Space-filling model

A molecular representation that depicts atoms as overlapping spheres scaled to their van der Waals radii. It emphasizes a molecule’s overall shape, surface, and occupied volume.

Van der Waals radius: A measure of an atom’s effective size based on nonbonded contacts with other atoms. These radii set the spheres’ sizes and therefore the model’s outer surface.
Protein structure: The three-dimensional arrangement of atoms in a protein molecule. Space-filling views show how densely folded protein atoms occupy volume.
Wire-frame model: A molecular representation drawn with lines for bonds and minimal depiction of atomic volume. It exposes connectivity and internal structure where spheres can conceal them.
Molecular model: A physical or visual representation of a molecule’s structure or behavior. Space-filling models are a type of molecular model.
Molecular geometry: The three-dimensional arrangement of atoms in a molecule. Geometry determines how the scaled atomic spheres overlap in the model.
Molecular docking: A computational method for predicting how molecules bind to one another. The model’s surfaces make steric complementarity at binding sites visible.
Skeletal formula: A shorthand drawing of an organic molecule in which carbon atoms and many hydrogens are implicit. Its compact notation prioritizes connectivity rather than three-dimensional occupied volume.
Atomic coordinates: Numerical positions specifying where atoms lie in a molecular structure. Coordinates place each sphere before its overlap with neighboring atoms is drawn.
Covalent bond: A chemical bond formed when atoms share one or more pairs of electrons. Covalent bonds connect the atoms whose positions the model displays.
Steric hindrance: Reduced chemical reactivity or binding caused by spatial crowding among atoms or groups. Overlapping spheres reveal crowding that can block molecular approaches.

Linked from 5 pages