Compact-packed crystal structure

A landmark achievement in RNA structure determination was the solution of the crystal structure of the 160 nucleotide long P4-P6 domain of the Tetrahyme-na group I intron [19,34,35,39]. The P4-P6-domain folds into a compact structure with a sharp turn that is stabilized by tight packing of the heHces. This newly discovered structural element was designated as the ribose-zipper because of the hydrogen bonds between ribose residues of the helices that participate in the structure. In addition, stabiHzation of RNA folds in P4-P6 occurs mainly via... 

What is less understood is the extent to which the presence of a LP is responsible for orientation effects in crystals and, more generally, for determining the type, compactness, and symmetry of crystal packing. The notion that a stereochemically active LP should have spatial extension implies that significant electron density is associated, locally, with the LP, and that this electron density extends radially and in a particular direction from the parent atom over an appreciable portion of space in the crystal. This effectively excludes other atoms from occupation of this space and creates a void in the crystal structure. 

Generally, a crystal is electrically neutral. This implies that the crystal should have an equal number of positive and negative charges. Thus, when oppositely charged ions come together to form a neutral crystal structure, each ion coordinates with as many ions of opposite charge as the size permits. This coordination principle dictates both electrical neutrality of the crystal structure and compact packing of the atoms within the structure. 

Figure 13-27 There are two crystal structures in which atoms are packed together as compactly as possible. The diagrams show the structures expanded to clarify the difference between them, (a) In the hexagonal close-packed structure, the first and third layers are oriented in the same direction, so that each atom in the third layer (A) Ues directly above an atom in the first layer A), (b) In the cubic close-packed structure, the first and third layers are oriented in opposite directions, so that no atom in the third layer (C) is directly above an atom in either of the first two layers A and B). In both cases, every atom is surrounded by 12 other atoms if the strucmre is extended indefinitely, so each atom has a coordination number of 12. Although it is not obvious from this figure, the cubic close-packed structure is face-centered cubic. To see this, we would have to include additional atoms and tilt the resulting cluster of atoms.

This leads to the appearance of both anti and syn rotational conformations, which coexist in the DBDI based PU macromolecules, (Fig. 2.4-2.6). As a result, in this latter case the PU macromolecules can adopt a more compact packing which enhances significantly the ability to order in crystalline structures involving predominantly the anti form [60]. Shown in Fig. 2.4 and 2.5 are the extended linear anti and contorted syn DBDI positions as compared to the conventional rigid 4,4-diphenylmethane diisocyanate (MDI) non-crystallizing (Fig. 2.6). 

Figure 13-27 There are two crystal structures in which atoms are packed together as compactly as possible. The diagrams showthe structures expanded to clarify the difference between them.

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