Molecular mechanics

Molecular mechanics models molecular structure and motion using classical mechanics, representing atoms as particles and interactions with parameterized energy functions.

Force field (chemistry): A parameterized mathematical model for calculating molecular energies and forces from atomic coordinates. It specifies the energy terms and parameters used in molecular mechanics.
Potential energy surface: A function giving a system's potential energy as a function of its nuclear coordinates. Molecular mechanics approximates this surface with a classical energy function.
Quantum mechanics: A physical theory describing matter and energy through quantum states and probabilistic measurement outcomes. Molecular mechanics replaces explicit quantum states with classical particles and fitted interactions.
Protein structure prediction: The computational inference of a protein's three-dimensional structure from its amino-acid sequence. Molecular mechanics can refine candidate structures and assess their conformational energies.
Molecular orbital method: A quantum-chemical description of electrons occupying molecular orbitals spread across a molecule. Its electronic treatment contrasts with the classical assumptions that motivated molecular mechanics.
Bond stretching: A molecular deformation in which the distance between two bonded atoms changes. Its energy term penalizes departures from preferred bond lengths.
Partial charge: A numerical representation of an atom's share of electron density in a molecule. Partial charges commonly determine electrostatic interactions between atoms.
Density functional theory: A quantum-mechanical method that approximates electronic energy from electron density. It can describe electronic rearrangements that fixed-parameter molecular mechanics cannot.
Molecular docking: A computational method for predicting how molecules bind and orient within a target site. Docking commonly uses force-field energies to score candidate ligand poses.
Westheimer's molecular mechanics: The early molecular-mechanics framework developed by Frank H. Westheimer and colleagues for molecular conformations. It helped establish classical energy functions as tools for analyzing molecular structure.

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