Packing van der Waals

FIGURE 1.12 Van der Waals packing is enhanced in molecules that are structurally complementary. Gln represents a surface protuberance on the protein lysozyme. This protuberance fits nicely within a pocket (formed by Tyr , Tyr , Phe and Trp ) in the antigen-binding domain of an antibody raised against lysozyme. (See also Figure 1.16.)... 

If we consider hydrocarbons at surfaces, we must set the saturated ones aside. These do not chemisorb at metal surfaces, but rather physisorb at low temperatures. No detailed structural determination has been performed for saturated hydrocarbons on metals. However, some structures have been obtained using the graphite basal plane as a substrate (cf. Suzanne etc) which give information about Van der Waals packing of such molecules, but no chemical reactions are involved. 

Potluri S, Yan AK, Chou JJ, Donald BR, Bailey-Kellogg C. Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing. Proteins 2006 65 203-219. 

A remarkable feature of this structure is that the van der Waals packing distance between double heUces is in agreement witft the glucoside lirik. This is a direct consequence of the IPMS character of the structure. The position of the polyglucan chain in relation to diis surface is illustrated in Fig. 8.5. Just as in quartz, there is a packing distance between the double helices that is related to the helical units. These links correspond to the labyrinths joining the double helices. The nature of these labyrinths of the Q surface space group 6422 is considered further below. 

Small organic molecules have been the subject of most surface-structure studies of molecular adsorbates. Most of these molecules are alkenes (such as ethylene) and aromatic molecules (such as benzene and substituted benzenes). Saturated hydrocarbons physisorb only at low temperatures and although some ordered surface structures have been obtained using graphite as a substrate, these structures exhibit van der Waals packing without forming stronger chemical bonds. 

Similar phenomena characterize the clathration behavior of the larger host tris(2,3-naphthalenedioxy)cyclotriphosphazene 13). Due to the boIki tack-bone, this host forms, in relation to the former structure type, a markedly expanded (withchaimelsof diameter 9-10 A at the narrowest point) and thus less stable structure. Evidently, the driving force for clathration of the substituted cyclotriphosphazene species is associated with their unusual paddle-wheel like shape. Van der Waals packing of these molecules in a high symmetry arrangement leaves substantial voids in the lattice which are fillta by guest components to lower the enthalpy of the total system. The potential use of this clathration behaviour for separation of hydrocarbons was envisioned already about fifteen years ago... 

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