BINDING FREE ENERGIES & EXTRACTION SELECTIVITY CALCULATIONS

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In this research project we are using free energy perturbation molecular dynamics simulations as implemented in AMBER 4.1 and AMBER 5.0 packages to estimate host-guest relative binding free energies of three spherands (spherical organic molecules preorganized for binding) and alkali metal ions (Li+, Na+, K+). Results of this study may be used to improve our ability to predict free energies of binding, which may be useful for computer aided drug design. The simulations were performed both in water and chloroform. Access to molecular graphics at the Computer Graphics Laoratory is essential in this study. During the data preparation stage it is important to position the cation in the middle of the spherand cavity. In some cases we also tried to add various amounts of water into the cavity. Picrate anion interacting with the spherand was introduced to simulate experimental conditions. Proper positioning and docking of these guests into the host would be a very painful process without 3D graphical insight.