A study of solvation energy using molecular dynamics and density functional theory

Open Access
Author:
Cai, Yusheng
Area of Honors:
Chemical Engineering
Degree:
Bachelor of Science
Document Type:
Thesis
Thesis Supervisors:
  • Scott Thomas Milner, Thesis Supervisor
  • Wayne Roger Curtis, Honors Advisor
Keywords:
  • Molecular Dynamics
  • Density Functional Theory
  • Solvation energy
  • Thermodynamic integration
  • Gromacs
  • proton
  • water
Abstract:
Chemical reactions typically take place in solvents, which can interact with reacting species and products, thereby shifting the free energy of reaction. Quantum calculations using density functional theory (DFT) are widely used to compute reaction free energies, however the calculation can only be performed in vacuum or in continuum dielectrics. Thus, DFT cannot account for solvation effects with any molecular detail. We propose to improve upon the DFT results by adding the difference in solvation free energy of reactants and products. Molecular dynamics simulations can obtain the solvation free energies by computing the work to slowly turn on interactions between a solute and surrounding solvent. We apply this approach to study the preferred state of a proton dissolved in water. First, DFT calculations were performed to obtain reaction energies for the reaction H2O + H3O+ -> H5O2+. Next, molecular dynamics simulations were performed on three aqueous solutes: H2O, H3O+, H5O2+. The reaction energy from DFT and solvation energy from simulations can then be combined to give a better estimate of the free energy of the reaction H2O + H3O+ -> H5O2+.