Molecular modelling
Methods to model molecular behaviour at the atomistic level.
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. These methods are used in computational chemistry, drug design, computational biology, and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The common feature of molecular modelling methods is the atomistic level description of the molecular systems, which may include treating atoms as the smallest individual unit or explicitly modelling subatomic particles.
- field
- Computational chemistry, drug design, computational biology, materials science
- methods
- Molecular mechanics, quantum chemistry, energy minimization, molecular dynamics
- key_concept
- Potential function, force field, atomistic level description
- common_force_fields
- Developed using chemical theory, experimental reference data, and high level quantum calculations
- coordinate_representations
- Cartesian coordinates, internal coordinates (Z-matrix or torsion angle representation), Natural Extension Reference Frame (NERF)
Lore & Background
Molecular modelling includes both theoretical and computational approaches. The simplest calculations can be performed by hand, but computers are required for any reasonably sized system. Molecular mechanics uses classical mechanics, describing atoms as point charges with mass, and interactions via spring-like bonds, Van der Waals forces, and Coulomb's law. The Lennard-Jones potential is commonly used for Van der Waals interactions. The collective mathematical expression is a potential function related to the system's internal energy.
Reader's Guide
Molecular modelling is significant because it enables the investigation of structure, dynamics, surface properties, and thermodynamics of inorganic, biological, and polymeric systems. Energy minimization methods find local energy minima, providing static pictures for comparing similar systems. Molecular dynamics simulations compute system behaviour over time by solving Newton's laws of motion, incorporating temperature effects. These methods are routinely used to study protein folding, enzyme catalysis, protein stability, conformational changes, and molecular recognition of proteins, DNA, and membrane complexes. The field relies on force fields—sets of parameters derived from chemical theory, experimental data, and quantum calculations—which vary in mathematical expression and parameters across different implementations.
Did You Know?
- Molecular modelling methods can treat atoms as the smallest individual unit or explicitly model subatomic particles like protons, neutrons, quarks, and electrons with photons.
- The Lennard-Jones potential is commonly used to describe Van der Waals forces in molecular mechanics.
- The Natural Extension Reference Frame (NERF) method is currently the fastest and most accurate torsion to Cartesian conversion.
- Molecular dynamics simulations involve solving Newton's second law, F = ma, to compute atomic trajectories in space and time.
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