Molecular mechanics uses classical mechanics to model molecular systems. The potential energy of all systems in molecular mechanics is calculated using force fields. Molecular mechanics can be used to study small molecules as well as large biological systems or material assemblies with many thousands to millions of atoms.
All-atomistic molecular mechanics methods have the following properties:
- Each atom is simulated as a single 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)
- Bonded interactions are treated as "springs" with an equilibrium distance equal to the experimental or calculated bond length
Variations on this theme are possible; for example, many simulations have historically used a "united-atom" representation in which methyl and methylene groups were represented as a single particle, and large protein systems are commonly simulated using a "bead" model that assigns two to four particles per amino acid.
... "On the molecular-orbital theory of conjugated organic compounds with application to the perturbed benzene ring" ... problem, virial theorem, and connected relations in quantum mechanics" ... Journal of Molecular Spectroscopy 3 (1–6) 46–66 ...
... Molecular mechanics or force field was first introduced apparently independently by Hill and by Westheimer in 1949, primarily applied to organic chemistry ... however, there is no unique way of treating polarization in molecular mechanics because it is of quantum mechanical origin ... the properties derived from the dynamic dependence of the force field itself on molecular fluctuations ...
... SPARTAN is a molecular modeling and computational chemistry application from Wavefunction, Inc ... It contains code for molecular mechanics, semi-empirical methods, ab initio models, density functional models, post-Hartree-Fock models, and thermochemical recipes including T1 ... Molecular mechanics calculations and quantum chemical calculations play an ever-increasing role in modern chemistry ...
... Molecular mechanics is one aspect of molecular modelling, as it refers to the use of classical mechanics/Newtonian mechanics to describe the physical basis behind the models ... Molecular models typically describe atoms (nucleus and electrons collectively) as point charges with an associated mass ... of the system with propagation of time are known as molecular dynamics This function, referred to as a potential function, computes the molecular potential energy as a sum of energy terms that describe the ...
... Such effects are unaccounted in the standard molecular mechanics ... to avoid "a central embarrassment of molecular mechanics, namely that energy minimization or molecular dynamics generally leads to a model that is less like the experimental structure" ... There is also an opinion that molecular mechanics may operate with energy which is irrelevant to protein folding or ligand binding ...
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