Investigation of solvent-mediated host-guest interactions and conformational changes in N-alkanes trapped under hydrophobic confinement

In numerous biological processes, biomolecules utilize their ability to recognize specific molecules through non-covalent interactions and bind with them using a "lock and key" mechanism. These processes involve a broad range of host receptor sites differing in their molecular architecture, which plays vital role in binding specific guests and inducing conformational changes in them. Inspired by the makeup of biological receptors, a large number of biomimetic hosts are artificially synthesized, which provides an excellent source to probe the molecular recognition process of such varying shaped host cavities.;In this dissertation, molecular simulation results of solvent-mediated interactions between three different shaped biomimetic hosts and a variety of non-polar guests are described. Initially, we analyze the association of a concave octaacid cavitand host with adamantane and a series of Lennard Jones guests in water. The strength of host-guest binding calculated by estimating the potential-of-mean force (PMF) indicate that adamantane is one of the best guests that can bind to the octaacid. The PMFs are mainly dominated by direct guest/octaacid interactions and are weakly opposed by indirect water-mediated forces. These simulations stand in difference to the standard interpretation of hydrophobic effect, which theorize the aggregation of non-polar species in water to be driven by their mutual insolubility.;Next, we investigate the confinement effect of a narrow cylindrical carbon nanotube (CNT) on the encapsulation and conformations of n-alkanes. Although alkanes in bulk water mainly adopt trans dominated extended form, the CNT confined alkanes undergo a significant trans to gauche conformational redistribution. The PMF between hexane and CNT demonstrates that hexane adsorption within CNT is favorable in water, but almost neutral in benzene. The association is weakly opposed by water-mediated forces and strongly opposed by benzene-mediated forces.;Finally, conformational changes and interactions of n-alkanes with a flat hydrophobic graphite surface are estimated to figure out the role of host curvature in the host-guest association process. We observe that while cylindrical curvature of CNT converts the n-alkanes into a gauche dominated helical structure, the flat surface of graphite change them into even more trans dominated extended form, than it can be observed in the bulk water.