Structural Biology Glossary
Van der Waals radii
Since the advent of quantum-mechanics it is well known that atoms are no hard spheres. Their electronic structure has to be described by wavefunctions and the radial part of these wavefunctions is defined between 0 and infinity. When atoms are approachung each other there is an overlap between their electronic wavefunctions and this may lead to various types of interactions. In this respect, the question How large is an atom? makes no sense.
On the other hand, the location of the atomic nuclei are accessible by experimental methods, like X-ray diffraction, for example. One can, for example, very precisely determine that distance d between the two hydrogen atoms in a hydrogen molecule and then conclude that the distance is two times the radius r of a hydrogen atom.
d H---------H r | r
Starting out from homonuclear interactions one can also derive values for heteronuclear contacts. Due to the very nature of this defintion the radii obtained depend on the type of interaction measured. For example, atom radii obtained from bonded intereactions are definitely different from the corresponding data obtained from non-bonded contacts. Van der Waals radii are determined from contact distances between non-bonded atoms. Comprehensive information on van der Waals radii can be obtained from WebElements. The most common elements in bioploymers (no metals) have the following radii.
|element||van-der-Waals radius / Å|
Note, that in other compilations slightly different values may be given. Conversion factors between different units are: 1 pm = 1 x 10-12 meter 100 pm = 1 Å 1000 pm = 1 nanometer (nm)
Evdw(Rij) = epsilon [(Rij,vdw / Rij )^12) - 2 (Rij,vdw/ Rij )^6].
The first term describes the repulsion and the second one the attraction.
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