Molecular Mechanics

From DrugPedia: A Wikipedia for Drug discovery

Revision as of 17:14, 8 August 2008

Molecular Mechanics or force-field methods use classical type models to predict the energy of a molecule as a function of its conformation. It is an empirical method of calculating the dynamics of molecules, in which bonds between atoms are represented by springs obeying Hooke's law, and additional terms representing bond angle bending, torsional interactions, and van der Waals-type interactions are included.

This allows predictions of:

• Equilibrium geometries and transition states
• Relative energies between conformers or between different molecules

Molecular mechanics can be used to supply the potential energy for molecular dynamics computations on large molecules. However, they are not appropriate for bond-breaking reactions.

Molecular mechanics methods are based on the following principles:

Nuclei and electrons are lumped into atom-like particles. Atom-like particles are spherical (radii obtained from measurements or theory) and have a net charge (obtained from theory). Interactions are based on springs and classical potentials. Interactions must be preassigned to specific sets of atoms. Interactions determine the spatial distribution of atom-like particles and their energies.

Functional Form

Schematic of targeted drug delivery

In its simplest representation, the molecular mechanics equation is

E = Es + Eb + Ew + Enb

where Es is the energy involved in the deformation of a bond, either by stretching or compression, Eb is the energy involved in angle bending, Ew is the torsional angle energy, and Enb is the energy involved in interactions between atoms that are not directly bonded.

Software Packages

• AMBER
• Ascalaph
• CHARMM
• Ghemical
• GROMOS
• GROMACS
• MDynaMix
• NAMD
• STR3DI32
• TINKER
• Zodiac