Paper Citing NAMD - Abstract
Liu, Peng; Cai, Wensheng; Chipot, Christophe; Shao, Xueguang
Thermodynamic Insights into the Dynamic Switching of a Cyclodextrin in a Bistable Molecular Shuttle
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1:1776-1780, JUN 17 2010
A prototypical molecular shuttle formed by dedecamethylene and 4,4'-bipyridinium units and an alpha-cyclodextrin (CD) was investigated employing molecular dynamics simulation. The free-energy profile characterizing the shutting process of the alpha-CD along the molecular thread was determined using the adaptive biasing force method, revailed two thermodynamically stable states separated by a pronounced energy barrier. The free-energy barrier with respect to the stable states is calculated to be +20.6 kcal/mol, in excellent agreement with the experimentally measured quantity. Partitioning of the free energy into contributions of different nature indicates that the shuttling process is primarily controlled by the favable inclusion of the cationic bipyridinium group by alpha-CD. The predominant contributions to the energy barrier stems from the disruption of the solvation shell of the charged group. Deciphering the molecular mechanism of the shuttling process is expected to help design new controllable molecular shuttles.
