Molecular modelling bond stretching energy

However, when it comes to reactions where bonds are being made and/or broken, it is clear that, at least for the vast majority of force fields that use polynomial expressions for the bond stretching energy, the normal model is inapplicable. Nevertheless, substantial application of molecular mechanics to such TS structures has been reported, with essentially three different approaches having been adopted. 

Molecular Mechanics Models. Methods for structure, conformation and strain energy calculation based on bond stretching, angle bending and torsional distortions, together with Non-Bonded Interactions, and parameterized to fit experimental data. 

The simple harmonic terms used to represent the energy of bond stretching in typical protein molecular mechanics force fields cannot model the making and breaking of chemical bonds. Also, molecular mechanics parameters are usually developed based on the properties of stable molecules, and so might not be applicable to transition states and intermediates. Molecular mechanics functions and parameters can be developed specifically for reactions, an approach that has been... 

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