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Standard molecular mechanics can describe only motions that leave bonding unchanged

Molecular mechanics (MM) describes molecular shape and behavior using potential energy functions adjusted to fit the properties of known molecules. MM methods lump nuclei and electrons into points representing atoms and operate on molecular descriptions with explicit, pre-defined bonds. Each MM system defines a potential energy function for a class of molecules, calculated as a sum of two-, three-, and four-atom terms, with each term containing geometric variables and atom-type based parameters. The functional form of these terms depends on the pattern of bonds among the atoms. Because the bonds are predefined and unchanging, MM methods cannot give realistic descriptions of molecular motions that make, break, or rearrange bonds.

Other, less standard approaches resemble molecular mechanics in using an empirical, non-quantum-mechanical potential function, but have functional forms that describe changes in bonding within special classes of structures. An example is the Brenner potential for hydrocarbons (in first- and second-generation [pdf] versions).

How can computational modeling describe general changes in bonding?

Previous  Quantum chemistry can describe motions, including changes in bonding

How does molecular mechanics describe molecules?

The NIH Guide to Molecular Modeling: Molecular Mechanics