molecularmodel

A molecular model is a representation of the arrangement and interactions of atoms within a molecule or material, used to study structure, properties, and dynamics. Models can be physical objects or computational simulations, and may range from simple diagrams to detailed simulations that predict behavior under different conditions. They are often built from experimental data and theoretical principles.

Physical models include ball-and-stick, space-filling, and wireframe forms that convey geometry, bonding, and steric effects. They are valuable for teaching, visualization, and intuition about conformations.

Computational models use quantum chemistry and molecular mechanics to predict structure and properties. Quantum methods (ab initio, density functional theory) treat electrons explicitly, while molecular dynamics and Monte Carlo simulations model motions and thermodynamics with approximate forces. Docking and coarse-grained models enable studies of large systems. Visualization and analysis rely on software such as PyMOL, Chimera, and VMD.

Model inputs often come from experimental structures determined by X-ray crystallography, NMR, or cryo-electron microscopy. Structural databases, notably the Protein Data Bank, provide coordinates used as starting points for modeling and validation.

Applications include drug discovery, materials design, catalysis, enzyme mechanism studies, and education. Molecular models help interpret experiments, test hypotheses, and guide experimental planning.

Limitations include simplifications and approximations, variable accuracy across methods, and finite computational resources. Dynamic processes or electronic effects may be challenging to capture fully, and models require validation against experimental data.