Molecular Mechanics

Molecular mechanics is a method of calculating molecular structure and energy with the help of experience and semi-empirical parameters based on the theory of classical mechanics, also known as force field method. The basic idea of this method is to treat a molecule as a collection of atoms held together by elastic force. If these atoms are too close, they will be affected by the repulsive force; if they are far away, the chemical bonds connecting them will be stretched or compressed, the bond angle will be distorted, and the internal gravity of the molecule will increase. The structure of each real molecule is the result of the balance of the above-mentioned effects. [At present, it is widely used to calculate the conformation and energy of molecules. This method can be traced back to the work of M. Born and R. Oppenheimer (1927), P.M. Morse (1929), and D.H. Andrews (1930).


In molecules and aggregates, chemical bonds have "natural" bond length and bond angle values. When these conditions are met, the energy of the system and the interaction between internal atoms should meet certain extreme conditions. The molecule should adjust its geometric shape (conformation) so that its bond length and bond angle values are as close to the natural values as possible, while also minimizing non-bonding effects.

All-atomistic molecular mechanics methods have the following properties:

  • Each atom is simulated as one particle
  • Each particle is assigned a radius (typically the van der Waals radius), polarizability, and a constant net charge (generally derived from quantum calculations and/or experiment)


In some tensioned molecular systems, the tension of the molecules can be calculated. But it was not until 1946 that T.L.Hill proposed to use van derWaals action energy and bond length and bond angle deformation energy to calculate the energy of the molecule to optimize the spatial configuration of the molecule.


There are three molecular mechanics methods in Gaussian. They are used for ONIOM calculations, but they can also be used as independent methods. These methods do not need to specify basis set keywords, and the following force fields can be used:

  • Amber: Use the latest version of Amber from the Amber website (
  • UFF


  • The main use of molecular mechanics is in the field of molecular dynamics. This uses a force field to calculate the force acting on each particle, and a suitable integrator to model the dynamics of the particle and predict the trajectory.
  • Another application of molecular mechanics is energy minimization, where the force field is used as an optimization criterion. This method uses appropriate algorithms (such as steepest descent) to find the molecular structure with the smallest local energy.
  • Molecular mechanics potential energy functions have been used to calculate binding constants, protein folding kinetics, [9] proton balance, active site coordinates, and design binding sites.
* For Research Use Only.