Molecular modelling

Density functional theory (DFT)

Water on quartz.
The minimum energy structure of a water molecule (red represents the oxygen atom, with white to represent the hydrogen atoms) on a the surface of a quartz cyrstal (yellow represents silicon, red oxygen and white, hydrogen).

Information obtained

  • Most stable structure in solids and for fluids in contact with them
  • Adsorption energies and geometries
  • Bonding character
  • Structural stability

Principle

DFT solves the Schrödinger’s equation to obtain the ground state wavefunction of the system of interest. From this, electron density distribution of the system can be obtained, from which other properties can be derived.

COSMO-RS — one approach to DFT predictions in solution

 

COSMO surfaces for water and phenol.
Example COSMO surfaces for water (left) and phenol (right) . The colours on the COSMO surface represent the screening charge density, which reflects the electron distribution in the molecule. Blue and red areas represent regions with high polarity whereas green areas represent nonpolar regions of the molecules.

Information obtained

  • Solvation energies
  • Partition coefficients
  • Liquid-liquid interfacial tension
  • pKa of acid and bases

Principle

COSMO-RS combines the COSMO implicit solvent model and statistical thermodynamics. It can describe important interactions in a solvent, such as electrostatics, dispersion and hydrogen bonding. [1]

Classical molecular dynamics (MD)

MD snapshot of aspartic acid on calcite.
A snapshot from an MD simulation of polyaspartic acid and a calcite (318) surface. The aspartic acid interacts through its charged and polar groups with the calcite calcium and carbonate ions. Hydrogen atoms are depicted in white, carbon atoms in cyan, nitrogen atoms in blue, oxygen atoms in red and calcium atoms in brown.
Calcite 104 with a mixture of ethanol and water. The figures below shows the separated distributions of ethanol and water.
Calcite {10.4} with a mixture of ethanol and water (top). In the figures below, the water and ethanol have been separated to show their distribution above the calcite slab Ethanol has a higher affinity for the calcite surface than water and it also is more stable at the interface between the fluid and the vacuum.[2]

Information obtained

  • Time evolution of a system
  • Local structural properties of materials and how fluids interact
  • Conformational sampling
  • Surface diffusion

Principle

Classical MD is a computational technique that follows the time evolution of a set of N-interacting atoms by integrating the equations of motion from classical mechanics. MD is a statistical mechanics method. It is a way to obtain a statistical ensemble with a set of configurations from which one can obtain average properties.

References

  1. A. Klamt, F. Eckert, W. Arlt, in Annual Review of Chemical and Biomolecular Engineering, Vol 1. (2010), vol. 1, pp. 101-122.
  2. K.S. Keller, M.H.M. Olsson, M. Yang, S.L.S. Stipp in Langmuir (2015), vol. Y, pp. XX-XX.