Molecules, Vol. 24, Pages 681: The Good, the Bad, and the Ugly: `HiPen`, a New Dataset for Validating (S)QM/MM Free Energy Simulations (Molecules)

Indirect (S)QM/MM free energy simulations (FES) are vital to efficiently incorporating sufficient sampling and accurate (QM) energetic evaluations when estimating free energies of practical/experimental interest. Connecting between levels of theory, i.e., calculating ? A l o w -> h i g h , remains to be the most challenging step within an indirect FES protocol. To improve calculations of ? A l o w -> h i g h , we must: (1) compare the performance of all FES methods currently available; and (2) compile and maintain datasets of ? A l o w -> h i g h calculated for a wide-variety of molecules so that future practitioners may replicate or improve upon the current state-of-the-art. Towards these two aims, we introduce a new dataset, `HiPen`, which tabulates ? A g a s M M -> 3 o b (the free energy associated with switching from an M M to an S C C - D F T B molecular description using the 3ob parameter set in gas phase), calculated for 22 drug-like small molecules. We compare the calculation of this value using free energy perturbation, Bennett`s acceptance ratio, Jarzynski`s equation, and Crooks` equation. We also predict the reliability of each calculated ? A g a s M M -> 3 o b by evaluating several convergence criteria including sample size hysteresis, overlap statistics, and bias metric ( ? ). Within the total dataset, three distinct categories of molecules emerge: the `good` molecules, for which we can obtain converged ? A g a s M M -> 3 o b using Jarzynski`s equation; `bad` molecules which require Crooks` equation to obtain a converged ? A g a s M M -> 3 o b ; and `ugly` molecules for which we cannot obtain reliably converged ? A g a s M M -> 3 o b with either Jarzynski`s or Crooks` equations. We discuss, in depth, results from several example molecules in each of these categories and describe how dihedral discrepancies between levels of theory cause convergence failures even for these gas phase free energy simulations.