scholarly journals The Good, the Bad, and the Ugly: “HiPen”, a New Dataset for Validating (S)QM/MM Free Energy Simulations

Molecules ◽  
2019 ◽  
Vol 24 (4) ◽  
pp. 681 ◽  
Author(s):  
Fiona Kearns ◽  
Luke Warrensford ◽  
Stefan Boresch ◽  
H. Woodcock

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 Δ A l o w → h i g h , remains to be the most challenging step within an indirect FES protocol. To improve calculations of Δ 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 Δ 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 Δ 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 Δ A g a s M M → 3 o b by evaluating several convergence criteria including sample size hysteresis, overlap statistics, and bias metric ( Π ). Within the total dataset, three distinct categories of molecules emerge: the “good” molecules, for which we can obtain converged Δ A g a s M M → 3 o b using Jarzynski’s equation; “bad” molecules which require Crooks’ equation to obtain a converged Δ A g a s M M → 3 o b ; and “ugly” molecules for which we cannot obtain reliably converged Δ 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.

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Vytautas Gapsys ◽  
Ahmet Yildirim ◽  
Matteo Aldeghi ◽  
Yuriy Khalak ◽  
David van der Spoel ◽  
...  

AbstractThe accurate calculation of the binding free energy for arbitrary ligand–protein pairs is a considerable challenge in computer-aided drug discovery. Recently, it has been demonstrated that current state-of-the-art molecular dynamics (MD) based methods are capable of making highly accurate predictions. Conventional MD-based approaches rely on the first principles of statistical mechanics and assume equilibrium sampling of the phase space. In the current work we demonstrate that accurate absolute binding free energies (ABFE) can also be obtained via theoretically rigorous non-equilibrium approaches. Our investigation of ligands binding to bromodomains and T4 lysozyme reveals that both equilibrium and non-equilibrium approaches converge to the same results. The non-equilibrium approach achieves the same level of accuracy and convergence as an equilibrium free energy perturbation (FEP) method enhanced by Hamiltonian replica exchange. We also compare uni- and bi-directional non-equilibrium approaches and demonstrate that considering the work distributions from both forward and reverse directions provides substantial accuracy gains. In summary, non-equilibrium ABFE calculations are shown to yield reliable and well-converged estimates of protein–ligand binding affinity.


2019 ◽  
Author(s):  
Javad Noroozi ◽  
William Smith

We use molecular dynamics free energy simulations in conjunction with quantum chemical calculations of gas phase reaction free energy to predict alkanolamines pka values. <br>


1977 ◽  
Vol 55 (5) ◽  
pp. 792-797 ◽  
Author(s):  
Robert L. Benoit ◽  
Michael F. Wilson ◽  
Sing-Yeung Lam

The solvent effect on the iodide–triiodide equilibrium has been investigated by means of calorimetric and potentiometric measurements. The aprotic solvents studied were nitromethane, nitrobenzene, sulfolane, acetonitrile, propylene carbonate, acetophenone, dimethylformamide, dimethylsulfoxide, and o-dichlorobenzene. The resulting enthalpy and free energy changes imply that the variations of the enthalpies and free energies of transfer of the iodide and triiodide ions probably are small and that there is an important non-coulombic contribution to these transfer parameters. Values were obtained for the enthalpy of formation of two solid triiodides, which together with values for other triiodides, cast doubt on reported calculated lattice enthalpies of triiodides and formation enthalpy of I3− ion in the gas phase. This latter formation enthalpy is found to be, from our solution data, more negative than −22 kcal mol−1.


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