Ball-and-stick three-dimensional representation

Figure 9.4 Ball and stick three-dimensional representation of PTFE.

Figure 11.29 Ball-and-stick three-dimensional representation of fluorinated ethylene propylene (FEP). Table 11.8 MIT Fold Endurance of Chemours Teflon FEP Resins [14]...

Figure 31-6 Three-dimensional ribbon representation of the structure of a complex of a soluble Fc fragment of a human IgGl molecule. Pro 329 of the IgG and Trp 87 and Trp 110 of the Fc-receptor fragment form a "proline sandwich/ which is shown in ball-and-stick form. The oligosaccharide attached to the Fc fragment of the antibody and the disulfide bridge between the two Cys 229 residues (at the N termini of the C2 domains of the heavy y chains) are also shown. The small spheres on the Fc receptor fragment are potential sites for N-glycosylation. From Sondermann et al.107 Courtesy of Uwe Jacob.

Furthermore, when modern tools for determining organic structures that involve actually measuring the distances between the atoms became available, these provided great convenience, but no great surprises. To be sure, a few structures turned out to be incorrect because they were based on faulty or inadequate experimental evidence. But, on the whole, the modern three-dimensional representations of molecules that accord with actual measurements of bond distances and angles are in no important respect different from the widely used three-dimensional ball-and-stick models of organic molecules, and these, in essentially their present form, date from at least as far back as E. Paterno, in 1869. 

What is the relationship between stereoisomers 19-22 This will be clearer if we translate each of the projection formulas into a three-dimensional representation, as shown in Figure 5-13. You will be helped greatly if you work through the sequence yourself with a ball-and-stick model. Drawn as Newman projections, 19-22 come out as shown in 19a-22a ... 

Figure 4.11. Graphic representations of protein 3D structure. Three-dimensional graphics of hen s egg-white lysozyme as visualized with RasMol (first and second rows, ILYZ.pdb) and Cn3D (third row, ILYZ.val) are shown from left to right (color type) in wireframe (atom), spacefill (atom), dots (residue), backbone (residue), ribbons (secondary structure), strands (secondary structure), secondary structure (secondary structure), ball-and-stick (residue), and tubular (domain) representations.

A structural model is a three-dimensional representation of the structure of a compound. There are two kinds of structural models ball-and-stick models and space-filling models. Figure 13.6 shows ball-and-stick models for the five isomers of C6Hi4. Notice that they show how the carbon and hydrogen atoms are bonded within the structures. 

Fig. 7.1 The tetramer of eco bound to a serine protease. Visualized as a cartoon of the canonical protease and eco interaction (a), and (b), as two views of the three dimensional solution of D102N trypsin in complex with eco [3]. Each eco molecule has three protein-protein interaction surfaces. The C-terminus forms an anti-parallel p ribbon to complete the ecotin dimer interface. The 80 s and 50 s loops form the primary binding site by interacting with the protease at the active site cleft in a sub-strate-like y -sheet conformation. The 60 s and lOO s loops of eco form the secondary binding site by interacting with the C-termi-nal a-helix of the protease. Note that each eco molecule contacts both of the protease molecules. Two eco molecules (black and medium grey) form a pair of interactions each with two protease molecules (light grey). The catalytic triad residues Ser-195, Asp-102 and His-57 are in black ball and stick representation. This figure was made with Molscript [37] and Raster 3D [38].

Fig. 7.4 The three-dimensional fold of three serine proteases, (a) Fiddler crab collagenase defined in complex with WT eco, (b) rat gran-zyme B in complex with [81-84 lEPD] eco, and (c) human factor Xa in complex with M84Reco. Each protease is shown in grey. The catalytic triad and amino acids contacting the ecotin molecule in the active site are shown in grey ball and stick representation. The ecotin mol-...

The three-dimensional representations and the ball-and-stick models for these alkanes indicate the tetrahedral geometry around each carbon atom. In contrast, the Lewis structures are not meant to imply any three-dimensional arrangement. Moreover, in propane and higher molecular weight alkanes, the carbon skeleton can be drawn in a variety of different ways and still represent the same molecule. 

Figure 9.6. Three-Dimensional Structure of Chymotrypsin. The three chains are shown in ribbon form in orange, blue, and green. The side chains of the catalytic triad residues, including serine 195, are shown as ball-and-stick representations, as are two intrastrand and interstrand disulfide bonds.

Figure 21-2 Representations of a molecule of methane, CH4. (a) The condensed and Lewis formulas for methane, (b) The overlap of the four sp carbon orbitals with the s orbitals of four hydrogen atoms forms a tetrahedral molecule, (c) A ball-and-stick model, (d) a space-filling model of methane, and (e) a three-dimensional representation that uses the wedged line to indicate a bond coming forward and a dashed line to represent a bond projecting backward.

Representations of the three-dimensional structure of methane, CH4. (a) Tetrahedral methane structure, (b) Ball and stick model of tetrahedral methane, (c) Three-dimensional representation of structure (b). 

Three-dimensional (3D) Shapes and Dynamics of Some Alkanes Before proceeding, it is worthwhile to appreciate the pretty 3D shapes of some alkanes. Figures 4.1a-c show ethane, propane, and butane using a ball-and-stick representation. 

What is lacking in these structures, however, is the three dimensionality of the molecule, which for 2-methylbutane is shown by the ball-and-stick molecular model in Figure 16.3(d). Depending on the purpose of the discussion, any of these representations can be used to describe the properties of the molecule. 

There are other ways with varying emphases and economy of ink. The digital representations are not confined to two dimensions (2D). Ball-and-stick and spacefilling assemblies capture the molecular information in a three-dimensional (3D) way. Computer graphics portray the electronics in 2D by transmitting the illusion of 3D. 

Figure 13.6 Conventions used for drawing three-dimensional ball-and-stick representations of molecules. 

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