(593g) Free Energy Landscape of Alkanes Confined within Supramolecular Complexes

Complex biological containers such as molecular chaperones aid in the non-covalent folding of proteins, confining them in their interiors thereby modifying the free energy landscapes of such proteins. Deep cavity cavitands, such as, octa-acid (OA) are host molecules that possesses a water-soluble outer coat and a deep hydrophobic pocket suitable for binding a range of non-polar guests in aqueous solution. Via the hydrophobic effect, OA readily assembles into dimeric capsules in the presence of suitably sized guests, forming 2:1 host−guest complexes. In difference to complex biological containers, the simplicity of OA provides an excellent test bed for studying both the forces associated with guest packing as well as the guest conformational motifs under molecular confinement that are not typically observed for unbound species. Alkane encapsulation experiments within dimeric OA capsules in water reveal a succession of packing motifs from extended, to helical, to hairpin, to spinning top structures with increasing chain length. Understanding of the interactions between the cavitand host and guest species in aqueous solution is required to understand the transition from one motif to another. Here we present a systematic molecular simulation study of n-alkane encapsulation in dimeric OA in vacuum and water to uncover the details and mechanics of host-induced conformational changes of the n-alkanes. Potentials of mean force determined via umbrella sampling from Replica Exchange Molecular Dynamics simulation between the end-to-end methyl groups of encapsulated n-alkanes are used to characterize the free energy landscape of each observed motif. Our results show that dihedral angle redistribution coupled with entropic and enthalpic changes influence conformational changes observed in encapsulated alkanes.