Dynamic and rotational analysis of cryptophane host-guest systems: Challenges of describing molecular recognition

Cryptophanes are aromatic hosts which bind a variety of guests. Here, we describe three 25 ns molecular dynamics simulations of a particular cryptophane in water. Simulations have been conducted on the uncomplexed cryptophane, the cryptophane-tetramethylammonium ion (TMA(+)) complex, and the cryptophane-neopentane (NEO) complex. TMA(+) and NEO are both tetrahedral species and are nearly isomorphic. In the current study, we examine how the presence of these guests influences motions of the host. Also examined are the preferred orientations and the motions of the guests relative to the cryptophane. This study demonstrates some of the many challenges of describing molecular recognition.