous liquids can be useful for CO2 capture from power plants and CH4 separation from shale gas. The effect of adsorbed water on the three-dimensional structure of ionic liquids [BMIM][Tf2N] near mica surfaces was investigated. It was shown that water, as a dielectric solvent and a molecular liquid, can alter layering and ordering of ions near mica surfaces. vi A three-way coupling between the self-organization of ions, the adsorption of interfacial water, and the electrification of the solid surfaces was suggested to govern the structure of ionic liquid near solid surfaces. The effects of electrode charge and surface curvature on adsorption of N2 molecules near electrodes immersed in water were studied. N2 molecules are enriched near neutral electrodes. Their enrichment is enhanced as the electrode becomes moderately charged but is reduced when the electrode becomes highly charged. Near highly charged electrodes, the amount of N2 molecules available for electrochemical reduction is an order of magnitude higher near spherical electrodes with radius ~1nm than near planar electrodes. The underlying molecular mechanisms are elucidated and their implications for development of electrodes for electrochemical reduction of N2 are discussed.

L'objectif de cette thèse est d'analyser la structure microscopique des mélanges de liquide avec des solvants utilisés comme électrolytes dans les dispositifs électrochimiques afin de caractériser l'effet de l'agrégation des ions sur les propriétés de transport de ces systèmes. En utilisant la simulation de dynamique moléculaire, les systèmes suivants ont été étudiés: (i) les solutions de LiPF6 dans le mélange carbonate de diméthyle / carbonate d'éthylène (1:1), (ii) les solutions de SBPBF4 dans l'acétonitrile, et (iii) les mélanges de liquides ioniques (ILs) C4mimX à température ambiante (X= BF4-, PF6-, TFO-, TFSI-) avec des solvants aprotiques dipolaires tels que l'acétonitrile, la γ-butyrolactone et le carbonate de propylène.Pour tous les systèmes, l'analyse des agrégats a montré la formation d'un réseau ionique continu avec l'augmentation de la concentration de l'électrolyte. Ceci affecte significativement la diffusivité et la viscosité dans ces solutions.L'analyse des polyèdres de Voronoi des mélanges ILs-solvants a montré qu'en dessous de la fraction molaire IL d'environ 0.2, les ions sont bien solv atés par les molécules de solvant, mais au-dessus de cette fraction molaire, ils commencent à former des paires de contact, tandis que les molécules de solvant, expulsées du voisinage des ions, s'autoassocient
The objective of this thesis is to analyze the microscopic structure of the series ion-molecular systems that widely used for practical electrochemistry and to characterize the effect of the ion aggregation on the transport properties of these systems. By using molecular dynamics simulation, the following systems were investigated: (i) the solutions of LiPF6 in dimethyl carbonate / ethylene carbonate mixture (1:1), (ii) the solutions of SBPBF4 in acetonitrile, and (iii) the mixtures of room-temperature ionic liquids (ILs) C4mimX (X= BF4-, PF6-, TFO-, TFSI-) with dipolar aprotic solvents such as acetonitrile, γ-butyrolactone and propylene carbonate.For all the systems the aggregate analysis showed the formation of the ionic continuous network with the increase of electrolyte concentration. This affects significantly diffusivity and viscosity in these solutions.Voronoi polyhedra analysis of ILs-solvent mixtures showed that below the IL mole fraction of about 0.2, the ions are well solvated by the solvent molecules, but above this mole fraction they start to form contact pairs, while the solvent molecules, expelled from the vicinity of the ions, self-associates

The electron density of an ion is strongly influenced by its environment in a condensed phase. When the environment changes, for example due to thermal motion, non-trivial changes in the electron density, and hence the interionic interactions occur. These interactions give rise to many-body effects in the potential. In order to represent this phenomenon in molecular dynamics (MD) simulations a method has been developed in which the environmentally-induced changes in the ionic properties are represented by extra dynamical variables. These extra variables are handled in an extended Lagrangian formalism by techniques analogous to those used in Car and Parrinello's ab initio MD method. At its simplest level (the polarizable-ion model or PIM) induced dipoles are represented. With the PIM it has proven possible to quantitatively account for numerous properties of divalent metal halides, which had previously been attributed to unspecific "covalent" effects. In the solid-state the prevalence of layered crystal structures is explained. Analogous non-coulombic features in liquid structures, in particular network formation in "strong" liquids like ZnCl₂ , have been studied as has network disruption by "modifiers" like RbCl. This work leads to an understanding of the relationship between the microscopic structure and anomalous peaks ("prepeaks") seen in diffraction data of such materials. The PIM was extended to include induced quadrupoles and their effect studied in simulations of AgCl. In the solid-state it is found that the both are crucial in improving the phonon dispersion curves with respect to experiment. In the liquidstate polarization effects lower the melting point markedly. For oxides the short-range energy has been further partitioned into overlap and rearrangement energies and electronic structure calculations are used to parameterize a model in which the radius of the anion is included as an additional degree of freedom. The Bl → B2 phase transition is studied in MgO and CaO and the differences between the new model and a rigid-ion model are analysed.

Yes
Ionic systems with enhanced proton conductivity are widely viewed as promising electrolytes in fuel cells and batteries. Nevertheless, a major challenge toward their commercial applications is determination of the factors controlling the fast proton hopping in anhydrous conditions. To address this issue, we have studied novel proton-conducting materials formed via a chemical reaction of lidocaine base with a series of acids characterized by a various number of proton-active sites. From ambient and high pressure experimental data, we have found that there are fundamental differences in the conducting properties of the examined salts. On the other hand, DFT calculations revealed that the internal proton hopping within the cation structure strongly affects the pathways of mobility of the charge carrier. These findings offer a fresh look on the Grotthuss-type mechanism in protic ionic glasses as well as provide new ideas for the design of anhydrous materials with exceptionally high proton conductivity.

abstract: Ionic liquids (ILs), or low-temperature liquid salts, are a class of materials with unique and useful properties. Made up entirely of ions, ILs are remarkably tunable and diverse as cations and anions can be mixed and matched to yield desired properties. Because of this, IL/water systems range widely—from homogeneous mixtures to multiphasic systems featuring ionic liquid/liquid interfaces. Even more diversity is added when particles are introduced to these systems, as hard particles or soft-matter microgels interact with both ILs and water in complex ways. This work examines both miscible ionic liquid/water mixture and two-phase, immiscible ionic liquid/water systems. Extensive molecular dynamics (MD) simulations are utilized in conjunction with physical measurements to inform theoretical understanding of the nature of these systems, and this theoretical understanding is related to practical applications—in particular, the development of a low-temperature liquid electrolyte for use in molecular electronic transducer (MET) seismometers, and particle self-assembly and transport at ionic liquid/liquid interfaces such as those in Pickering emulsions. The homogenous mixture of 1-butyl-3-methylimidazolium iodide and water is examined extensively through MD as well as physical characterization of properties. Molecular ordering within the liquid mixture is related to macroscopic properties. These mixtures are then used as the basis of an electrolyte with unusual characteristics, specifically a wide liquid temperature range with an extremely low lower bound combined with relatively low viscosity allowing excellent performance in the MET sensor. Electrolyte performance is further improved by the addition of fullerene nanoparticles, which dramatically increase device sensitivity. The reasons behind this effect are explored by testing the effect of graphene surface size and through MD simulations of fullerene and a silica nanoparticle (for contrast) in [BMIM][I]/water mixtures. Immiscible ionic liquid/water systems are explored through MD studies of particles at IL/water interfaces. By increasing the concentration of hydrophobic nanoparticles at the IL/water interface, one study discovers the formation of a commingled IL/water/particle pseudo-phase, and relates this discovery to previously-observed unique behaviors of these interfaces, particularly spontaneous particle transport across the interface. The other study demonstrates that IL hydrophobicity can influence the deformation of thermo-responsive soft particles at the liquid/liquid interface.
Dissertation/Thesis
Doctoral Dissertation Chemical Engineering 2016

Submitted in fulfillment of the requirements of the Degree of Doctor of Technology: Chemistry, Durban University of Technology, 2010.
The thermodynamic properties of mixtures involving ionic liquids (ILs) with alcohols or alkyl acetate or nitromethane at different temperatures were determined. The ILs used were methyl trioctylammonium bis(trifluoromethylsulfonyl)imide ([MOA]+[Tf2N]-) and 1-butyl-3- methylimidazolium methyl sulphate [BMIM]+[MeSO4]-. The ternary excess molar volumes (􀜸􀬵􀬶􀬷 E ) for the mixtures {methyl trioctylammonium bis (trifluoromethylsulfonyl)imide + methanol or ethanol + methyl acetate or ethyl acetate}and (1- butyl-3-methylimidazolium methylsulfate + methanol or ethanol or 1-propanol + nitromethane) were calculated from experimental density values, at T = (298.15, 303.15 and 313.15) K and T = 298.15, respectively. The Cibulka equation was used to correlate the ternary excess molar volume data using binary data from literature. The 􀜸􀬵􀬶􀬷 E values for both IL ternary systems were negative at each temperature. The negative contribution of 􀜸􀬵􀬶􀬷 E values are due to the packing effect and/or strong intermolecular interactions (ion-dipole) between the different molecules. The density and speed of sound of the binary solutions ([MOA]+[Tf2N]- + methyl acetate or ethyl acetate or methanol or ethanol), (methanol + methyl acetate or ethyl acetate) and (ethanol + methyl acetate or ethyl acetate) were also measured at T = ( 298.15, 303.15, 308.15 and 313.15) K and at atmospheric pressure. The apparent molar volume, Vφ , and the apparent molar isentropic compressibility, κφ , were evaluated from the experimental density and speed of sound data. A Redlich-Mayer type equation was fitted to the apparent molar volume and apparent molar isentropic compressibility data. The results are discussed in terms of solute-solute, solute- solvent and solvent-solvent interactions. The apparent molar volume and apparent molar isentropic compressibility at infinite dilution, 􀜸φ 􀬴 and κφ 􀬴, respectively of the binary solutions have been calculated at each temperature. The 􀜸φ 􀬴 values for the binary v systems ([MOA]+[Tf2N]- + methyl acetate or ethyl acetate or methanol or ethanol) and (methanol + methyl acetate or ethyl acetate) and (ethanol + methyl acetate or ethyl acetate) are positive and increase with an increase in temperature. For the (methanol + methyl acetate or ethyl acetate) systems 􀜸φ 􀬴 values indicate that the (ion-solvent) interactions are weaker. The κφ 􀬴 is both positive and negative. Positive κφ 􀬴, for ([MOA] + [Tf2N]- + ethyl acetate or ethanol), (methanol + ethyl acetate) and (ethanol + methyl acetate or ethyl acetate) can be attributed to the predominance of solvent intrinsic compressibility effect over the effect of penetration of ions of IL or methanol or ethanol. The positive κφ 􀬴 values can be interpreted in terms of increase in the compressibility of the solution compared to the pure solvent methyl acetate or ethyl acetate or ethanol. The κφ 􀬴 values increase with an increase in temperature. Negative κφ 􀬴, for ([MOA] + [Tf2N]- + methyl acetate or methanol), and (methanol + methyl acetate) can be attributed to the predominance of penetration effect of solvent molecules into the intra-ionic free space of IL or methanol molecules over the effect of their solvent intrinsic compressibility. Negative κφ 􀬴 indicate that the solvent surrounding the IL or methanol would present greater resistance to compression than the bulk solvent. The κφ 􀬴 values decrease with an increase in the temperature. The infinite dilution apparent molar expansibility, 􀜧φ 􀬴 , values for the binary systems (IL + methyl acetate or ethyl acetate or methanol or ethanol) and (methanol + methyl acetate or ethyl acetate) and (ethanol + methyl acetate or ethyl acetate) are positive and decrease with an increase in temperature due to the solution volume increasing less rapidly than the pure solvent. For (IL + methyl acetate or ethyl acetate or methanol or ethanol) systems 􀜧φ 􀬴 indicates that the interaction between (IL + methyl acetate) is stronger than that of the (IL + ethanol) or (IL + methanol) or (IL + ethyl acetate) solution. For the (methanol + methyl acetate or ethyl acetate) systems 􀜧φ 􀬴 values vi indicate that the interactions are stronger than (ethanol + methyl acetate or ethyl acetate) systems.

Submitted in fulfillment of the academic requirements for the Masters Degree in Technology: Chemistry, Durban University of Technology, 2008.
The thermodynamic properties of binary liquid mixtures involving ionic liquids (ILs) with alcohols were determined. ILs are an important class of solvents since they are being investigated as environmentally benign solvents, because of their negligible vapour pressure, and as potential replacement solvents for volatile organic compounds (VOCs) currently used in industries. Alcohols were chosen for this study because they have hydrogen bonding and their interaction with ILs will help in understanding the intermolecular interactions. Also, their thermodynamic properties are used for the development of specific chemical processes. The excess molar volumes of binary mixtures of {1-ethyl-3-methylimidazolium ethylsulfate + methanol or 1-propanol or 2-propanol}, {trioctylmethylammonium bis (trifluoromethyl-sulfonyl) imide + methanol or ethanol or 1-propanol}, {1-buty-3-methylimidazolium methylsulfate + methanol or ethanol or 1-propanol} were calculated from experimental density values, at T = (298.15, 303.15 and 313.15) K. The Redlich-Kister smoothing polynomial was fitted to the excess molar volume data. The partial molar volumes of the binary mixtures {1-ethyl-3-methylimidazolium ethylsulfate + methanol or 1-propanol or 2-propanol}, {trioctylmethylammonium bis (trifluoromethyl-sulfonyl) imide + methanol or ethanol or 1-propanol}, {1-buty-3-methylimidazolium methylsulfate + methanol or ethanol or 1-propanol} were calculated from the Redlich-Kister coefficients, at T = (298.15, 303.15 and 313.15) K. This information was used to better understand the intermolecular interactions with each solvent at infinite dilution. iii The isentropic compressibility of {trioctylmethylammonium bis (trifluoromethyl-sulfonyl) imide + methanol or ethanol or 1-propanol}, were calculated from the speed of sound data at T = 298.15 K.

碩士
國立交通大學
應用化學系所
95
This study investigates on obtaining a water model suited to long simulation time of macromolecules in solution and constructing a simulation system of aqueous solutions. Comparison between other models revealed that flexible three-center model has been already used in many large-scale simulation and it’s provided with experimental data. Because the model works well with short-range truncation suited to high-speed computation. It’s tested by comparing the structural, dynamic and thermodynamic properties of water in aqueous solution, at several temperature and density, with the other models and experimental data. Our program also was tested by calculation such properties and fitted these literature very well. Therefore, the aims of research divide into three parts: First is tested for many water properties comparing with literature；Second investigates on the structural and dynamic properties of brine solutions；the other simulates charged aqueous nanodroplets for different condition, which were different temperatures, the number of ions, the type of ion and the size of droplets, in vacuum and these nanodroplets were given some additional velocity ranging from 1 m/s to 200 m/s to observe two nanodroplets bumped into or merged each other or merged . Studies show that ionic solvation shell effects strongly on the water structure in aqueous solution, like Cl- anion makes water more slow meaning ionic solvation shells are rigid. Computation of Bond time correlation functions shows that Cl--water pair can hold longer than water-water pair. The rigidity can play an important role in charged aqueous nanodroplets. At several conditions, the nanodroplet including Cl- ions were stable. Giving two nanodroplets a velocity in a direction to overcome the surface energy of the droplet made a formation of bridge structure and giving more kinetic energy performed the merged process. To calculate the surface area and volume of a nanodroplet, there are the merged nanodroplet and a nanodroplet had the same number water molecules and ions of the merged nanodroplet, we use the molecular modeling software TINKER implemented the algorithms of solvent accessible surface. The result of computation can prove the merged nanodroplet is the stable structure.

Amphiphilic molecules are interesting building blocks of self-assembled structures for a variety of biotechnological purposes, due to their hydrophobic and hydrophilic moieties. Some of them are deemed as biocompatible, capable of carrying biomolecules, while being highly tuneable and controlled with external cues. Such properties are advantageous in drug delivery applications. Ionic liquids have gained relevance since their discovery as not only responsive and adjustable, but also as promising alternatives to conventionally used solvents. This project aims to use molecular dynamics to the study of ammonium-based ionic liquids in the extraction and delivery of biomolecules, specifically gallic acid and ibuprofen. A multiscale strategy was followed to simulate systems using the GROMACS package for classical molecular dynamics simulations. High-resolution descriptions were used to create a novel coarse-grained model to reproduce the phase behaviour and partition studies. The partition of gallic acid and ibuprofen in the studied ionic liquid solutions was assessed, as well as the particular orientation of the biomolecule in the supramolecular structure of the ionic liquids, as well as the interactions generating each outcome. A pH-driven effect was verified as the main parameter affecting the studied systems. This work has the potential to pave the way for a transferable, transversal platform to analyse and test different biomolecule-IL combinations in aqueous solutions in order to save time and experimental resources in diverse applications.
As moléculas anfifílicas são elementos de elevado potencial de estruturas auto-organizadas para vários fins biotecnológicos, devido às suas componentes hidrofóbica e hidrofílica. Parte destas são biocompatíveis, capazes de transportar biomoléculas e altamente ajustáveis e controláveis por fatores externos. Estas propriedades são particularmente relevantes em aplicações de libertação controlada de fármacos. Os líquidos iónicos são cada vez mais utilizados desde a descoberta da sua sensibilidade a estímulos, ajustabilidade e possível uso como alternativas sustentáveis a solventes convencionais. Este trabalho teve como objetivo utilizar dinâmica molecular para estudar líquidos iónicos à base de iões amónio para extração e libertação de biomoléculas, particularmente ácido gálico ou ibuprofeno. Foi utilizada uma estratégia de simulação em várias escalas com o pacote de simulação em dinâmica molecular clássica GROMACS, onde modelos com alta resolução foram usados para criar modelos de grão-grosso novos, mais eficientes em estudos de partição e comportamento de fases. Foi averiguada a partição de ácido gálico e ibuprofeno nas soluções de líquido iónico em questão, bem como a orientação da biomolécula na estrutura supramolecular do líquido iónico e as interações que levaram à mesma. Foi verificado um efeito à base do pH como o principal fator a afetar os sistemas estudados. Este trabalho tem o potencial de dar origem a uma plataforma transversal e transferível para analisar e testar várias combinações de biomoléculas e líquidos iónicos em soluções aquosas de forma a poupar tempo e recursos experimentais em diversas aplicações.
Mestrado em Biotecnologia

碩士
國防大學中正理工學院
應用化學研究所
91
In this article we studied the amines (N(CH3)nH3-n) combined with different kinds of molecule to create the intermolecular hydrogen bonding and inter-ionic hydrogen bonding complex, from that way, discussing the influence of molecular structure stability by two kinds of hydrogen bonding systems. In the intermolecular hydrogen bonding system, we chosen amines combined with nitric acid (HNO3) or hydrogen halide (HX,X=F, Cl or Br) complex, to compare and analyze the affect of hydrogen bonding by methyl group and steric effect. However, in the part of ionic-inter hydrogen bonding, selected the amines combined with hydrogen halide complex for researching object, to discuss the distinction of intermolecular hydrogen bonding and inter-ionic hydrogen bonding. As the result of calculation, we found that methyl group really could strength the stability at intermolecular hydrogen bonding. Along with the addition of temperature because of steric effect and entropy, the stability sequence of Gibbs free energy (△G) would have different variations. In the amines combined with hydrogen halide complex, when methyl group added gradually and atomic number of halogen atom became augmented (Cl or Br), contrasted the migration of hydrogen atom position in hydrogen bonding system, we could find the tendency of total system transferred from intermolecular hydrogen bonding to inter-ionic hydrogen bonding. In the case of inter-ionic hydrogen bonding system, its binding energy between ions including both the coulombic attraction energy and hydrogen bonding energy. In this system, the overall energy between this ionic pairs is decreased whenever the number of CH3 is increasing due to proton accept or electron donor effect of methyl group.

Diffusion is a fundamental process which plays a crucial role in many processes occurring in nature. It is governed by the Fickian laws of diffusion. The laws of diffusion explain how diffusive flux is related to the concentration gradient. However, diffusion occurs even when there is no concentration gradient. Chapter 1 introduces diffusion and related concepts such as random walk, Brownian motion, etc. Present understanding with relation to ionic conduction and diffusion in polar solvents and the anomalies observed in the variation of ionic conductivity with ionic radii has also been discussed. Walden’s rule states that the product of limiting ionic conductivity and viscosity is constant for a given ion in different solvents and it is inversely proportional to ionic radius in a given solvent. However, experimental observations indicate that in a given solvent limiting ionic conductivities show an increase followed by a decrease with increase in ionic radii. This is often referred to as the breakdown of Walden’s rule. Several theories have been proposed in the past to explain the breakdown in Waldens rule. Solvent-berg model, continuum based theories and microscopic theories are some of theories that have been proposed. These theories are discussed briefly. The limitations in these theories are also outlined. There are several computer simulation investigations of ions in water and these are discussed. Also described is diffusion of hydrocarbons in zeolites. Various interesting observations such as window effect, nest effect, single file diffusion and the levitation effect are discussed. In Chapter 2, we have analysed the experimental ionic conductivity data as a function of the ionic radius for monovalent cations and anions in aqueous solution. Molecular dynamics simulations on LiCl and CsCl dissolved in water are also reported. The results suggest that the activation energy is responsible for the anomalous dependence of ionic conductivity on ionic radii. It is seen that ions with high conductivity posses low activation energy. The reason for the variation of activation energy with ionic radii are explained in terms of Derouane’s mutual cancellation of forces or levitation effect. This provides an alternative to the existing theories. Experimental limiting ionic conductivity, λ0 of different alkali ions in water shows markedly different dependences on pressure. Existing theories such as that of Hubbard-Onsager are unable to explain this dependence on pressure of the ionic conductivity for all ions. Experimental ionic conductivity data shows that smaller ions such as Li+ exhibit a monotonic increase in λ0 with pressure. Intermediate sized ions such as K+ exhibit an increase in λ0 followed by a decrease at still higher pressures. Larger ions such as Cs+ exhibit a monotonic decrease in λ0 with increase in pressure. In the present thesis, we have explored this intriguing behaviour shown by alkali ions in water in the next few chapters. In Chapter 3, we report molecular dynamics investigation of potassium chloride solution (KCl) at low dilution in water at several pressures between 1 bar and 2 kbar. Two different potential models have been employed. One of the models successfully reproduces the experimentally observed trend in ionic conductivity of K+ ion in water over 0.001-2 kbar range at 298K. We also propose a theoretical explanation, albeit at a qualitative level, to account for the dependence of ionic conductivity on pressure in terms of the previously studied Levitation Effect. A number of properties of the solvent in the hydration shell are also reported. In Chapter 4, residence times of water in the solute and water hydration shell are reported for KCl in water as a function of pressure. Two different approaches – Impey, McDonald and Madden’s approach as well as the recently proposed stable state picture (SSP) of Laage and Hynes yield somewhat different values for the residence times. The latter suggests that the hydration shell is more labile. As pressure is varied, the analysis suggests drastic changes in the hydration shell around water and little or no change in the hydration shell of the ions at higher pressures. The residence times τIMM as well as τSSP show a decrease with increase in pressure upto 1.5 kbar and a small increase beyond this pressure. This correlates with the dependence of the ionic conductivity of potassium ion on pressure. Similar correlation is also seen for chloride ion between ionic conductivity and residence time in hydration shell. However, no such correlation is seen in the case of water. We also report variation of residence time as a function of t∗, the minimum time that a water has to leave the hydration shell to be excluded from it. In Chapter 5, a molecular dynamics study of LiCl dissolved in water is reported at several pressures between 1 bar and 4 kbars at 240K. Structural properties such as radial distribution function, distribution of the angle between ion-oxygen and dipole vector of water in the hydration shell, angle between ion-oxygen and OH vector, oxygen-ion oxygen angle for water in the hydration shell, mean residence times by two different approaches are reported. Self-diffusivity of both Li+ and Cl− exhibit an increase with pressure in agreement with the experimentally observed trend. We also report the velocity autocorrelation function as a function of pressure. We show that the changes in these can be understood in terms of the levitation effect. For the first time we report the self part of the intermediate scattering function, Fs(k, t), at different pressures. These show for Li+ at small wavenumber k, a bi-exponential decay with time at low pressures. At higher pressures when the ionic conductivity is high, Fs(k, t) exhibits a single exponential decay. We also report wavenumber dependence of the ratio of the full width at half maximum to 2Dk2. These changes in these properties can be accounted for in terms of the levitation effect. The changes in the void structure of water with pressure plays a crucial role in the changes in ionic conductivity of both the ions. In Chapter 6, a detailed molecular dynamics study of self-diffusivity of model ions in water is presented as a function of pressure. First, we have obtained the dependence of self-diffusivity on ionic radius for both cations and anions by varying the radius of the ion, rion. Self-diffusivity exhibits an increase with ionic radius when rion is small and reaches a maximum at some intermediate value, before decreasing with increase in rion for rion > . The velocity autocorrelation function for different sizes of cations as well as anions suggest that the ion with maximum self-diffusivity has facile motion with little back scattering. These trends can be understood in terms of the levitation effect which relates the dependence of self-diffusivity on ionic radius to the bottleneck radius of the pore network provided by the solvent or water. The ratio ζ, defined as the full width at half maximum of the self part of the dynamic structure factor at wavenumber k to its value (2Dk2) at k = 0 is seen to increase with k for ions far away from the diffusivity maximum while a decrease with k is observed for ions closer to the diffusivity maximum. Calculations have also been carried out at pressures of 0.001, 2 and 4 kbars to obtain the variation of ionic conductivity with pressure for model ions of several different sizes. It is shown that for small ions (rion < ), self-diffusivity increases with pressure or exhibits an increase followed by a decrease. In contrast, we show that whenever ionic radius is large, (rion > ), a decrease in self-diffusivity with increase in pressure is seen. We suggest that there is a relation between the dependence of self-diffusivity on ionic radius and its dependence on pressure. The nature of this relationship arises through the levitation effect. Increase in pressure leads to decrease in the bottleneck radius, thus increasing the levitation parameter. For small ions (rion < ), this will lead to increase in diffusivity whereas for large ions (rion > ) this will lead to decrease in diffusivity. For small ions (rion < ), the increase in pressure leads to lowered back scattering in the velocity autocorrelation function. In contrast to this, for large ions (rion ≥ ), any increase in pressure leads to increase in back scattering in the velocity autocorrelation function. For the 1.7 °A anion, the ratio ζ is seen to exhibit a minimum at intermediate k and increase with k at large k for 0.001 kbar pressure. This changes to a less pronounced minimum at 2 kbars and by 4 kbars to a nearly monotonically decreasing function of k. These changes suggest, in agreement with the predictions of the levitation effect, the approach of the bottleneck radius to values similar to that of the ionic radius of 1.7 °A on increasing pressure to 4 kbars. Thus, this work offers an unification in our understanding of the dependence of ionic conductivity on ionic radius and pressure. It is seen that when the ionic radius is varied the numerator of the expression for levitation parameter is varied whereas by varying the pressure, the denominator is varied. The variation of diffusivity with density of the host medium and degree of disorder of the host medium is explored in Chapter 7. The system consists of a binary mixture of a relatively smaller sized solute (whose size is varied) and a larger sized solvent interacting via Lennard-Jones potential. Calculations have been performed at three different reduced densities of 0.7, 0.8 and 0.933. These simulations show that diffusivity exhibits a maximum for some intermediate size of the solute when the solute diameter is varied. The maximum is found at the same size of the solute at all densities which is at variance with the prediction of the levitation effect. In order to understand this anomaly, we have carried out additional simulations in which we have varied the degree of disorder at constant density and find that the diffusivity maximum gradually disappears with increase in disorder. We have also carried out simulations in which we have kept the degree of disorder constant but changed only the density. We find that the maximum in diffusivity is now seen to shift to larger distances with decrease in density. In these simulations we have characterized the disorder by constructing the minimal spanning tree. These results are in excellent agreement with the predictions of the levitation effect. They suggest that the effect of disorder is to shift the maximum in diffusivity towards smaller solute radius while that of the decrease in density is to shift it towards larger solute radius. Thus, in real systems where the degree of disorder is lower at higher density and vice versa, the effect due to density and disorder have opposing influences. These are confirmed by the changes seen in the velocity autocorrelation function, self part of the intermediate scattering function and activation energy. In Chapter 8 we report a molecular dynamics study of the dependence of diffusivity of the cation on cation radii in molten superionic salt containing iodine ion. In this study, we have employed modified Parinello-Rahman-Vashistha interionic pair potential proposed by Shimojo et al (F. Shimojo and M. Kobayashi, J. Phys. Soc. Jpn 60, 3725 (1991)). Our results suggest that the diffusivity of the cation exhibits an increase followed by a decrease as the ionic radius is increased. Several other properties like velocity auto correlation function, intermediate scattering function, activation energy are reported. The next two chapters deal with diffusion of hydrocarbon isomers containing aromatic moiety. Chapter 9 reports structure, energetics and dynamic properties of the three isomers of trimethyl benzene in β-zeolite. Monte Carlo and molecular dynamics simulations have been performed at 300K. Of the three isomers, it is observed that 1,2,4-trimethyl benzene(124 TMB) shows fast dynamics inside the channels of β-zeolite. It is seen that both translational and rotational diffusivities are in the order D (124 TMB) > D (123 TMB) > D (135 TMB). 124 TMB seems to perform jumps between perpendicular channels more frequently whereas 123 and 135 isomers experience more hindrance to these jumps. It is also shown that there is a lower energetic barrier for 124 TMB across the window that separates two perpendicular channels in β-zeolite. Reorientational correlation functions suggest that reorientation of C6 axis (axis perpendicular to the plane of the phenyl ring) is highly restricted in case of 135 TMB. Reorientation of C2 axis (axis on the plane of the phenyl ring) seems to be more facile than that of C6 axis in case of both 123 TMB and 135 TMB. And interestingly, C6 and C2 axis reorientations are equally facile in case of 124 TMB. Chapter 10 presents molecular dynamics simulation results carried out on an equimolar binary mixture of cumene (isopropyl benzene) and pseudo-cumene (1,2,4-trimethyl benzene) in zeolite-NaY at four different temperatures. We compare different structural, energetic and dynamic properties of cumene and pseudo-cumene in zeolite-NaY. Our results suggest that both translational and rotational diffusivities are higher for cumene as compared to pseudo-cumene. Potential energy landscapes show that there is an energetic barrier for diffusion past the 12 MR window plane that separates two neighboring super cages. Such an energetic barrier is large for pseudo-cumene (3 kJ/mol) as compared to that of cumene (1.5 kJ/mol). Activation energies corresponding to both translational and rotational diffusion suggest that pseudo-cumene encounters larger energetic barriers for both translation and rotation as compared to cumene. Reorientational correlation functions suggest that reorientation of C2 axis is more facile than that of C6 axis in case of both cumene and pseudo-cumene. Activation energies corresponding to reorientational relaxations suggest that C6 axis encounters larger energetic barriers as compared to C2 axis in case of both cumene and pseudo-cumene. Chapter 11 discusses the main conclusions of the thesis and directions for future work.

Diffusion is a fundamental process which plays a crucial role in many processes occurring in nature. It is governed by the Fickian laws of diffusion. The laws of diffusion explain how diffusive flux is related to the concentration gradient. However, diffusion occurs even when there is no concentration gradient. Chapter 1 introduces diffusion and related concepts such as random walk, Brownian motion, etc. Present understanding with relation to ionic conduction and diffusion in polar solvents and the anomalies observed in the variation of ionic conductivity with ionic radii has also been discussed. Walden’s rule states that the product of limiting ionic conductivity and viscosity is constant for a given ion in different solvents and it is inversely proportional to ionic radius in a given solvent. However, experimental observations indicate that in a given solvent limiting ionic conductivities show an increase followed by a decrease with increase in ionic radii. This is often referred to as the breakdown of Walden’s rule. Several theories have been proposed in the past to explain the breakdown in Waldens rule. Solvent-berg model, continuum based theories and microscopic theories are some of theories that have been proposed. These theories are discussed briefly. The limitations in these theories are also outlined. There are several computer simulation investigations of ions in water and these are discussed. Also described is diffusion of hydrocarbons in zeolites. Various interesting observations such as window effect, nest effect, single file diffusion and the levitation effect are discussed. In Chapter 2, we have analysed the experimental ionic conductivity data as a function of the ionic radius for monovalent cations and anions in aqueous solution. Molecular dynamics simulations on LiCl and CsCl dissolved in water are also reported. The results suggest that the activation energy is responsible for the anomalous dependence of ionic conductivity on ionic radii. It is seen that ions with high conductivity posses low activation energy. The reason for the variation of activation energy with ionic radii are explained in terms of Derouane’s mutual cancellation of forces or levitation effect. This provides an alternative to the existing theories. Experimental limiting ionic conductivity, λ0 of different alkali ions in water shows markedly different dependences on pressure. Existing theories such as that of Hubbard-Onsager are unable to explain this dependence on pressure of the ionic conductivity for all ions. Experimental ionic conductivity data shows that smaller ions such as Li+ exhibit a monotonic increase in λ0 with pressure. Intermediate sized ions such as K+ exhibit an increase in λ0 followed by a decrease at still higher pressures. Larger ions such as Cs+ exhibit a monotonic decrease in λ0 with increase in pressure. In the present thesis, we have explored this intriguing behaviour shown by alkali ions in water in the next few chapters. In Chapter 3, we report molecular dynamics investigation of potassium chloride solution (KCl) at low dilution in water at several pressures between 1 bar and 2 kbar. Two different potential models have been employed. One of the models successfully reproduces the experimentally observed trend in ionic conductivity of K+ ion in water over 0.001-2 kbar range at 298K. We also propose a theoretical explanation, albeit at a qualitative level, to account for the dependence of ionic conductivity on pressure in terms of the previously studied Levitation Effect. A number of properties of the solvent in the hydration shell are also reported. In Chapter 4, residence times of water in the solute and water hydration shell are reported for KCl in water as a function of pressure. Two different approaches – Impey, McDonald and Madden’s approach as well as the recently proposed stable state picture (SSP) of Laage and Hynes yield somewhat different values for the residence times. The latter suggests that the hydration shell is more labile. As pressure is varied, the analysis suggests drastic changes in the hydration shell around water and little or no change in the hydration shell of the ions at higher pressures. The residence times τIMM as well as τSSP show a decrease with increase in pressure upto 1.5 kbar and a small increase beyond this pressure. This correlates with the dependence of the ionic conductivity of potassium ion on pressure. Similar correlation is also seen for chloride ion between ionic conductivity and residence time in hydration shell. However, no such correlation is seen in the case of water. We also report variation of residence time as a function of t∗, the minimum time that a water has to leave the hydration shell to be excluded from it. In Chapter 5, a molecular dynamics study of LiCl dissolved in water is reported at several pressures between 1 bar and 4 kbars at 240K. Structural properties such as radial distribution function, distribution of the angle between ion-oxygen and dipole vector of water in the hydration shell, angle between ion-oxygen and OH vector, oxygen-ion oxygen angle for water in the hydration shell, mean residence times by two different approaches are reported. Self-diffusivity of both Li+ and Cl− exhibit an increase with pressure in agreement with the experimentally observed trend. We also report the velocity autocorrelation function as a function of pressure. We show that the changes in these can be understood in terms of the levitation effect. For the first time we report the self part of the intermediate scattering function, Fs(k, t), at different pressures. These show for Li+ at small wavenumber k, a bi-exponential decay with time at low pressures. At higher pressures when the ionic conductivity is high, Fs(k, t) exhibits a single exponential decay. We also report wavenumber dependence of the ratio of the full width at half maximum to 2Dk2. These changes in these properties can be accounted for in terms of the levitation effect. The changes in the void structure of water with pressure plays a crucial role in the changes in ionic conductivity of both the ions. In Chapter 6, a detailed molecular dynamics study of self-diffusivity of model ions in water is presented as a function of pressure. First, we have obtained the dependence of self-diffusivity on ionic radius for both cations and anions by varying the radius of the ion, rion. Self-diffusivity exhibits an increase with ionic radius when rion is small and reaches a maximum at some intermediate value, before decreasing with increase in rion for rion > . The velocity autocorrelation function for different sizes of cations as well as anions suggest that the ion with maximum self-diffusivity has facile motion with little back scattering. These trends can be understood in terms of the levitation effect which relates the dependence of self-diffusivity on ionic radius to the bottleneck radius of the pore network provided by the solvent or water. The ratio ζ, defined as the full width at half maximum of the self part of the dynamic structure factor at wavenumber k to its value (2Dk2) at k = 0 is seen to increase with k for ions far away from the diffusivity maximum while a decrease with k is observed for ions closer to the diffusivity maximum. Calculations have also been carried out at pressures of 0.001, 2 and 4 kbars to obtain the variation of ionic conductivity with pressure for model ions of several different sizes. It is shown that for small ions (rion < ), self-diffusivity increases with pressure or exhibits an increase followed by a decrease. In contrast, we show that whenever ionic radius is large, (rion > ), a decrease in self-diffusivity with increase in pressure is seen. We suggest that there is a relation between the dependence of self-diffusivity on ionic radius and its dependence on pressure. The nature of this relationship arises through the levitation effect. Increase in pressure leads to decrease in the bottleneck radius, thus increasing the levitation parameter. For small ions (rion < ), this will lead to increase in diffusivity whereas for large ions (rion > ) this will lead to decrease in diffusivity. For small ions (rion < ), the increase in pressure leads to lowered back scattering in the velocity autocorrelation function. In contrast to this, for large ions (rion ≥ ), any increase in pressure leads to increase in back scattering in the velocity autocorrelation function. For the 1.7 °A anion, the ratio ζ is seen to exhibit a minimum at intermediate k and increase with k at large k for 0.001 kbar pressure. This changes to a less pronounced minimum at 2 kbars and by 4 kbars to a nearly monotonically decreasing function of k. These changes suggest, in agreement with the predictions of the levitation effect, the approach of the bottleneck radius to values similar to that of the ionic radius of 1.7 °A on increasing pressure to 4 kbars. Thus, this work offers an unification in our understanding of the dependence of ionic conductivity on ionic radius and pressure. It is seen that when the ionic radius is varied the numerator of the expression for levitation parameter is varied whereas by varying the pressure, the denominator is varied. The variation of diffusivity with density of the host medium and degree of disorder of the host medium is explored in Chapter 7. The system consists of a binary mixture of a relatively smaller sized solute (whose size is varied) and a larger sized solvent interacting via Lennard-Jones potential. Calculations have been performed at three different reduced densities of 0.7, 0.8 and 0.933. These simulations show that diffusivity exhibits a maximum for some intermediate size of the solute when the solute diameter is varied. The maximum is found at the same size of the solute at all densities which is at variance with the prediction of the levitation effect. In order to understand this anomaly, we have carried out additional simulations in which we have varied the degree of disorder at constant density and find that the diffusivity maximum gradually disappears with increase in disorder. We have also carried out simulations in which we have kept the degree of disorder constant but changed only the density. We find that the maximum in diffusivity is now seen to shift to larger distances with decrease in density. In these simulations we have characterized the disorder by constructing the minimal spanning tree. These results are in excellent agreement with the predictions of the levitation effect. They suggest that the effect of disorder is to shift the maximum in diffusivity towards smaller solute radius while that of the decrease in density is to shift it towards larger solute radius. Thus, in real systems where the degree of disorder is lower at higher density and vice versa, the effect due to density and disorder have opposing influences. These are confirmed by the changes seen in the velocity autocorrelation function, self part of the intermediate scattering function and activation energy. In Chapter 8 we report a molecular dynamics study of the dependence of diffusivity of the cation on cation radii in molten superionic salt containing iodine ion. In this study, we have employed modified Parinello-Rahman-Vashistha interionic pair potential proposed by Shimojo et al (F. Shimojo and M. Kobayashi, J. Phys. Soc. Jpn 60, 3725 (1991)). Our results suggest that the diffusivity of the cation exhibits an increase followed by a decrease as the ionic radius is increased. Several other properties like velocity auto correlation function, intermediate scattering function, activation energy are reported. The next two chapters deal with diffusion of hydrocarbon isomers containing aromatic moiety. Chapter 9 reports structure, energetics and dynamic properties of the three isomers of trimethyl benzene in β-zeolite. Monte Carlo and molecular dynamics simulations have been performed at 300K. Of the three isomers, it is observed that 1,2,4-trimethyl benzene(124 TMB) shows fast dynamics inside the channels of β-zeolite. It is seen that both translational and rotational diffusivities are in the order D (124 TMB) > D (123 TMB) > D (135 TMB). 124 TMB seems to perform jumps between perpendicular channels more frequently whereas 123 and 135 isomers experience more hindrance to these jumps. It is also shown that there is a lower energetic barrier for 124 TMB across the window that separates two perpendicular channels in β-zeolite. Reorientational correlation functions suggest that reorientation of C6 axis (axis perpendicular to the plane of the phenyl ring) is highly restricted in case of 135 TMB. Reorientation of C2 axis (axis on the plane of the phenyl ring) seems to be more facile than that of C6 axis in case of both 123 TMB and 135 TMB. And interestingly, C6 and C2 axis reorientations are equally facile in case of 124 TMB. Chapter 10 presents molecular dynamics simulation results carried out on an equimolar binary mixture of cumene (isopropyl benzene) and pseudo-cumene (1,2,4-trimethyl benzene) in zeolite-NaY at four different temperatures. We compare different structural, energetic and dynamic properties of cumene and pseudo-cumene in zeolite-NaY. Our results suggest that both translational and rotational diffusivities are higher for cumene as compared to pseudo-cumene. Potential energy landscapes show that there is an energetic barrier for diffusion past the 12 MR window plane that separates two neighboring super cages. Such an energetic barrier is large for pseudo-cumene (3 kJ/mol) as compared to that of cumene (1.5 kJ/mol). Activation energies corresponding to both translational and rotational diffusion suggest that pseudo-cumene encounters larger energetic barriers for both translation and rotation as compared to cumene. Reorientational correlation functions suggest that reorientation of C2 axis is more facile than that of C6 axis in case of both cumene and pseudo-cumene. Activation energies corresponding to reorientational relaxations suggest that C6 axis encounters larger energetic barriers as compared to C2 axis in case of both cumene and pseudo-cumene. Chapter 11 discusses the main conclusions of the thesis and directions for future work.