The two most common computational methodologies for estimating free energy differences (Free Energy Perturbation, FEP and Thermodynamic Integration, Tl) have been used to study the conformational preference of a cyclodextrinic catenane. A strategy based on the use of several FEP simulations and an averaging of the results has been shown as the best approach for properly evaluating the conformational ΔG in this large and flexible system. The stereoisomer (conformer) where the (2,6-di-0-methyl)-j3-cyclodextrin is over the bitolyl station is shown to be preferred by about 1 kcal/mol, in agreement with the experimentally available data. © 2006 American Scientific Publishers.
|Journal||Journal of Computational and Theoretical Nanoscience|
|Publication status||Published - 1 Jan 2006|
- Free energy perturbation
- Molecular dynamics