In all states of matter, atoms and molecules are in motion. Molecular dynamics is the study of how these motions occur and how they can affect the physical and chemical properties of matter. The synthesis of polymeric materials from gaseous or liquid precursors can be described by how the molecular building blocks assemble themselves. Two adjacent atoms in a molecule may vibrate at a certain frequency, which can allow for the optical absorption of an infrared (IR) photon with an energy equal to the vibrational energy. These absorptions are associated with types of chemical bonds, helping to elucidate the chemical structure of the molecule.
Molecular dynamics can also describe bulk properties of materials, such as viscosity or diffusion coefficients. It can also be used to predict how chemical reactions occur, based on how atoms can move together and become bonded to each other.
Because of the complex nature of molecular motion, especially in large molecules such as proteins, simulations of simpler systems are often used to establish models. Starting from the simplest descriptions of the forces involved as two atoms approach each other in free space, and adding information about the electronic structure, a more complete picture of how a molecular structure forms can be created. Once these simpler models can be validated with experimental data, more complex structures can be simulated.