Flexible molecules

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Modelling of internal degrees of freedom, usual techniques:

Bond distances[edit]

Atoms linked by a chemical bond (stretching) using the harmonic spring approximation:

However, this internal coordinates are very often kept constrained (fixed bond distances)

Bond Angles[edit]

Bond sequence: 1-2-3:

Bond Angle:

Two typical forms are used to model the bending potential:

Dihedral angles. Internal Rotation[edit]

Bond sequence: 1-2-3-4 Dihedral angle () definition:

Consider the following vectors:

  • ; Unit vector in the direction of the 2-3 bond
  • ; normalized component of ortogonal to
  • ; normalized component of ortogonal to

For molecules with internal rotation degrees of freedom (e.g. n-alkanes), a torsional potential is usually modelled as:


Van der Waals intramolecular interactions[edit]

For pairs of atoms (or sites) which are separated by a certain number of chemical bonds:

Pair interactions similar to the typical intermolecular potentials are frequently used (e.g. Lennard-Jones potentials)