Date of Award
Doctor of Philosophy (PhD)
The parameters of monovalent ions for the AMOEBA force field were revised. High level quantum mechanics results, relative solvation free energies of monovalent ions, lattice energies and lattice constants of salt crystals were used to calibrate the parameters. The revised parameters were validated against the quantum optimized structures and energies of ion-water dimers and ion-water clusters, and against thermodynamic properties of salt solutions at different concentrations measured in experiments, e.g. mean ionic activity coefficients, self-diffusion coefficients of water. In the simulations the sodium ion is found to qualitatively differ from larger cations in aqueous solution. Direct ionic interactions are predominant for potassium and larger cations, while sodium salt solutions at similar concentrations are dominated by ion-water interactions.
A novel stochastic isokinetic integrator proposed by Tuckerman, et al. was extended and generalized in three respects. First, the Nos-Hoover chain algorithm was implemented in the original integrator. Next, the functional form of the isokinetic constraint was generalized so that it was no longer restricted to multiples of kBT. Finally, the isokinetic constraint was extended to be able to constrain the kinetic energies of multi-dimensional velocities, instead of only one degree of freedom as in its original form.
An application of conformational sampling with molecular dynamics method, predictions of the binding free energies of cucurbituril and ligands in the SAMPL6 challenge, is presented. A great improvement in the prediction accuracy was made by more accurate torsional parameters of cucurbituril and by revised protocols annihilating the intra-molecular van der Waals and key torsions in the ligands.
Corresponding methods for all portions of this work have been implemented in the Tinker software package, some of which are also available in the Tinker-OpenMM library.
Chair and Committee
Jay W. Ponder
Gregory R. Bowman, Richard Mabbs, Garland R. Marshall, Lee G. Sobotka,
Wang, Zhi, "Polarizable Force Field Development, and Applications to Conformational Sampling and Free Energy Calculation" (2018). Arts & Sciences Electronic Theses and Dissertations. 1661.