
Molecular Mechanics


Molecular mechanics is the description of molecular structure by Nowtonian mechanics. Molecular mechanics is mainly used to conver 1D or 2D representation of molecules into 3D structures, study the internal degrees of fredom of molecules, molecular movement and molecular interaction. The figure at the bottom displays the terms included in a forcefield. These are stretch, bend, torsion and nonbonded interactions. Last mentioned consists of two terms, a van der Waal and an electrostatic term. The summ of all these terms gives the conformational energy of the molecule studied. This energy is meaningless on its own, but the relative energy difference between two molecules is a good approximation for the enthalpy difference.
When a molecule structure is converted from 2D to 3D, an equation is obtained by applying the force field to the molecule. This equation is solved by finding the closest minima. This is called a minimisation. General mathematical algorithms like newtonrapson and steepest descendare used for solving (minimising) the force field equation.


In this example a 2D molecular structure of CP99994 (a selective NK1 antagonist from Pfizer) was minimised using TNCG and the MMFFs94 force field. It took 40 steps before the minimisation converged. The force field equation consisted of 16 stretch terms, 25 bend terms, 60 torsion terms and 64 nonbonded terms.
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