Skeletal model

Fig. 2. Stmcture of the mineral 2eohte chaba2ite is depicted by packing model, left, and skeletal model, right. The sihcon and aluminum atoms He at the corners of the framework depicted by soHd lines. In this figure, and Figure 1, the soHd lines do not depict chemical bonds. Oxygen atoms He near the midpoint of the lines connecting framework corners. Cation sites are shown in three different locations referred to as sites I, II, and III.

The following bond density surface for hex-5-en-l-yne clearly allows you to see whicf atoms are connected. It does not, however, distinguish single, double and triple carbon-carbon bonds as clearly as a simple skeletal model. 

Fig. 10. Electron density projection along -strand direction—hydrogen-bonding direction (a-axis) horizontal, and intersheet direction (c-axis) vertical—and skeletal models of polyGln8 (Q8) and polyGln45 (Q45) assemblies. The unit cell for both peptides was monoclinic, with lattice constants a = 9.73 A, b = 7.14 A, c = 8.16 A, and y = 95.7° for Q8, and a = 9.66 A, b = 7.10 A, c = 8.33 A, and y = 94.0° for Q45. The side chains are nearly overlapped in the hydrogen-bonding direction. This difference in side chain conformation and disorder likely accounts for the differences in observed intensity between their diffraction patterns.

Chapter 9, Model Frameworks and Template Packages, shows how recurring patterns of types, collaborations, and refinement can be captured using the idea of a framework a template package. The resulting model can then be used as a skeletal model that is applied with various specializations to different problems. Frameworks enable you to define new modeling constructs. 

In the enumeration of chirality elements of flexible molecules all arrangements are taken into account which are permitted by the given constraints under the observation conditions. Here, one must always assume a rigid skeletal model and freely rotating ligandsF That arrangement for which the lowest number of chirality elements is found equal zero determines the number of chirality elements for the whole ensemble. 

Rigid skeletal models can be indexed in any arbitrary manner but once an assignment of skeletal indices has been made, it must be retained. 

Matkovic, V. (1991). Calcium metabolism and calcium requirements during skeletal modeling and consolidation of bone mass. Am. J. Clin. Nutr. 54, 245S-260S. 

Fio. 2. Stereoscopic view of a skeletal model of RNase-S deduced from the 3.5-A resolution map and chemical sequence data. The small balls locate sulfur atoms. Die large ball hanging from the top support plate shows the van der Waals size of a paraffinic hydrogen atom. 

Fig. 21. The symbolic EF hand on the left represents helix E (forefinger), the calcium binding loop (middle finger enclosing an Ca2+C>6 octahedron), and helix F (thumb). The a-carbon skelet models of the carp MCBP EF hand (right) (after Tufty and Kretsinger203))...

A ball-and-stick drawing is a simple skeletal model, in which the representation of the bond is generalized to a cylinder, and a disc is added at the position of each atom. Additional information may thereby be displayed in that different atom types may be distinguished by size and shading, and bonds of different appearance may be drawn. To create the line segments corresponding to a pure skeletal model, one needs only copy the coordinates of each pair of bonded atoms as the line segment end-points. To create ball-and-stick pictures, one must ... 

Formal chemical bonds as lines in space represent only a drastically oversimplified representation of chemical bonding, a mere skeletal model, introduced and in use since the early days of chemistry when there was no hope yet to detect, model, visualize, and understand the intricate, fuzzy, three-dimensional features and the wealth of shape information of molecular electron densities. 

FIGURE 7. Stereo diagram of one subunit of flavocytochrome b. Only residues ln486 are shown, the remainder being involved in intermolecular interactions. The flavin-binding domain is at the top and the cytochrome domain is at the bottom. The flavin and heme groups are shown as skeletal models. 

FIGURE 8. stereo diagram of p-cresol methylhydroxylase. The flavoprotein subunit is on the left and the cytochrome subunit is on the right. The flavin-binding domain of the flavoprotein subunit is on the bottom and the catalytic domain is on the top. Skeletal models of the heme and FAD prosthetic groups are also shown. 

FIGURE 11. stereo diagram of phthalate dioxygenase reductase. The FMN- and NADPH-binding domains are on the top and the 2Fe-2S binding domain is on the bottom. The FMN and 2Fe-2S prosthetic groups are shown as skeletal models. 

FIGURE 12. Stereo diagram of the complete fimiarate reductase complex. The FAD-binding subunit is at the top, the iron-sulfur subunit is in the center and die two membrane anchoring subunits that provide die binding sites for two molecules of menaquinone are at the bottom. In this molecule electron h ansfer occiffs from menaquinone at die bottom to FAD at die top during reduction of fumarate by menaquinone. Skeletal models of two molecules of menaquinone, a 3Fe-4S, a 4Fe-4S, a 2Fe-2S, an FAD molecule and one molecule of oxalate are included. 

A wire skeletal model of lysozyme was constructed and then modified to accommodate the a-lacuilbumin sequence, by changing side chains that differ between them and by rearranging the main chain to accommodate the various deletions. 

Skeletal models. An even simpler image is achieved with a skeletal model, which shows only the molecular framework. In skeletal models, atoms are not shown explicitly. Rather, their positions are implied by the junctions and ends of bonds. Skeletal models are frequently used to depict larger, more complex structures. 

Figure 29.5. L-Shaped tRNA Structure. A skeletal model of yeast phenylalanyl-tRNA reveals the L-shaped structure. The CCA region is at the end of one arm, and the anticodon loop is at the end of the other.

Figure I.l A ball and stick model of the allyl alcohol molecule is shown. The formal bonding pattern is well recognizable in such "skeletal" models, however, the actual three-dimensional shape of the fuzzy "body" of the molecular electron density, ultimately responsible for chemical bonding, is not well represented.

It has been common practice to fit a skeletal model to the electron density map, usually by means of a Richards comparator, a device with a half-silvered mirror that enables an observer to see a reflected image of a wire model projected within the three-dimensional map.14 The model is adjusted by varying the torsional angles and in some cases distorting the interbond angles to allow for departures from ideal values, until the atoms are in positions that appear best to satisfy the electron density. It must be emphasized that the fit is a subjective one and that it is impossible to make an objective assessment. Errors in coordinates from models fit to maps at resolutions of 2-2.5 A are usually estimated to be in the 0.2- to 0.5-A range,s although errors much in excess of this may be made. 

Figure 3.18 The Watson-Crick double helical structure of DNA illustrated by the crystal structure of an oligonucleotide. (a) Skeletal model representation, in stereo (note the tilting of the base pairs in certain cases this is responsible for causing the DNA double helix to coil up, for example, into the nucleosome, a key component of the chromosome). (b) Space filling representation, in stereo, (c) Beevers molecular model. Figures kindly provided by Dr W. N. Hunter with permission.

All reverse turns where found by visual inspection of skeletal models. A computer search was then made to find other sets of four residues in which i+i, v>i+2, and were within 30 of the values for the turn. In most cases this lead to either no new turns... 

In the chicken skeletal model, the structural homology between the RLC and calmodulin was used to delineate the interaction sites (Rayment et al., 1993a). A cluster of hydrophobic residues, including phenylalanine, tryptophan, and methionine, would participate in the binding. The region of Lys-834-Gln-852 of the gizzard smooth muscle HC (Yanagisawa et al.,... 

Figure 3.8 Crystal structure of polyoxy methylene. (a) Skeletal model open circle, oxygen atom solid circle, methylene group, (b) Electron density map on a cylindrical section of radius 0.691 A, which is cut open flat for presentation purpose. (From Uchida and Tadokoro.25)...

FIGURE 1.16 Molecular representations. Comparison of (A) space-filling, (B) ball-and-stick, and (C) skeletal models of ATP. 

A third more diffuse group of resonances is those carbons bearing electron-withdrawing groups or which are allylic, e.g., C-16 in venalstonine and C-20 in tabersonine. The remaining carbons are those associated with aliphatic carbons, and in many cases close chemical shift approximations can be accomplished by application of established equations or, preferably, good skeletal models. 

Molecular models are very useful when looking at these reactions and I would recommend that every chemist interested in terpenoids should possess a set. Ball and stick models or skeletal models are more useful for following carbocation rearrangements than are space filling ones. There are many types of models available any of which will serve the purpose. The choice is up to the reader s personal preferences and budget. Models are particularly useful for those who have difficulty in visualising structures in three dimensions. 

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