Synthetic adenine receptors: Direct calculation of binding affinity and entropy

A novel method fur calculating binding free energies is applied to a series of water-soluble adenine receptors that have been characterized experimentally. The calculations use a predominant states method, "Mining Minima", to identify and account for the low-energy conformations of the free and bound species. The CHARMM force field is used to estimate potential energies, and an adjusted form of the generalized Born/ surface area model is used to estimate solvation energies as a function of conformation. The computed binding free energies agree with experiment to within 2.9 kJ/mol(0.7 kcal/mol) and reproduce observed trends across the series of receptors. Preorganization of two rotatable bonds enhances the calculated affinity of one receplor/ adenine complex by -2.5 kJ/mol (-0.6 kcal/mol), and the change in translational/rotational entropy (-T Delta S-trans/rot(degrees)) is 30 kJ/mol (7 kcal/mol). The concept of the translational/rotational entropy change upon binding in the present model is compared with others previously presented in the literature.