Ball-and-stick three-dimensional

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

Phthalic Acid. While catechol and sahcylate could chelate individual titanium sites, phthaUc acid isomers are more likely to inteact with two diffeent surface Ti sites, due to the position of the two carboxylic add groups. Figure 21 -7 shows a proposed ball and stick three-dimensional molecular model of surface Ti complexation by phthalic add (Moser, 1991). 

Figure 21-7. Proposed ball and stick three-dimensional molecular model for surface Ti(lV) complexation by phthalic acid isomers (taken with permission from Moser, 1991).

Figure 2.11 The molecuiar structure of the enantiomers of limonene (a, c) the chemical structure and ball-and-stick three-dimensional model of S-limonene (b, d) corresponding illustrations for R-limonene.

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]...

A molecule is a three-dimensional array of atoms. In fact, many of a molecule s properties, such as its odor and chemical reactivity, depend on its three-dimensional shape. Although molecular and structural formulas describe the composition of a molecule, they do not represent the molecule s shape. To provide information about shapes, chemists frequently use ball-and-stick models or space-filling models. 

Chemists use a variation on the ball-and-stick model to depict more clearly the three-dimensional character of molecules, as shown for methane in Figure 9-1 Icf. The central carbon atom is placed in the plane of the paper, hi these models, solid lines represent bonds lying in the plane of the paper, solid wedges represent bonds that protmde outward from the plane of the paper, and dashed wedges represent bonds extending backward, behind the plane. 

Lewis structure and ball-and-stick models of ethane (a) and propane (b). All the carbon atoms have tetrahedral shapes, because each has four pairs of electrons to separate in three-dimensional space. 

A) Three-dimensional structural diagram of the hromochloromethane molecule, BrCICH2 (B) Ball-and-stick model... 

Visualization of conformers There are four conventional methods for visualization of three-dimensional structures on paper. These are the ball and stick method, the sawhorse method, the wedge and broken line method and the Newman projection method. Using these methods, the staggered and eclipsed conformers of ethane can be drawn as follows. 

It is convenient for many purposes to have models available for inspection in order to realize fully the three-dimensional aspect of molecular and lattice structures. "Bafl-and-stick" models of various stages of sophistication are useful when it is necessary to be able to see through the structure under consideration. Space-filling models of atoms with both covalent and van der Waals radii are particularly helpful when steric effects are important. The space-filling models and the more sophisticaied stick models tend to be rather expensive, but there are several inexpensive modifications of the "ball-and-stick type available. It is extremely useful to have such a set at hand when considering molecular structures. 

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. 

Use ball-and-stick models or suitable three-dimensional drawings to determine which members of the following sets of formulas represent identical compounds, provided free rotation" is considered to be possible around all single bonds (except when these bonds are present in a cyclic structure) ... 

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 ... 

Look at the following computer-generated ball-and-stick models of water, ammonia, and methane. Each of these molecules—and every other molecule as well— has a specific three-dimensional shape. Often, particularly for biologically important molecules, three-dimensional shape plays a crucial part in determining the molecule s chemistry. 

The polymerized 2-cyano acrylate (n=8) shown in Fig. 2.15a is a simple model to demonstrate a polymer of n=8, and the correct atom-bond configuration of substituents and conformational molecular structure is shown in Fig. 2.15b in a planar or two-dimensional form, and the three-dimensional stick and ball models in Fig. 2.16a and b rotated about the T-axis 90°. 

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.

Fig. 8. MolScript (Kraulis, 1991) diagram of the three-dimensional structure of />NB esterase variant 8G8 (Spiller et al., 1999). Mutated residues are shown in black ball-and-stick. Catalytic residues are shown in white ball-and stick. Black portions indicate stabilized loop regions.

C A ball-and-stick model shows atoms as spheres and bonds as sticks. It accurately shows how the bonds within a molecule are oriented in three-dimensional space. The distances between the atoms are exaggerated, however. In this model, you can see the differences in the shapes of carbon dioxide and water. 

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. 

Ball-and-stick models showing the three-dimensional structures of cellulose and starch were given in Figure 5.2. 

The illustration program is a key component of the visual emphasis in Organic Chemistry. Besides traditional skeletal (line) structures and condensed formulas, there are numerous ball-and-stick molecular models and electrostatic potential maps to help students grasp the three-dimensional structure of molecules (including stereochemistry) and to better understand the distribution of electronic change. 

Figure 3.44. Three-Dimensional Structure of Myoglobin. (A) This ball-and-stick model shows all nonhydrogen atoms and reveals many interactions between the amino acids. (B) A schematic view shows that the protein consists largely of a helices. The heme group is shown in black and the iron atom is shown as a purple sphere. 

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