Space-filling model

[1] They are distinguished from other 3D representations, such as the ball-and-stick and skeletal models, by the use of the "full size" space-filling spheres for the atoms.

Crystallographic data are the starting point for understanding static molecular structure, and these data contain the information rigorously required to generate space-filling representations (e.g., see these crystallographic models); most often, however, crystallographers present the locations of atoms derived from crystallography via "thermal ellipsoids" whose cut-off parameters are set for convenience both to show the atom locations (with anisotropies), and to allow representation of the covalent bonds or other interactions between atoms as lines.

In short, for reasons of utility, crystallographic data historically have appeared in presentations closer to ball-and-stick models.

In 1952, Robert Corey and Linus Pauling described accurate scale models of molecules which they had built at Caltech.

The two spheres were then firmly held together by a metal rod inserted into the pair of opposing bushing (with fastening by screws).

A space-filling model of n -octane , the straight chain (normal) hydrocarbon composed of 8 carbons and 18 hydrogens, formulae: CH 3 CH 2 (CH 2 ) 4 CH 2 CH 3 or C
8 H
18 . Note, the representative shown is of a single conformational "pose" of a population of molecules, which, because of low Gibbs energy barriers to rotation about its carbon-carbon bonds (giving the carbon "chain" great flexibility), normally is composed of a very large number of different such conformations (e.g., in solution).
An example of a three-dimensional, space-filling model of a complex molecule, THC , the active agent in marijuana.
An example of a 3D, space-filling model of a simple molecule, sulfur dioxide , SO 2 , showing the electrostatic potential surface , computed for the molecule using the Spartan software suite of computational chemistry tools. It is shaded from blue for electropositive areas to red for electronegative areas. The surface was generated by calculating the energy of interaction of a spherical point positive charge (e.g., a proton, H +, ) with the molecule's atoms and bonding electrons, in a series of discrete computational steps. Here, the electrostatic surface emphasizes the electron deficiency of the sulfur atom, suggesting interactions in which it might engage, and chemical reactions it might undergo.
An example of a 3D, space-filling model of a very complex macromolecule , a protein , the cell membrane -spanning β2 adrenoreceptor , a G protein-coupled receptor , in this image, viewed as if looking down onto the extracellular surface. The electrostatic potential surface was applied to a model with atom positions determined by crystallography ( PDB code 2RH1); the electrostatic surface was computed using Adaptive Poisson-Boltzmann Solver (APBS) freeware. [ 3 ] It is again shaded blue for electropositive areas to red for electronegative areas. Somewhat apparent, in stick representation in yellow, red and blue, in a groove at the top of the receptor , is a small molecule ligand bound to it, the agent carazolol , a partial inverse agonist which, through this binding, antagonizes binding of the normal ligand, the neurotransmitter /hormone epinephrine . In response to binding epinephrine , this receptor, in conjunction with an L-type calcium channel , mediates physiologic responses such as smooth muscle relaxation and bronchodilation . All of such binding interactions and the function of the receptor in signal transduction are mediated by electrostatic effects, and in modern structure work they are often studied using similar space filling models.
A space-filling model of cyclohexane C
6 H
12 . Carbon atoms, partially masked, are in grey, and hydrogen atoms are presented as white spheres.