Organic moleculesstructure and chemistry

Organic matter and organic compounds are integral components of all environmental reservoirs; it is therefore important to understand some of the basic facts about their structure and chemistry. Organic molecules contain carbon, hydrogen and often some other non-metallic elements such as oxygen, nitrogen, sulphur or halogens such as chlorine. Organic molecules are often complex structures, typically a skeleton of carbon atoms arranged in chains, branched chains or rings. It is more convenient to draw these complex structures as a simple picture (Fig. 2.4) rather than write the formula. The atoms in organic molecules are usually held together by covalent bonds, depicted as lines joining atoms (Section 2.3.1 & Fig. 2.4).

The simplest organic compounds contain only hydrogen atoms bonded to the carbon skeleton and are known as hydrocarbons, for example methane, the main

Fig. 2.4 Organic molecules. (a) Methane. (b) Ethane. (c) Ethene—note the double bond. (d) Benzene—the double bonds become delocalized so may be symbolized by a circle. It is conventional to omit the H atoms from pictorial representations of benzene. Compounds based on benzene are called aromatic compounds, for example (e) benzo[«]pyrene—a polycyclic aromatic hydrocarbon (PAH). The benzene ring is particularly stable, which enables it to be the building block of larger molecules such as this one. See also Figs 3.4, 4.28 and 4.34.

constituent of natural gas (Fig. 2.4a). When all the carbon atoms in a compound are joined by single bonds (Section 2.3.1) the structure is called aliphatic or saturated. Simple straight-chain aliphatic hydrocarbons are known as normal alkanes (n-alkanes), for example ethane (Fig. 2.4b). Molecules that contain one or more double-bonded (Section 2.3.1) carbon atoms are known as unsaturated molecules. Ethene is an example (Fig. 2.4c), but you are probably more familiar with the term unsaturated in relation to fats in foods. A particularly stable structure forms when double-bonded (Section 2.3.1) carbon atoms alternate with single bonded carbon atoms, i.e.:

It is easy to imagine this structure bent around upon itself into a ring or cycle, such that the first carbon atom in the chain also bonds with the sixth carbon atom (Fig. 2.4d). These six-carbon cyclic structures are very common and are known as aromatic compounds as many of them have a distinctive odour. Benzene is the simple hydrocarbon with this ring structure (Fig. 2.4d); it can be formally described as an unsaturated aromatic hydrocarbon. It is possible for stable aromatic rings of this type to be fused together into larger multiple ring structures. These complex but stable structures are known as polycyclic. The polycyclic aromatic hydrocarbons or PAHs (e.g. benzo[«]pyrene, Fig. 2.4e) are becoming quite familiar in well-publicized cases of urban air pollution (see Section 3.7). The presence of aliphatic or aromatic hydrocarbon groups in a molecule are often denoted by the symbol, R, when the specific identity of the molecule is unimportant (e.g. see eqns. 4.9 & 4.10).

To simplify the depiction of organic molecules it is usual not to label each carbon and hydrogen atom of the basic structure. Hydrogen atoms are usually omitted, while the position of each carbon atom in the 'skeleton' is indicated by the change in angle of the line drawing (Fig. 2.4d). Also, quite often, the bond system of aromatic rings is represented as a circle (Fig. 2.4d). This shows that the bonds are delocalized, i.e. the bonds between all the six carbon atoms are identical and intermediate in strength between single and double bonds.

2.7.1 Functional groups

Atoms of other elements, typically oxygen, nitrogen and sulphur, are incorporated into the basic hydrocarbon structures, usually as peripheral components known as functional groups (Table 2.1). Each functional group confers specific properties on the compound, and can be a major factor in determining the chemical behaviour of the compound. Functional groups include the hydroxyl (-OH), carboxyl (-COOH), amino (-NH2) and nitro groups (-NO2). The -OH and

Table 2.1 Important functional groups in environmental chemistry. Modifed from Killops and Killops (1993). Reproduced with kind permission of the authors.


Group name

Resulting compound name



Alcohol (R = aliphatic group)

Phenol (R = aromatic group)



Aldehyde (R = H)


Ketone (R = aliphatic or aromatic group)

—C = O


Carboxylic acid










* Ethers make bonds in biopolymers such as cellulose (see Box 4.11).

* Ethers make bonds in biopolymers such as cellulose (see Box 4.11).

-COOH functional groups, for example, increase the polarity of the molecule (see Box 4.14), increasing its aqueous solubility. Organic molecules are often described collectively by the functional groups they contain, for example the car-boxylic acids all contain -COOH, an example being ethanoic (acetic) acid:

carboxyl group

The word acid indicates that these substances act as a weak acid (see Box 3.3) in water, releasing H+ by dissociation from the carboxyl group (see Box 4.5). Some molecules contain more than one functional group, for example the amino acids contain both -COOH and -NH2:

ammo group



\ : 1

/ ;



/ : 1

W ^-

H : H

O !

carboxyl group carboxyl group

Amino acids also behave as weak acids due to the -COOH group, so they can release H+ ions by dissociation, for example in the simple amino acid glycine:


However, the amino functional group (-NH2) is also able to accept an H+ ion and act as a base (see Box 3.3), i.e.:

The amino acids thus have the unusual ability to form dipolar ions, denoted by the + sign on the amino group and the—sign on the COO. This property makes amino acids highly soluble in polar solvents like water or ethanol, each polar end attracted to the suitable solvent (see Box 4.14).

2.7.2 Representing organic matter in simple equations

Organic matter is implicated in many chemical reactions in natural environments. Organic matter is typically a mixture of materials derived from a number of different plants, which are themselves composed from a variety of complex biopolymers (see Box 4.10). The precise chemistry of organic matter in a soil or sediment is thus not usually known. This problem is usually avoided by using simple compounds such as carbohydrates to represent organic matter. Carbohydrates have the general formula Cn(H2O)n (where n is an integer), which shows they contain only carbon, hydrogen and oxygen, the latter two elements in the same ratio as in water. In this book organic matter is often represented by the generic formula CH2O. A specific example might be the sugar glucose, i.e.:

H—C—C—C—C—C—C=O, which gives the forumla CgH^Ofi


Again, it is easy to see that glucose might form a six-carbon cyclic unit. However this molecule cannot be considered aromatic because it lacks the double bonds found in the benzene ring. Compounds like glucose that contain elements other than carbon in the ring structure are called heterocyclic.



The drawing shows a three-dimensional representation of the molecule with, for example, some OHs sticking up from the ring and some hanging downward. Common sugars, for example sucrose —the main component of domestic sugar —are made of short chains of these six-carbon (C6) units. In the case of sucrose just two C6 units are present (disaccharide), whereas polymers such as cellulose (see Box 4.10) are made of much longer chains, giving rise to the term polysaccharide.

Use of the simple carbohydrate formula to represent organic matter has the advantage of simplifying reactions, but it also means the reactions are very approximate representations of the complexities found in nature (see e.g. Box 4.10).

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