Hydrocarbon frameworks and functional groups

Some molecular structures are shown below. These molecules are aU amino acids, the constituents of proteins. Look at the number of carbon atoms in each molecule and the way they are bonded together. Even within this small class of molecules there s great variety—glycine nd alaninehaxe only 

In methionine the atoms are arranged in a single chain in leucine the chain is branched. In proliney the chain bends back on itself to form a ring. 

That isn t to say the carbon atoms aren t important they just play quite a different role from those of the oxygen, nitrogen, and other atoms they are attached to. We can consider the chains and rings of carbon atoms we find in molecules as their skeletons, which support the functional groups and allow them to take part in chemical interactions, much as your skeleton supports your internal organs so they can interact with one another and work properly, 

We will see later how the interpretation of organic structures as hydrocarbon frameworks supporting functional groups helps us to understand and rationalize the reactions of organic molecules. It also helps us to devise simple, clear ways of representing molecules on paper. You saw in Chapter 1 how we represented molecules on paper, and in the next section we shall teach you ways to draw (and ways not to draw) molecules—the handwriting of chemistry. This section is extremely important, because it will teach you how to communicate chemistry, clearly and simply, throughout your life as a chemist. 

Below is another organic structure—again, you may be familiar with the molecule it represents it is a fatty acid commonly called linoleic acid. 

We shall return to amino acids as examples several times In this chapter, but we shall leave detailed discussions about their chemistry till Chapters 24 and 49, when we look at the way in which they polymerize to form peptides and proteins, 

You may well have seen diagrams like these last two in older books—they used to be easy to print (in the days before computers) because all the atoms were in a line and all the angles were 90°. But are they realistic We will consider ways of determining the shapes and structures of molecules in more detail in Chapter 3, but the picture below shows the structure of linoleic acid determined by X-ray crystallography. 

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Here, then, is one rationalization of the observation that reactive sites in molecules are normally associated with functional groups. The bromine atom confers polarity on an otherwise effectively non-polar hydrocarbon framework, and ionic reagents might be expected to react at polar sites for electrostatic reasons. 

Although allylic brommations and chlormations offer a method for attaching a reactive functional group to a hydrocarbon framework we need to be aware of two important limitations For allylic halogenation to be effective m a particular synthesis... 

Aliphatic compounds comprise hydrocarbons and their derivatives in which the molecular skeletons consist of tetrahedral carbon atoms connected by C-C single bonds. These tetrahedral carbon atoms can be arranged as chains, rings, or finite frameworks, and often with an array of functional groups as substituents on various sites. The alkanes CMH2n+2 and their derivatives are typical examples of aliphatic compounds. 

The hydrocarbon framework is made up of chains and rings of carbon atoms, and it acts as a support for the functional groups. 

Because functional groups are the key to the chemistry of molecules, clear diagrams must emphasize the functional groups, and let the hydrocarbon framework fade into the background. Compare the diagrams below ... 

When you draw diagrams like these to indicate the three-dimensional shape of the molecule, try to keep the hydrocarbon framework in the plane of the paper and allow functional groups and other branches to project forwards out of the paper or backwards into it,... 

This quick architectural tour of some of the molecular edifices built by nature and by man serves justas an introduction to some of the hydrocarbon frameworks you will meet in the rest of this chap-ter and of this book. Yet, fortunately for us, however complicated the hydrocarbon framework might be, it serves only as a support for the functional groups. And, by and large, a functional group in one molecule behaves in much the same way as it does in another molecule. What we now need to do, and we start in the next section, is to introduce you to some functional groups, and to explain why it is that their attributes are the key to understanding organic chemistry. 

These four functional groups have similar properties—though alkyl iodides are the most reactive and alkyl fluorides the least. PVC (polyvinyl chloride) is one of the most widely used polymers—it has a chloro group on every other carbon atom along a linear hydrocarbon framework. Methyl iodide (Mel), on the other hand, is a dangerous carcinogen, since it reacts with DNA and can cause mutations in the genetic code. 

Systematic names can be divided into three parts one describes the hydrocarbon framework one describes the functional groups and one indicates where the functional groups are attached to the skeleton. 

Draw good diagrams of saturated hydrocarbons with seven carbon atoms having (a) linear, (b) branched, and (c) cyclic frameworks. Draw molecules based on each framework having both ketone and carboxylic acid functional groups. 

The hydrocarbon framework of organic molecules is unreactive. Functional groups such as NH2 and OH are nucleophilic because they have nonbonding lone pairs. Carbonyl compounds and alkyl halides are electrophilic functional groups because they have low-energy LUMOs (it for 0=0 and G for C-X, respectively). 

Nonactivated tertiary hydrocarbon sites of enantiopure compounds 210 are oxyfunctionalized enantiospecifically by perfluoro-a.r-2- -butyl-3- -propyloxaziridine 80 under remarkably mild reaction conditions (Equation 8) <19990L281>. The reaction occurs with retention of the configuration at the oxidized stereogenic center and the enantiospecificity is highly independent of both the carbon framework of the substrate as well as functional groups (Table 16). 

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