# Flexible molecules

Revision as of 16:32, 30 July 2007 by Carl McBride (talk | contribs)

Modelling of internal degrees of freedom, usual techniques:

## Contents

## 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:

or

## 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)