Van der Waals contacts

Restraints can facilitate docking a substrate molecule to a binding site. Restraints can also facilitate the interaction of two molecules in solution. In both cases, it is unlikely that two different neutral molecules would come into van der Waals contact with each other without the use of restraints. 

Studies of cyclodecane derivatives by X-ray crystallographic methods have demonstrated that the boat-chair-boat conformation is adopted in the solid state. (Notice that boat is used here in a different sense than for cyclohexane.) As was indicated in Table 3.7 (p. 146), cyclodecane is significantly more strained than cyclohexane. Examination of the boat-chair-boat conformation reveals that the source of most of this strain is the close van der Waals contacts between two sets of three hydrogens on either side of the molecule. 

When two atoms approach each other so closely that their electron clouds interpenetrate, strong repulsion occurs. Such repulsive van der Waals forces follow an inverse 12th-power dependence on r (1/r ), as shown in Figure 1.13. Between the repulsive and attractive domains lies a low point in the potential curve. This low point defines the distance known as the van der Waals contact distance, which is the interatomic distance that results if only van der Waals forces hold two atoms together. The limit of approach of two atoms is determined by the sum of their van der Waals radii (Table 1.4). 

The stmcture of the compound 67b was determined by X-ray (95JA6388). The length of the Te=Se bond (2.445 A) is 0.1 A shorter that in bis(2-ethylcarboxy-phenyltellurenyl) selenide (81CSC1353), which points to a greater double bond character of this bond in the former compound. Selenoxide 67b has a boat conformation. The length of the transannular Te- N bond (2.620 A) is appreciably shorter than the corresponding van der Waals contact (3.70 A). The intramolecular coordination Te- N bond thus formed contributes to the stabilization of the boat conformation of the compounds 67. 

The work of Melander and Carter (1964) on 2,2 -dibromo-4,4 -di-carboxybiphenyl-6,6 -d2 (1) has been referred to above in the introductory and theoretical sections, where it was pointed out that the availability of two detailed theoretical computations of the inversion barrier (Westheimer and Mayer, 1946, Westheimer, 1947 Hewlett, 1960) made this system especially attractive for the study of steric isotope efifects. Furthermore, in the preferred initial-state conformation the two bromines are probably in van der Waals contact (cf. Hampsoii and Weissberger, 1936 Bastiansen, 1950), and thus initial-state steric effects are unaffected by deuterium substitution in the 6 and 6 positions. The barrier calculations provided two different theoretical values for the non-bonded H Br distance in the transition state which, together with the corresponding H Br potential function, could be inserted in equation (10) to yield values for A AH. For... 

The (5 )-enantioselectivity of MeHNL can be explained considering Fig. 1. As shown in the figure, the carbonyl oxygen is hydrogen bonded to SerSO and Thrll. One methyl group of acetone (Cl) is held in position by van der Waals contacts to Leu 149, Thrll and He 12. The side chains of these residues define a... 

Also deoxycholic acid (6) crystallizes in an inclusion lattice with channel-shaped cavities 13). Figure 3 shows that they are formed by facing molecules of deoxycholic acid, 4). This characteristic structural unit is a double layer of head-to-tail linked deoxycholic acid molecules at which specific H-bridges between hydroxy and carboxy groups are the decisive fact. The channels as such (e.g. in case of the orthorhombic crystal, see Fig. 3) are lined with lipophilic groups. Thus only van der Waals contacts are kept between the included guest molecules (also for polar molecules like acetone, Fig. 3) and the molecules of the channel wall. 

Thus, the two Pc rings of the LnPc2 complexes have a skew angle of about 45° only in the case of the fairly strong it-it contact between the two Pc rings. When the interplanar distance is greater than the usual van der Waals contacts, the skew angle is decreased dramatically. 

Such a structure cannot be constructed for a ribopolynucleotide, since the extra oxygen atom would result in too close a van der Waals contact. However, x-ray photographs of ribonucleic acids from various sources are found to be identical, which suggests that, irrespective of differences in composition, there is an underlying configuration which is common to all... 

Changes in the pteridine ring affect the contacts between DHFR and the p-aminobenzoic acid (PBH) moiety. PBH maintains van der Waals contact with Phe31 in all four structures (1, 3, 5 and 6) with contact distances ranging within 0.4 A of one another. Contact is also observed with Leu54 in all four structures with distances ranging from 3.0 A to 2.8 A. Only in... 

Table 5.1. Properties of binary B - -HA hydrogen-bonded complexes (see Fig. 5.1), showing the H-bond energy A b-h, H-bond length Rb-e, van der Waals contact distance f B---H(vdW), cind covalent-bond elongation A/sAn (relative to isolated monomer)...

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