Van der Waals radius, for hydrogen

Fig. 8-2.—The planar configuration of cis-azobenzene, drawn to scale using 1.0 A for the van der Waals radius for hydrogen. Steric interactions of hydrogen atoms prevent the assumption of this configuration.

The van der Waals radius for carbon is taken as 1.35 A in the Stuart models, which is also about 0.3 A too small, but this is of minor importance compared with the hydrogen radius in determining the spatial character of the methyl group. 

The electron density around the hydrogen will also be significantly dependent on the nature of the X atom, e.g. electronegative atoms such as oxygen or nitrogen will lead to a smaller effective van der Waals radius for the hydrogen, than if it is bonded to carbon. 

An alternative measure of steric requirements was suggested by Charton who defined a steric scale v which is the difference between the van der Waals radius for a symmetrical substituent and hydrogen (Vx = U 1.20). The steric parameter can be incorporated into the free energy relationship by the additive function (Equation 16) where z is the similarity coefficient, analogous to 5, for the steric effect. 

The discretization is done with each molecule at the centre of each grid. The empty space not filled by the molecule is necessary for the algorithm. To perform the discretization, each grid cell within which an atomic position is found is turned orf. Grid cells whose centre is within 1.8 A of any atomic position are also turned orf. This value of 1.8 A is chosen to approximate an effective van der Waals radius for an atom combined with any hydrogen atoms that are bound to it. Thus the surface of the resulting grids will represent the atomic surface of the molecules. 

The problem is to determine the distance between nearest neighbors. The value in general adopted for the Van der Waals radius of hydrogen ... 

Conformational (steric) effects and ring strains contribute to strain energies. It is the van der Waals radii, and not the atomic radii, which are decisive in these cases. For example, fluorine has a smaller van der Waals radius than hydrogen, since the larger fluorine atomic mass leads to lower vibrational amplitudes. Thus, hydrogen produces a greater steric effect than fluorine the polymerization enthalpy of tetrafluoroethylene is more negative... 

In the area calculations, it is customary to use van der Waals radii for atoms, although for hydrogen / h = I 0 A and for water Rw = I -4 A is usually taken. While the van der Waals radius of hydrogen (1.2 A) places the surface outside that of the oxygen (1.5 A), water molecules touching are still usually only 2.78 A apart. 

---