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Molecular simulations are computer experiments that allow us to investigate thermodynamic and transport properties of complex chemical systems. Here, we have investigated self-assembly of organogelators and analysed the diffusion characteristics of small molecules in the nanopores of zeolites. Molecular gels are attractive soft-materials with viscoelastic properties with applications in drug delivery, tissue engineering, sensing, etc. Small organic amphiphilic gelators act as a building block of complex 3-dimensional network in molecular gels. Due to time and length scale differences, the understanding and characterization of early stage aggregation of gelators is difficult using experimental techniques. Classical and quantum mechanical approaches have been used to understand the self-assembly of gelator molecules and to rationalize the gelation. We have used density functional theory (DFT) to derive new quantity namely, pseudo-cohesive energy density to rationalize the gelation of di-Fmoc-L-lysine. Molecular dynamics is used to probe the self-assembly and conformation of gelators in DMSO-water. We have also studied the self-assembly of 12-hydroxyoctadecanamide in octane. We used DFT to calculate the dimer energy in the vacuum and meta-dynamics simulation to calculate potential of mean force in the condensed phase. Interestingly, we found that, dimer energetics was not sufficient to elucidate bulk aggregation behavior, such as, probability distribution of different dimers in aggregation. We also observed different types of branched and mesh-like networks in the aggregation, which are analogous to the network found through experimental imaging techniques. Zeolites are crystalline materials with well defined nanoporous channels and act as molecular sieves. They are attractive for catalytic applications due to their tunable Bronsted and Lewis acidity. A wide array of zeolite polymorph offers versatile micro and meso-porous channels to accommodate small molecules like glucose to big and complex lignocellulose molecules for undergoing chemical transformations. In this current study, we present the transport properties of -glucose into Faujisite zeolite framework. We have investigated the trajectory of the glucose molecule into porous material and found that, the diffusivity of glucose inside zeolite pore is two order of magnitude smaller than that of bulk solutions. We have also observed the variable loading rate of glucose molecule inside pore at different temperatures.

Biodiesel is one of the most widely used biofuels in the world, due in part to its simplicity of production, compatibility with existing engines, and reduction of green house gas emissions. However, technical difficulties with biodiesel include: (1) the need of highly refined oil for ASTM compliance, (2) incompatibility with the petroleum-diesel pipeline distribution system, and (3) a relatively small inventory of expensive feedstocks. Issues (1) and (2) could be overcome by the production of biofuels using chemical processes associated with petroleum refining. Catalytic lipid cracking could result in green diesel, a fuel chemically similar to conventional diesel but derived from a clean renewable feedstock. The impact of phosphorus poisoning on catalytic cracking of lipids has been studied in this work using both homogeneous and heterogeneous catalysts. Catalytic cracking of model lipids was shown to occur in a homogeneous liquid phase with triflic acid, a superacid 100 times more acidic than sulfuric acid. Products obtained from the reaction were heavily oxygenated and generally unsuitable for fuel use, suggesting the need for heterogeneous catalytic cracking. Reaction kinetics show a high linear dependence on Brönsted system acidity, with an overall reaction order of 3. The affect of phosphorus on heterogeneous acid cracking was then studied. Since lipid feedstocks contain small amounts of phospholipids knowledge of the interactions between phospholipids and zeolites is crucial to a system-wide understanding of the lipid cracking process. Phosphorus-containing compounds were used to poison ZSM-5 (a solid zeolite catalyst) in order to simulate the cracking of phospholipids. Model compounds were then cracked over the poisoned zeolite, with differences in product distribution and kinetics based on phosphorus loading recorded. It was shown that phosphorous has a dramatic effect on both conversion and product distribution of cracking reactions. It is believed that phosphorous binds irreversibly to heterogeneous active sites, causing the majority of deactivation. To address the issue of limited feedstock availability, research was also undertaken to find new lipids sources for biofuel use. It was determined that lipids extracted from microorganisms grown in a municipal wastewater treatment system could be suitable. However, any phosphorous must be removed before catalytic cracking of the extracted lipids.

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