Three-dimensional shape

Table 1 3 lists the dipole moments of various bond types For H—F H—Cl H—Br and H—I these bond dipoles are really molecular dipole moments A polar molecule has a dipole moment a nonpolar one does not Thus all of the hydrogen halides are polar molecules To be polar a molecule must have polar bonds but can t have a shape that causes all the individual bond dipoles to cancel We will have more to say about this m Section 1 11 after we have developed a feeling for the three dimensional shapes of molecules... 

So far we have emphasized structure in terms of electron bookkeeping We now turn our attention to molecular geometry and will see how we can begin to connect the three dimensional shape of a molecule to its Lewis formula Table 1 6 lists some simple com pounds illustrating the geometries that will be seen most often m our study of organic chemistry... 

Use your Learning By Modeling software to reproduce the models shown in Figure 2 7 so that you can better view their three dimensional shapes... 

FIGURE 2 13 Tube (top) and space filling bottom) models of (a) pentane (b) 2 methylbutane and (c) 2 2 dimethylpropane The most branched isomer 2 2 dimethylpropane has the most compact most spherical three dimensional shape... 

In this chapter we explored the three dimensional shapes of alkanes and cycloalkanes The most important point to be taken from the chapter is that a molecule adopts the shape that minimizes its total strain The sources of strain m alkanes and cycloalkanes are... 

The three dimensional shapes of many proteins are governed and stabilized by S—S bonds connecting what would ordinarily be remote segments of the molecule We 11 have more to say about these disulfide bridges m Chapter 27... 

Some heavier gauge flexible materials, usually containing nylon, are thermoformed, ie, heated and formed into three-dimensional shapes. Such stmctures are used to provide high gas-barrier, heat-sealable containment for processed meat or cheese. 

Newer resins include polysulfone, polyethersulfone, polyetherimide, and polyetherketone. Some of these newer materials are high temperature thermoplastic, not thermoset, resins. They are being promoted for the design of injection-molded printed circuit boards in three-dimensional shapes for functional appHcations as an alternative to standard flat printed circuit boards. Only semiadditive or fully additive processing can be used with these devices. 

Avery s studies shed light on the function of DNA. Chargaff s touched on structure in that knowing the distribution of A, T, G, and C in DNA is analogous to knowing the fflnino acid composition of a protein, but not its sequence or three-dimensional shape. 

When the polypeptide chains of protein molecules bend and fold in order to assume a more compact three-dimensional shape, a tertiary (3°) level of structure is generated (Figure 5.9). It is by virtue of their tertiary structure that proteins adopt a globular shape. A globular conformation gives the lowest surface-to-volume ratio, minimizing interaction of the protein with the surrounding environment. 

The Ball and Wire model is identical to the Wire model, exeept that atom positions are represented by small spheres. This makes it possible to identify all atom locations in all molecules. The Tube model is identical to the Wire model, except that bonds, whether single, double or triple, are represented by single colored tubes. The tubes are useful because they better eonvey the three-dimensional shape of a molecule. The Ball and Spoke model is a variation on the Ibbe model atom positions are represented by colored spheres, making it possible to see all atom locations in all molecules. 

The present review intends to be illustrative rather than comprehensive, and focuses on the results of this study leading to the hypothesis 9 — the three-dimensional shape similarity between interacting groups in reacting molecules is responsible for more specific and precise molecular recognition than would otherwise be achieved — and on the explanation of biological recognition on this basis. 

The similarity recognition hypothesis presented here would be applicable to the specific and precise discrimination in chemical and biological systems. It is hoped that this review will serve to stimulate further work on the physicochemical origin of the shape-similarity effect on specific molecular recognition, for example, work on weak interactions specific for the three-dimensional shape of interacting groups. 

The two individual line-bond structures for acetate are called resonance forms, and their special resonance relationship is indicated by the doubleheaded arrow between them. The only difference between resonance forms is the placement of the r and nonbonding valence electrons. The atoms themselves occupy exactly the same place in both resonance forms, the connections between atoms are the same, and the three-dimensional shapes of the resonance forms are the same. 

Cyclohexane adopts a strain-free, three-dimensional shape, called a chair conformation because of its similarity to a lounge chair, with a back, a seat, and a footrest (Figure 4.7). Chair cyclohexane has neither angle strain nor torsional strain—all C—C-C bond angles are near 109°, and all neighboring C-H bonds are staggered. 

I The tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape. 

Figure 26.7 A representation of protein denaturation. A globular protein loses its specific three-dimensional shape and becomes randomly looped.

Proteins have four levels of structure. Primary structure describes a protein s amino acid sequence secondary structure describes how segments of the protein chain orient into regular patterns—either a-helix or /3-pleated sheet tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape and quaternary structure describes how individual protein molecules aggregate into larger structures. 

Conformation (Section 3.6) The three-dimensional shape of a molecule at any given instant, assuming that rotation around single bonds is frozen. 

A note on good practice Dashed and solid wedge-shaped bonds are commonly used when displaying organic structures to convey a sense of the three-dimensional shapes. The dashed wedge-shaped bonds go into the page and the solid wedge-shaped bonds come toward us. The thin lines are in the plane of the paper. 

The three-dimensional shape or structure of a polymer is dependent on the shape and type of monomer and the ways the monomers are hnked together. A linear polymer is one in which the monomers are connected in a chainlike manner. Although called linear, such polymers should not be thought of as straight lines. They form random coils as seen in a plate of spaghetti. 

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. 

C07-0084. The conventional method of showing the three-dimensional shape of an orbital is an electron contour surface. What are the limitations of this representation ... 

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