Fundamental computational studies towards advancement of alternative fuel applications

Abstract

Ensuring the wide-spread use of alternative fuels such as biodiesels and cellulosic biofuels is a crucial step towards attaining our ultimate goal of sustainable development. However, a number of issues plague the application of alternative fuels, such as their biological instability, production inefficiencies, storage and handling problems. On the bright side, the increasing affordability of high performance computational hardware and software has made scientific computing an important tool to understand systems from a molecular perspective. This thesis utilizes computational approaches to gain a fundamental understanding of specific problems in the aforementioned hurdles that affect alternative fuel applications. Hydrocarbon biodegradation is an increasing cause of concern to the navy and petroleum industries since it causes bio-corrosion. The free radical nature of the fumarate addition reaction has challenged experimental efforts to understand the enzymatic machinery that drives biodegradation. We utilize multiple computational approaches to provide insight into the structural basis as well as compare the susceptibility of aromatic and n-alkyl hydrocarbon fuels to biodegradation. Ionic liquids (ILs) have been the latest development in the effort to better utilize cellulosic feed-stocks for production of bio-fuels and value added chemicals. Interactions between ionic liquid components and the functional groups of cellulose has been a key enabling factor in the dissolution and conversion of poly and oligosaccharides to value-added platform chemicals. We employ atomistic simulations to characterize these interactions at the molecular level and evaluate their impact on the conformational orientation of glucose and cellobiose in ILs. The widespread utilization of biodiesel as an alternative lubricant and transportation fuel has been limited by its associated storage and handling issues. We lay the foundations to characterize the aggregation events of component fatty acid methyl esters that lead to these issues, by demonstrating the applicability of a charge modified generalized amber force field to accurately estimate their physical properties and provide insights into their molecular-level ordering. The fundamental insights gained from this body of research are crucial for an enhanced understanding of, and the development of solutions, to overcome the obstacles that hinder the wide-spread application of alternative fuels.