Van der Waals overlap

In this study several theoretical measures of fit of the allylic diradical 3 in the crystal lattice were used. One was van der Waals overlap of the cisoid and transoid diradicals with the cavity of surrounding neighbors. The transoid allylic diradical required a 10% overlap increase compared with 1% overlap increase for formation of the cisoid counterpart from reactant. Thus the preference for the five-membered ring photoproduct in the crystal lattice photolysis is understood, because only that reaction pathway may occur via an intermediate that can fit in the lattice cavity. 

Table 8.1 Van der Waals Overlaps of Alternative Diradicals En Route to 13a and 13b ...

Figure 2 Dependence of the potential energy U of two atoms on their distance r (Lennard Jones potential). Coming from an infinite distance r, the energy decreases (attraction due to electrostatic interactions) until a minimum distance r jn is reached from thereon repulsion due to increasing van der Waals overlap of the atoms results a is the distance for which the interaction energy is zero (reproduced from Figure 3.1 of ref. [59] with permission from Cambridge University Press, Cambridge, UK).

Set counter, c = 1. Perform TAD (1000 high-temperature steps followed by 3000 annealing steps) using Es as the target function. The torsion angle bounds of the current subdomain determine the dihedral angle restraint functions. In addition to the NOE-derived distance restraints, sterically based distance restraints are added to prevent van der Waals overlaps. 

The modified constrained global optimization was also applied to the Compstatin structure prediction problem using the same constraint function and parameters [104]. The goal of introducing TAD as a component of the upper bound solution approach is to increase the number of feasible points available for initialization of the constrained local minimization. Initially, TAD is used in combination with simple van der Waals overlap restraints to drive the distance violations to zero. 

The space filling model developed by Corey, Pauling, and Koltun is also known as the CPK model, or scale model [197], It shows the relative volume (size) of different elements or of different parts of a molecule (Figure 2-123d). The model is based on spheres that represent the "electron cloud . These atomic spheres can be determined from the van der Waals radii (see Section 2.10.1), which indicate the most stable distance between two atoms (non-bonded nuclei). Since the spheres are all drawn to the same scale, the relative size of the overlapping electron clouds of the atoms becomes evident. The connectivities between atoms, the bonds, are not visualized because they are located beneath the atom spheres and are not visible in a non-transparent display (see Section 2.10). In contrast to other models, the CPK model makes it possible to visualize a first impression of the extent of a molecule. 

Dienes would be expected to adopt conformations in which the double bonds are coplanar, so as to permit effective orbital overlap and electron delocalization. The two alternative planar eonformations for 1,3-butadiene are referred to as s-trans and s-cis. In addition to the two planar conformations, there is a third conformation, referred to as the skew conformation, which is cisoid but not planar. Various types of studies have shown that the s-trans conformation is the most stable one for 1,3-butadiene. A small amount of one of the skew conformations is also present in equilibrium with the major conformer. The planar s-cis conformation incorporates a van der Waals repulsion between the hydrogens on C—1 and C—4. This is relieved in the skew conformation. 

Figure 16.7 On a surface generated by overlapping van der Waals spheres there will be areas (hatch) which are inaccessible to a solvent molecule (dotted sphere)...

In sharp contrast to the stable [H2S. .SH2] radical cation, the isoelectron-ic neutral radicals [H2S.. SH] and [H2S. .C1] are very weakly-bound van der Waals complexes [125]. Furthermore, the unsymmetrical [H2S.. C1H] radical cation is less strongly bound than the symmetrical [H2S.. SH2] ion. The strength of these three-electron bonds was explained in terms of the overlap between the donor HOMO and radical SOMO. In a systematic study of a series of three-electron bonded radical cations [126], Clark has shown that the three-electron bond energy of [X.. Y] decreases exponentially with AIP, the difference between the ionisation potentials (IP) of X and Y. As a consequence, many of the known three-electron bonds are homonuclear, or at least involve two atoms of similar IP. 

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