What is Molecular Modeling?
Molecular modeling, also known as molecular mechanics, is a method to calculate the structure and energy of molecules based on nuclear motions. Electrons are not considered explicitly, but rather it is assumed that they will find their optimum distribution once the positions of the nuclei are known. This assumption is based on the Born-Oppenheimer approximation of the Schrödinger equation. The Born-Oppenheimer approximation states that nuclei are much heavier and move much more slowly than electrons. Thus, nuclear motions, vibrations and rotations can be studied separately from electrons; the electrons are assumed to move fast enough to adjust to any movement of the nuclei. In a very crude sense molecular modeling treats a molecule as a collection of wieghts connected with springs, where the weights represent the nuclei and the springs represent the bonds. A force field is used to calculate the energy and geometry of a molecule. It is a collection of atom types (to define the atoms in
