Designing an Optimum Guest for a Host Using Multimolecule Free Energy Calculations:  Predicting the Best Ligand for Rebek's “Tennis Ball”

We have predicted that difluoromethane (CH 2 F 2 ) will be the highest-affinity guest for Rebek's “tennis ball” host 1 using a new approach to multimolecule free energy calculations. The method, which we call chemical-Monte Carlo/Molecular Dynamics (CMC/MD), was first tested by calculating the relative free energies of solvation of a variety of molecules. Subsequently, we have used it to compare nine possible guests binding to the “tennis ball” host and predict that CH 2 F 2 will bind more tightly to this host than CH 4, the strongest binding guest studied to date. This prediction has been supported by standard thermodynamic integration free energy calculations in which CH 4 was mutated into CH 2 F 2 both in solution and in the host. Our results show the full power of such multimolecule calculations namely, that they can be used to rapidly calculate and rank the relative binding free energies of many molecules from a single simulation, accelerating the discovery of novel ligands or guests.