Molecular Mechanics

Molecular mechanics (MM) rests on a view of molecules as balls held together by springs, ignoring electrons. The potential energy of a molecule can be written as the sum of terms involving (at least) bond, stretching, angle bending, dihedral angles, and nonbonded interactions. Giving these terms explicit mathematical forms constitutes devising a forcefield, and giving actual numbers to the constants in it constitutes parameterizing the forcefield. Calculations on large biomolecules are a very important application of MM, and the pharmaceutical industry designs new drugs with the aid of MM. Organic synthesis now makes use of MM, which enables chemists to estimate which products are likely to be favored in a reaction and to devise realistic routes to a target molecule. In molecular dynamics (MD), MM is often used to generate the forces acting on molecules and hence to calculate their motions.