Contact Distances

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Covalent bond distances and angles tell us how the atomic nuclei are arranged in space but they do not tell us anything about the outside surfaces of molecules. The distance from the center of an atom to the point at which it contacts an adjacent atom in a packed structure such as a crystal is known as the vander Waals radius. The ways in which biological molecules fit together are determined largely by the van der Waals contact radii. In every case they are approximately equal to the covalent radius plus 0.08 nm. Van der Waals radii are not as constant as covalent radii because atoms can be“squeezed” a little, but only enough to decrease
the contact radii by 0.005–0.01 nm. The radii of spacefilling molecular models are usually made a little smaller than the actual scaled van der Waals radii to permit easier assembly.

Packing of molecules of suberic acid HOOC–(CH2) 6 –COOH in a crystal lattice as determined by neutron diffraction. 2 Notice the pairs of hydrogen bonds that join the carboxyl groups at the ends of the molecules and also the close contact of hydrogen atoms between the chains. Only the positions of the hydrogen nuclei were determined; the van der Waals radii have been drawn around them. However, the radii were originally determined from X-ray and neutron diffraction data obtained from many different crystalline compounds.