Molecular structure space-filling mode

Fig. 11.2 A view of molecular packing in the Ni(NCS)2(4-methylpyridine)4 layered structure [2] (host molecules shown in the capped sticks mode, hydrogen atoms are omitted for the sake of clarity). Guest azulene molecules are shown in the space filling mode, the two layers of the guest non-related by crystal symmetry are distinguished by different colors...

Larger structures may be built with the Molecular Design kits offered by Academic Press and used in either the skeletal or the space-filling mode. It is claimed that two turns of DNA can be built with such a kit in 6 hours, and a molecule of tRNA in 3 days. Firm locking of otherwise freely rotating bonds is a feature of these models. 

In order to represent 3D molecular models it is necessary to supply structure files with 3D information (e.g., pdb, xyz, df, mol, etc.. If structures from a structure editor are used directly, the files do not normally include 3D data. Indusion of such data can be achieved only via 3D structure generators, force-field calculations, etc. 3D structures can then be represented in various display modes, e.g., wire frame, balls and sticks, space-filling (see Section 2.11). Proteins are visualized by various representations of helices, / -strains, or tertiary structures. An additional feature is the ability to color the atoms according to subunits, temperature, or chain types. During all such operations the molecule can be interactively moved, rotated, or zoomed by the user. 

In the regions intermediate between these limiting cases, normal modes of vibration "erode" at different rates and product distributions become sensitive to the precise conditions of the experiment. Intramolecular motions in different product molecules may remain coupled by "long-range forces even as the products are already otherwise quite separated" (Remade Levine, 1996, p. 51). These circumstances make possible a kind of temporal supramolecular chemistry. Its fundamental entities are "mobile structures that exist within certain temporal, energetic and concentration limits." When subjected to perturbations, these systems exhibit restorative behavior, as do traditional molecules, but unlike those molecules there is no single reference state—a single molecular structure, for example—for these systems. What we observe instead is a series of states that recur cyclically. "Crystals have extension because unit cells combine to fill space networks of interaction that define [dissipative structures] fill time in a quite... 

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