Atomic radii van der Waals

Atom Van der Waals radius, nm Covalent radius, nm Atom represented to scale... 

Compare ethane with hexachloroethane, CgClg. The chlorine atoms are much larger than hydrogen atoms (van der Waals radius H. about 130 pm Cl, about 180 pm) and now they do physically get in the way of each other. This is reflected in the increase in the rotational barrier from 12 kJ mol-1 in C2H6to 45 kJ mol-1 in C2CI6 (although other factors also contribute). 

As an example, let us consider the MFTA model of the HIV-1 reverse transcriptase inhibition by the tetrahydroimidazobenzodiazepinone (TIBO) derivatives. The model is based on the atomic charge Q, atomic van der Waals radius R and group lipophilicity Lg as the local descriptors (V=73, Np=5, i = 0.887, g = 0.686). Figure 5.5 shows the molecular supergraph with the superimposed structure of one training set compound. 

Figure 5.6 Complementarity between the major MFTA descriptor contributions to activity of the TIBO inhibitors of HIV-1 reverse transcriptase and the molecular properties of the biotarget protein a) atomic charge (Q) and electrostatic potential (EP) (b) atomic van der Waals radius (i ) and molecular surface (c) local lipophilicity (Lg) and molecular lipophilic potential (MLP) - see text for details.

To calculate FRAU descriptors, first the frontier surface of each atom is determined by drawing a sphere around each atom with radius equal to or larger than the atomic van der Waals radius. The surface of this sphere is taken as the atomic surface. The part of the atomic surface overlapping with the sphere of another atom is called interior surface, and the atomic surface minus the interior surface is called frontier surface. Then, a number of points are evenly distributed on the atomic surface. 

Let us take the helium atoms in the equilateral triangle configuration with the side length R = 2.52 A. This value corresponds to 90% of the double helium atom van der Waals radius ... 

By virtue of its tetrahedral symmetry, the HCH bonds in CH4 are all 109.5°. In this configuration, the H---H distances are all 1.78 A. The van der Waals radius of an atom is defined such that whenever the distance between two atoms equals the sum of their van der Waals radii, their interatomic repulsion is RT. Since the H-atom van der Waals radius is 1.2 A, any distance less than 2.4 A between H-atom centers will produce significant repulsion between the electron clouds of the two H atoms. There have been many theoretical attempts to quantify this repulsion its magnitude is given approximately by an empirical formula proposed by Huggins ... 

Atom van der Waals Radius (rvdw)" Ionic Radius Covalent Radii (r ) ... 

Let us take the helium atoms in the equilateral triangle configuration with the side length R = 2.52 A. This value corresponds to 90% of the double helium atom van der Waals radius (1.40 A). The MP2 calculation, gives the energy for the three atoms equal to Ehcs = —8.5986551 a.u., for a pair of the atoms = —5.7325785 a.u., and for a single atom Ehc = —2.8663605... 

Let us now discuss possible choices of reference system for particular types of steric questions. As one simple example, we may consider evaluation of an atomic van der Waals radius / vdw by bringing up a probe species (e.g.. He) to the atom until the steric exchange energy increment (value at / vdw minus value at... 

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