Paper Citing NAMD - Abstract
Liu, Peng; Chipot, Christophe; Cai, Wensheng; Shao, Xueguang
Unveiling the Underlying Mechanism for Compression and Decompression Strokes of a Molecular Engine
JOURNAL OF PHYSICAL CHEMISTRY C, 118:12562-12567, JUN 12 2014
Manufacturing at the molecular level engines to power nanocars represents a challenge in the development of nanomachines. A molecular engine formed of beta-cyclodextrin (beta-CD), aryl, and amide moiety has been studied by means of molecular dynamics simulations combined with free-energy calculations. The compression and decompression strokes involving the binding processes of the (Z)- and (E)-isomers of this engine with 1-adamantanol (AD) have been elucidated by determining the underlying potentials of mean force (PMFs). The difference in the binding-free energies, considered as the work generated by and stored within this engine, is calculated to be +1.5 kcal/mol, in remarkable agreement with the experimentally measured quantity. Partitioning the PMFs into physically meaningful free-energy components suggests that the two binding processes are primarily controlled by the favorable inclusion of AD by the beta-CD. The work generated by the engine is harnessed to push the alkyl moiety from the hydrophobic cavity of the CD to water, to modify a dihedral angle by a twisting motion about the C-C alpha bond, and to increase the tilt angle between the mean plane of the sugar unit, which connects the amide moiety, and the mean plane CD. By deciphering the intricate mechanism whereby the present molecular engine operates, our understanding of how similar nanomachines work is expected to be improved significantly, helping in turn the design of novel, more effective ones.
