Molecular modelling

Molecular modelling uses computational representations of molecules to predict their structures, properties, and behavior. Its methods range from classical force fields to quantum-mechanical calculations.

Molecular mechanics: A method that models molecular energy and motion using atoms, bonds, and parameterized force fields. It provides the classical framework for calculating molecular structures and energies.
Molecular geometry: The three-dimensional arrangement of atoms in a molecule, described by distances, angles, and torsions. A molecular model encodes geometry as coordinates or internal structural variables.
Computer-aided drug design: The use of computational methods to identify and optimize candidate medicines. Molecular models help rank compounds and guide changes to drug candidates.
Quantum chemistry: The application of quantum mechanics to explain and predict the properties of atoms and molecules. Molecular modelling includes quantum-chemical methods alongside less explicit approximations.
Force field (chemistry): A mathematical function and parameter set for estimating a molecule’s potential energy from its atomic configuration. Its terms and parameters determine how molecular mechanics represents interactions.
Potential energy surface: A function giving a system’s potential energy as its nuclear coordinates vary. Optimization and simulation rely on how energy changes across molecular configurations.
Protein structure prediction: The computational prediction of a protein’s three-dimensional structure from its amino-acid sequence or related data. It uses molecular information to infer structures that are difficult to determine experimentally.
Ab initio methods: Electronic-structure methods derived from quantum mechanics with limited empirical parameterization. They offer a more direct physical basis than classical parameterized force fields.
Molecular dynamics: A simulation method that calculates atomic motion by numerically integrating equations of motion. It uses molecular energy models to trace how structures change over time.
Born–Oppenheimer approximation: An approximation that separates electronic and nuclear motion because nuclei move much more slowly than electrons. It underlies many calculations of molecular structure and electronic energy.

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