Date of Award


Degree Type


Degree Name

Master of Science (MS)




Computer simulations using molecular dynamics (MD) on classical molecular mechanical

(MM) interatomic potentials can provide valuable information and quantitative

predictions about these systems. In MD calculations binding free energies of ions to

host molecules can be studied if correct ion solvation free energies in aqueous solution

are obtained. However, no MM models exist that parametrize various Zn2+ and

transition metals consistently and consider both structural and thermodynamic data


The first part of our work focused on MD free energy perturbation (FEP) simulations

to derive MM interaction parameters for Zn2+ and Mg2+ ions in aqueous

solution. To obtain these parameters the absolute solvation free energies were calibrated

against the experimentally determined solvation free energies, using the TIP3P

water model, which is integrated in the Q-package from Aqvist. In addition to the

traditional single charge (SC) model a distributed charge model (DC) was developed

and tested to study the impact of charged ghost atoms on the solvation free

energy. Furthermore, the structural properties of the system were taken into consideration

to obtain a parameter set that reproduces both the experimentally observed

solvation free energies and the structure of the rst solvation shell. The results for

Zn2+ in aqueous solution showed that solvation free energies and metal-oxygen radial

distribution functions in aqueous solution are not coinciding with the experimentally

observed data simultanously. The developed distributed charge (DC) model increased

the solvation free energies substantially for various charge distributions compared to

the traditional single charge (SC) model. However, the radial distribution functions

were altered as well when performing molecular dynamics simulations with the DC

model. As far as the simulation of the solvent is concerned, the continuum Born

model overestimates the solvation free energy for realistic Zn2+ ionic radii whereas the explicit model underestimates solvation energies for realistic Zn2+-O distances.

During the second part of this work a Metal Center Parameter Analyzer (MCPA)

code was developed in python to automate gas-phase simulations for the ZnF2(H2O)3

complex for a given range of force eld parameter values. In particular, a random

number generator has been integrated in our MCPA code. The results that were

found with this MCPA code revealed that there are particular force field parameters

sets which produce Zn-O and Zn-F mean distances that coincide with the distances

obtained from ab initio calculations for some DC models. Our extensive numerical

data will guide the design of the next-generation of the DC models of metal ions.

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Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License.