Shapes of Larger Molecules

Although the molecules and ions we have considered contain only a single central atom, the VSEPR model can be extended to more complex molecules. For the acetic acid molecule, for example, 

Electron-domain geometry Tetrahedral Trigonal planar Tetrahedral 

The structure of the acetic acid molecule is shown in FIGURE 9.9. 

Eyedrops for dry eyes usually contain a water-soluble polymer called poly(vinyl alcohol), which is based on the unstable organic molecule vinyl alcohol  

Predict the approximate values for the H—O—C and O—C—C bond angles in vinyl alcohol. 

With larger molecules than the ones we have been considering, we usually do not specify a shape for the entire molecule. Instead, we describe the shape around each of the main atoms in the structure. For example, in methyl alcohol we say that the shape around the carbon atom is tetrahedral and the shape around the oxygen atom is bent. 

The air we breathe is a mixture of many gases. Mostly air consists of O, Ar, and water 

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Shapes of larger molecules are composites of the shapes around each central atom. 

Predicting the Shapes of Larger Molecules (10.4) Example 10.4 For Practice 10.4 Exercises 41-42, 45-46... 

Reasonable prediction can be made of the permeabiUties of low molecular weight gases such as oxygen, nitrogen, and carbon dioxide in many polymers. The diffusion coefficients are not compHcated by the shape of the permeant, and the solubiUty coefficients of each of these molecules do not vary much from polymer to polymer. Hence, all that is required is some correlation of the permeant size and the size of holes in the polymer matrix. Reasonable predictions of the permeabiUties of larger molecules such as flavors, aromas, and solvents are not easily made. The diffusion coefficients are complicated by the shape of the permeant, and the solubiUty coefficients for a specific permeant can vary widely from polymer to polymer. 

Dispersion forces increase in strength with the number of electrons, because larger electron clouds are more polarizable than smaller electron clouds. For molecules with comparable numbers of electrons, the shape of the molecule makes an important secondary contribution to the magnitude of dispersion forces. For example. Figure 11-11 shows the shapes of pentane and 2,2-dimethylpropane. Both of these molecules have the formula C5 H12, with 72 total electrons. Notice that 2,2-dimethylpropane has a more compact structure than pentane. This compactness results in a less polarizable electron cloud and smaller dispersion forces. Accordingly, pentane has a boiling point of 36 °C, while 2,2-dimethylpropane boils at 10 °C. 

Exclusion chromatography separates solutes that differ in size and shape. The technique is used extensively in the investigation of macromolecules and in the separation of small molecules from an interfering matrix of larger molecules. 

One potential problem that can occur with slightly larger molecules (typically of m.w. > 600) is that the NOE response in both NOE and 2-D (NOESY) experiments is related to the tumbling rate of molecules in solution. The larger the molecule, the slower it will tumble and at a certain point, all expected enhancements will be nullified. This null point depends not only on the tumbling rate (and therefore the size, or more accurately, the shape of the molecule) but also on the field strength of the... 

Tn spite of intensive research by countless numbers of capable scientists for the past 30 years our methods for precise separation and characterization of larger molecules do not have the discrimination needed to solve many of the problems now posed by what we have already learned about the behavior of such substances. This is true even with naturally occurring biopolymers where the amazing selectivity of the synthetic processes of living tissues permits the isolation of preparations which show the behavior expected if the individual molecules of the preparation should be really all of the same size, shape, and composition. Research with biopolymers can therefore be considered in a different category from that so important for industrial polymers since in many cases it relates to single molecular species. The importance of the latter point depends... 

In the larger peptide antibiotic compounds comprising the class of lantibiotics, the shape of the molecule is determined by several cyclic peptides, including two annulated peptide rings, present within one molecule, giving the lantibiotic a unique way to interact with the target molecule lipid II and subsequent pore-forming capabilities in phospholipid membranes [2]. 

Estimates of X (i.e. when A, is assumed to be 0) using eqn (52) or more complicated versions thereof (78) have turned out to be somewhat less than successful. It is usually difficult to use the spherical approximation (Fig. 4) for the shape of organic molecules, and other, more complex treatments produce problems of their own. Thus the intuitively satisfying model for electron transfer between two aromatic species, parallel orientation of the molecular planes at collision distance, cannot be fitted to the triaxial ellipsoidal model discussed in Section 4. Instead, one has to assume that electron transfer takes place over a considerably larger distance. This expansion of the transition state seems to be fairly constant for different compounds and can be included as an ad hoc (at least at present) parameter in the calculation of X. 

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