Hydrocarbon frameworks
Carbon as an element is unique in the variety of structures it can form. It is unusual because it forms strong, stable bonds to the majority of elements in the periodic table, including itself. It is this ability to form bonds to itself that leads to the variety of organic structures that exist, and indeed to the possibility of life existing at all. Carbon may make up only 0.2% of the earth’s crust, but it certainly deserves a whole branch of chemistry all to itself.
Chains
The simplest class of hydrocarbon frameworks contains just chains of atoms. The fatty acids we met earlier have hydrocarbon frameworks made of zig-zag chains of atoms, for example. Polythene is a polymer whose hydrocarbon framework consists entirely of chains of carbon atoms. The wiggly line at each end of this structure shows that we have drawn a piece in the middle of the polythene molecule. The structure continues indefinitely beyond the wiggly lines.
At the other end of the spectrum of complexity is this antibiotic, extracted from a fungus in 1995 and aptly named linearmycin as it has a long linear chain. The chain of this antibiotic is so long that we have to wrap it round two corners just to get it on the page.
We haven’t drawn whether the CH3 and OH groups are in front of or behind the plane of the paper because, at the time of writing this book, the stereochemistry of linearmycin is unknown.
Names for carbon chains
It is often convenient to refer to a chain of carbon atoms by a name indicating its length. You have probably met some of these names before in the names of the simplest organic molecules, the alkanes. There are also commonly used abbreviations for these names: these can be very useful in both writing about chemistry and in drawing chemical structures, as we shall see shortly.
You may notice that the abbreviations for the names of carbon chains look very much like the symbols for chemical elements: this is deliberate, and these symbols are sometimes called ‘organic elements’. They can be used in chemical structures just like element symbols. It is often convenient to use the ‘organic element’ symbols for short carbon chains for tidiness.
Here are some examples. Structure 1 to the right shows how we drew the structure of the amino acid methionine on p. 20. The stick representing the methyl group attached to the sulfur atom does, however, look a little odd. Most chemists would draw methionine as structure 2, with ‘Me’ representing the CH3 (methyl) group. Tetraethyllead used to be added to petrol to prevent engines ‘knocking’, until it was shown to be a health hazard. Its structure (as you might easily guess from the name) is easy to write as PbEt4 or Et4Pb.
Remember that these symbols (and names) can be used only for terminal chains of atoms. We couldn’t abbreviate the structure of lysine to 3, for example, because Bu represents 4 and not 5.
Before leaving carbon chains, we must mention one other very useful organic element symbol, R. R in a structure can mean anything—it’s a sort of wild card. For example, structure 6 would indicate any amino acid, if R = H it is glycine, if R = Me it is alanine. . . As we’ve mentioned before, and you will see later, the reactivity of organic molecules is so dependent on their functional groups that the rest of the molecule can be irrelevant. In these cases, we can choose just to call it R.
Carbon rings
Rings of atoms are also common in organic structures. You may have heard the famous story of Auguste Kekulé first realizing that benzene has a ring structure when he dreamed of snakes biting their own tails. You have met benzene rings in phenylalanine and aspirin. Paracetamol also has a structure based on a benzene ring.
When a benzene ring is attached to a molecule by only one of its carbon atoms (as in phenylalanine, but not paracetamol or aspirin), we can call it a ‘phenyl’ group and give it the organic element symbol Ph.
While Ph always means C6H5, Ar can mean any substituted phenyl ring, in other words phenyl with any number of the hydrogen atoms replaced by other groups. Of course Ar = argon too but there is no confusion as there are no organic compounds of argon.
Like R, the ‘wild card’ alkyl group, Ar is a ‘wild card’ aryl group. The compound known as muscone has only relatively recently been made in the laboratory. It is the pungent aroma that makes up the base-note of musk fragrances. Before chemists had determined its structure and devised a laboratory synthesis the only source of musk was the musk deer, now rare for this very reason. Muscone’s skeleton is a 13-membered ring of carbon atoms.
The steroid hormones have several (usually four) rings fused together. These hormones are testosterone and oestradiol, the important human male and female sex hormones.
Some ring structures are much more complicated. The potent poison strychnine is a tangle of interconnecting rings.
One of the most elegant ring structures is shown above and is known as buckminsterfullerene. It consists solely of 60 carbon atoms in rings that curve back on themselves to form a football-shaped cage. Count the number of bonds at any junction and you will see they add up to four so no hydrogens need be added. This compound is C60. Note that you can’t see all the atoms as some are behind the sphere.
Rings of carbon atoms are given names starting with ‘cyclo’, followed by the name for the carbon chain with the same number of carbon atoms. Structure 1 shows chrysanthemic acid, part of the naturally occurring pesticides called pyrethrins (an example appears in Chapter 1), which contains a cyclopropane ring. Propane has three carbon atoms. Cyclopropane is a three-membered ring. Grandisol (structure 2), an insect pheromone used by male boll weevils to attract females, has a structure based on a cyclobutane ring. Butane has four carbon atoms. Cyclobutane is a four-membered ring. Cyclamate (structure 3), formerly used as an artificial sweetener, contains a cyclohexane ring. Hexane has six carbon atoms. Cyclohexane is a sixmembered ring.
Branches
Hydrocarbon frameworks rarely consist of single rings or chains, but are often branched. Rings, chains, and branches are all combined in structures like that of the marine toxin palytoxin that we met at the beginning of the chapter, polystyrene, a polymer made of sixmembered rings dangling from linear carbon chains, or of β-carotene, the compound that makes carrots orange.
Just like some short straight carbon chains, some short branched carbon chains are given names and organic element symbols. The most common is the isopropyl group. Lithium diisopropylamide (also called LDA) is a strong base commonly used in organic synthesis.
Iproniazid is an antidepressant drug with i-Pr in both structure and name. ‘Isopropyl’ may be abbreviated to i-Pr, iPr, or Pri. We shall use the first in this book, but you may see the others used elsewhere.
Isomers are molecules with the same kinds and numbers of atoms joined up in different ways. n-propanol, n-PrOH, and isopropanol, i-PrOH, are isomeric alcohols. Isomers need not have the same functional groups—these compounds are all isomers of C4H8O:
The isobutyl (i-Bu) group is a CH2 group joined to an i-Pr group. It is i-PrCH2–. Two isobutyl groups are present in the reducing agent diisobutyl aluminium hydride (DIBAL). The painkiller ibuprofen (marketed as Nurofen®) contains an isobutyl group. Notice how the invented name ibuprofen is a medley of ‘ibu’ (from i-Bu for isobutyl) + ‘pro’ (for propyl, the threecarbon unit shown in brown) + ‘fen’ (for the phenyl ring). We will talk about the way in which compounds are named later in this chapter.
There are two more isomers of the butyl group, both of which have common names and abbreviations. The sec-butyl group (s-butyl or s-Bu) has a methyl and an ethyl group joined to the same carbon atom. It appears in an organolithium compound, sec-butyl lithium, used to introduce lithium atoms into organic molecules.
The tert-butyl group (t-butyl or t-Bu) group has three methyl groups joined to the samecarbon atom. Two t-Bu groups are found in butylated hydroxy toluene (BHT E321), an antioxidant added to some processed foods.
Primary, secondary, and tertiary The prefixes sec and tert are really short for secondary and tertiary, terms that refer to the carbon atom that attaches these groups to the rest of the molecular structure.
This quick architectural tour of some of the molecular edifices built by nature and by humans serves just as an introduction to some of the hydrocarbon frameworks you will meet in the rest of this chapter and 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 explain why it is that their attributes are the key to understanding organic chemistry.
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