BINDING FREE ENERGIES & EXTRACTION SELECTIVITY CALCULATIONS

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In our research project free energy perturbation molecular dynamics simulations as implemented in AMBER 4.1 and AMBER 5.0 packages are used 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 are performed both in water and chloroform. Molecular graphics is used to prepare the input structure as well as to evaluate the processes invoved in cation binding. It is very 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. Molecular graphcs is a necessary tool to correctly position the guests into the host cavity.