Molecular Mechanics : Mathematical And Differentiable Potential Energy Function

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Computational Chemistry Molecular Mechanics uses an analytical and differentiable potential energy function, (R), for describing the interactions between a set of atoms specified by their Cartesian coordinates R. Unlike first principles of quantum mechanical calculations, molecular mechanics might be thought of as simply a fitting procedure, attempting to obtain as accurately as possible a representation of (R) with no particular regard for theoretical foundations. However, it is found that the most successful fitting procedures, having generic utility, lead to terms in the potential that can be ascribed to chemically meaningful interactions. For example, molecular mechanics potentials typically have simple analytic terms that provide an…show more content…
The interaction potential Ѵ(R) describes both bonding and nonbonding interactions. The bonding interactions are usually formulated as a strain energy that is zero at some ideal configuration of the atoms and describe how the energy increases as the ideal configuration is deformed. Bonding interactions usually refer to atoms in the following relationships: directly bonded (a 1–2 bond stretch relationship), geminal to each other (a 1–3 angle bending relationship), vicinal to each other (a 1–4 dihedral angle rotation relationship). The nonbonded interactions usually include the following: an exchange repulsion when atoms get too close, a long range attraction arising from dispersion forces, electrostatic interactions coming from the interaction of charges, dipoles, quadrupoles, etc. The exchange repulsion and dispersive attraction combine in what is referred to as a van der Waals term. Sometimes a potential is added to account for hydrogen bonding
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