Biochemistry - The Chemical Reactions of Living Cells, Volume 3 - D. Metzler 1980

Construction of Molecular Models
Spatial Models

In these models, atomic radii approach Structure/103.html">Van der Waals radii (Table 2-1, Vol. 1, p. 68). Constructing a model with radii of this exact size is virtually impossible due to overly dense packing that hinders assembly. A compromise solution that yields visually acceptable molecular models is to use styrofoam spheres with a diameter of 3.8 cm for C, H, O, and N atoms, and 5.1 cm for P and S atoms. If 0.5 cm is trimmed from the spheres representing C, O, and N along each bond axis, the remaining 1.4 cm will roughly correspond to a covalent radius of 0.07 nm at a scale of 2 cm = 0.1 nm (1 Å). For hydrogen atoms, 1.3 cm is trimmed from the spheres, yielding the required covalent radius of 0.03 nm. A sphere radius of 1.9 cm corresponds to 0.095 nm, which is approximately ²/₃ of the actual van der Waals radii of C, N, and O, and 0.8 of the hydrogen radius. It is also convenient to use a scale of 1.25 cm = 0.1 nm. This exact scale is used in commercially available CPK models developed by the American Society of Biological Chemists, Inc. Using this scale allows for the combination of custom-made and ready-made models. For H and C atoms, spheres with a diameter of 2.54 cm are used, while for O and N, the diameters are 3.8 cm and 3.18 cm, respectively.

Spheres should be trimmed carefully when building space-filling models to maintain the correct covalent radius. The easiest way to do this is to first mark the centers of the regions to be cut by inserting toothpicks into the sphere. If a tetrahedron is required, the corresponding points are determined using a cardboard template as described above. The spheres are trimmed by placing them into holes drilled in a metal sheet; the diameter of these holes should be such that the exact portion of the sphere to be cut off protrudes from the other side of the metal sheet. This protruding part is then sliced off with a very sharp knife. The holes in the metal, such as aluminum, must be cut with high precision, but the time spent making such a template is well worth it, as the template is durable.

Large, flat chemical structures, such as nucleotide Base Pairs in DNA, can be cut out from styrofoam sheets.