Paper Citing NAMD - Abstract
Rodriguez-Ropero, Francisco; Zanuy, David; Aleman, Carlos
Molecular dynamics of a calix[4]arene-containing polymer in dichloromethane solution: Ability of the solvent molecules to fill the cavity of the macrocycle
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1233-1241, JUN 2008
The structure and dynamics of the dichloromethane solvent around the calix[4]arene units contained in the molecular actuator poly(calix[4]arene bis-bithiophene) have been examined using a 1-mu s molecular dynamics simulation. Results indicate that a solvent molecule fills the cavity associated to the cone conformation of the macrocycle during a significant period of time, especially when the actuator is not contracted. The position of such solvent molecule presents a fourfold symmetry with a maximum orientation toward the center of each ring contained in the calix[4]arene. Frequently, the solvent molecule located inside the cavity is rapidly exchanged for another molecule of the bulk. Thus, the number of dichloromethane molecules that reside more than 0.5 ns inside the cavity is relatively small. Finally, we detected that a significant number of solvent molecules are able to migrate from the cavity of one calix[4]arene to the cavity/ies of other/s, suggesting that the dynamics of the bulk solvent is important for the formation of these inclusion complexes. (C) 2007 Wiley Periodicals, Inc.
