Structure drawings space-filling models

Draw two isomers of 3-hexene in line notation, one with two ethyl groups on the same side of the C=C unit and one with the two ethyl groups on opposite sides of the C=C unit. Use a molecular modeling program or a model kit to show both structures as space-filling models. 

FIGURE 27 20 Heme shown as (a) a structural drawing and as (b) a space filling model The space filling model shows the coplanar arrangement of the groups surrounding iron... 

Figure 29-6 Some protein-RNA interactions within the ribosome. (A) A space-filling model of the 23S and 5S RNA with associated proteins from the ribosome of Haloarcula marismortui. The CCA ends of bound tRNA molecules in the A, P, and E sites are also included. The view is looking into the active site cleft. The proteins with e after the number are related to eukaryotic ribosomal proteins more closely than to those of E. coli.17 Courtesy of T. A. Steitz. (B) Three-dimensional structure of a 70S ribosome from Thermus thermophilus. The 30S subunit is to the right of the 50S subunit. Courtesy of Yusupov et al.33a (C) Stereoscopic view of the helix 21 to helix 23b region of the 16S RNA with associated proteins S6 (upper left), S18 (upper center, front), and S15 (lower back) from T. thermophilus. Courtesy of Agalarov et at.31 (D) Simplified in vitro assembly map of the central domain of the 30S bacterial ribosome. Courtesy of Gloria Culver. (E) Contacts of proteins with the central (platform) domain of the 16S RNA component. The sequence shown is that of Thermus thermophilus. Courtesy of Agalarov et al. (F) Three drawings showing alternative location of the four copies of protein L7/L12. The N-terminal and C-terminal...

The next most important aspect of a molecular compound is its shape. The pictorial representation of molecules that most accurately shows their shapes comes from the use of computer graphics that show computed structures. An example is the space-filling model of an ethanol molecule, shown in (5). The atoms are represented by colored spheres (they are not the actual colors of the atoms ) that fit into one another. Another representation of the same molecule, called a ball-and-stick model, is shown in (6). Each ball represents the location of an atom, and the sticks represent the bonds. Although this kind of model does not represent the actual molecular shape as well as a space-filling model, it is easier to draw and interpret. 

Each representation of a protein or nucleic acid conveys to the viewer different aspects of its structure line drawings give the bones, space-filling models the flesh, and schematic diagrams the gestalt of the design. No single representation of a protein or nucleic acid is adequate for all purposes, but the combination of several is more powerful than the total of all taken independently. 

The picture of molecules being composed of structural units, functional groups , which behave similarly in different molecules forms the very basis of organic chemistry. The drawing of molecular structures where alphabetic letters represent atoms and lines represent bonds is used universally. Organic chemists often build ball and stick, or CPK space-filling, models of their molecules to examine their shapes Force, field methods are... 

Figure 54. Drawing of the proposed helical conformation of oligomer 11 (n= 8), where R = Sn-Pr. Side (bottom left) and top (bottom right) view of the space-filling model of the crystal structure of pyridine—pyrimidine oligomer 11 (n = 8) in a helical conformation.

Fig. 4.9 Crystallographic structure of bacteriorhodopsin (A, PDB 1C3W) [64]. Trp86, Trpl82, and Tyrl 85 are shown in space-filling model together with the retinal chromophore in stick (A) or space-filling (B) drawing.

The following Lewis structure represents a molecule of formaldehyde, CH2O. Draw a geometric sketch, a ball-and-stick model, and a space-filling model for this molecule. 

The Lewis structure shows the two O-H covalent bonds and the two lone pairs on the oxygen atom. The space-filling model provides the most accurate representation of the electron charge clouds for the atoms and the bonding electrons. The ball-and-stick model emphasizes the molecule s correct molecular shape and shows the covalent bonds more clearly. The geometric sketch shows the structure with a two-dimensional drawing. 

A Figure 2.17 Different representations of the methane (CH4) moiecuie. Structural formulas, perspective drawings, ball-and-stick models, and space-filling models. 

Model and schematic representations of the DNA double helix. The space-filling model at the left shows the base pairs in the helix interior, in planes perpendicular to the main helical axis. The center drawing shows the structure more schematically, ihcluding the dimensions of the double helix. At the far right is a sohematio method for showing base pairing in the two strands. 

Draw the sawhorse diagram of syn- and anti-2,2,5,5-tetramethylhexane sighting down the C3-C4 bond. If you have access to a computer modehng program, convert this structure to its 3D structure (both a ball and a stick drawing and a space-filling model). Comment on the steric hindrence found in each rotamer. 

The molecules within these magnifications are depicted using space-filling models to help students develop the most accurate picture of the molecular world. Similarly, many molecular formulas are portrayed not only with structural formulas but with spacefilling drawings as well. Students are not meant to understand every detail of these formulas-since they are not scientists, they do not need to-rather, they should begin to appreciate the beauty and form of the molecular world. Such an appreciation will enrich their lives as it has enriched the lives of those of us who have chosen science and science education as our career paths. 

In the top part of Figure 22.20, the sugar-phosphate backbone is in red, and the bases are shown in blue. The bottom part shows you a space-filling model. Here, your perspective is of a segment of the whole molecule. Figure 22.21 is a schematic drawing similar to Figure 22.20 (top), but its purpose is to show you how the structure of DNA leads to the mechanism for its duplication. 

Figure 1. Calixcrown extractant adopted for CSSX, as complexed with Cs+ ion. Left chemical drawing of the complex. Right a space-filling view of part of a crystal structure of the model complex Cs2Calix[4]arene-bis(benzo-crown-6)(N03)2 3CHCl3 [69] showing the good fit of the Cs+ ion inside the calixarene cavity the crown ether atoms have been removed for clarity.

Figure IIB. A space-filling representation of the framework drawing of psilocin depicted in Figure llA. The molecular structures depicted in the figures in this chapter are two-dimensional, line-drawing representations of the molecules that show how the atoms are connected and allow for ready comparison of similarity between molecules. Molecules actually have three-dimensional shapes in which each of the constituent atoms occupies a volume defined by its cloud of electrons. Linus Pauling and two of his colleagues, Robert Corey and Walter Koltun, first developed a form of molecular models to depict the 3-dimensional space-filling aspect of molecules in the way shown in this figure.

Fig. 6.4 A d-dimensional copolymer model in absence of self-interactions, that is a non-directed walk in a d-dimensional space filled with two solvents (above and below one of the (hyper-)planes of the reference system), may be reduced to a (1 -t l)-directed walk model, since the energy depends only on the sign of the component of S perpendicular to the (hyper-)plane. In the figure we draw on the left a walk in a two-dimensional space the increments are uniformly distributed on a circumference of fixed radius. The walk is then mapped on the right to a directed walk, by projecting on the vertical component. Of course the distribution of the increments of the directed walk is easily computed. We stress that the substantial difference between the resulting model and the one we have treated is that the walk crosses the interface without touching it, so in order to mimic the procedure we have used up to now, one has to introduce a more complex renewal structure, for example the sequence of successive visits to the opposite half-plane and the corresponding overshoot variables.

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