Paper Citing NAMD - Abstract
Rodriguez, Javier; Semino, Rocio; Laria, Daniel
Building up Nanotubes: Docking of "Janus" Cyclodextrins in Solution
JOURNAL OF PHYSICAL CHEMISTRY B, 113:1241-1244, FEB 5 2009
Using molecular dynamics experiments, we analyze the association of "Janus" 6-amino-6-deoxy-2O-carboxymethyl-beta-cyclodextrins (JCD) in aqueous solutions. In JCD dimers, the free energy associated with the primary-rim-secondary-rim docking shows a stable minimum of similar to-45 kcal mol(-1). Trimers in solution are also remarkably stable, exhibiting minimal distortions in their spatial and orientational distributions. The resulting geometrical docking shows the incipient characteristics of flexible nanotubes in solution, with eventual water interchange between the central channel and the bulk at the junctions between monomers. Structural and dynamical properties of the trapped water filling the nanotube are dictated to a large exent by the charge density at the rims.
