Section 1.4: Functional groups and organic nomenclature
1.4A: Common functional groups in organic compounds
Functional groups are structural units within organic compounds that are defined by specific bonding arrangements between specific atoms. As we progress in our study of organic chemistry, it will become extremely important to be able to quickly recognize the most common functional groups, because they are the key structural elements that define how organic molecules react. For now, we will only worry about drawing and recognizing each functional group, as depicted by Lewis and line structures. Much of the remainder of your study of organic chemistry will be taken up with learning about how the different functional groups tend to behave in organic reactions.
We have already seen some examples of very common functional groups: ethene, for example, contains a carbon-carbon double bond. This double bond is referred to, in the functional group terminology, as an alkene.
The carbon-carbon triple bond in ethyne is the simplest example of an alkyne function group.
What about ethane? All we see in this molecule is carbon-hydrogen and carbon-carbon single bonds, so in a sense we can think of ethane as lacking a functional group entirely. However, we do have a general name for this ‘default’ carbon bonding pattern: molecules or parts of molecules containing only carbon-hydrogen and carbon-carbon single bonds are referred to as alkanes.
If the carbon of an alkane is bonded to a halogen, the group is now referred to as a haloalkane (fluoroalkane, chloroalkane, etc.). Chloroform, CHCl3, is an example of a simple haloalkane.
We have already seen the simplest possible example of an alcohol functional group in methanol. In the alcohol functional group, a carbon is single-bonded to an OH group (this OH group, by itself, is referred to as a hydroxyl). If the central carbon in an alcohol is bonded to only one other carbon, we call the group a primary alcohol. In secondary alcohols and tertiary alcohols, the central carbon is bonded to two and three carbons, respectively. Methanol, of course, is in class by itself in this respect.
The sulfur analog of an alcohol is called a thiol (the prefix thio, derived from the Greek, refers to sulfur).
In an ether functional group, a central oxygen is bonded to two carbons. Below are the line and Lewis structures of diethyl ether, a common laboratory solvent and also one of the first medical anaesthesia agents.
In sulfides, the oxygen atom of an ether has been replaced by a sulfur atom.
Ammonia is the simplest example of a functional group called amines. Just as there are primary, secondary, and tertiary alcohols, there are primary, secondary, and tertiary amines.
One of the most important properties of amines is that they are basic, and are readily protonated to form ammonium cations.
Phosphorus is a very important element in biological organic chemistry, and is found as the central atom in the phosphate group. Many biological organic molecules contain phosphate, diphosphate, and triphosphate groups, which are linked to a carbon atom by the phosphate ester functionality.
Because phosphates are so abundant in biological organic chemistry, it is convenient to depict them with the abbreviation 'P'. Notice that this 'P' abbreviation includes the oxygen atoms and negative charges associated with the phosphate groups.
We will have much more to say about the structure of the phosphate group in chapter 10.
There are a number of functional groups that contain a carbon-oxygen double bond, which is commonly referred to as a carbonyl. Ketones and aldehydes are two closely related carbonyl-based functional groups that react in very similar ways. In a ketone, the carbon atom of a carbonyl is bonded to two other carbons. In an aldehyde, the carbonyl carbon is bonded on one side to a hydrogen, and on the other side to a carbon. The exception to this definition is formaldehyde, in which the carbonyl carbon has bonds to two hydrogens.
Molecules with carbon-nitrogen double bonds are called imines, or Schiff bases.
If a carbonyl carbon is bonded on one side to a carbon (or hydrogen) and on the other side to a heteroatom (in organic chemistry, this term generally refers to oxygen, nitrogen, sulfur, or one of the halogens), the functional group is considered to be one of the ‘carboxylic acid derivatives’, a designation that describes a grouping of several functional groups. The eponymous member of this grouping is the carboxylic acid functional group, in which the carbonyl is bonded to a hydroxyl (OH) group.
As the name implies, carboxylic acids are acidic, meaning that they are readily deprotonated to form the conjugate base form, called a carboxylate (much more about carboxylic acids in the acid-base chapter!).
In amides, the carbonyl carbon is bonded to a nitrogen. The nitrogen in an amide can be bonded either to hydrogens, to carbons, or to both. Another way of thinking of an amide is that it is a carbonyl bonded to an amine.
In esters, the carbonyl carbon is bonded to an oxygen which is itself bonded to another carbon. Another way of thinking of an ester is that it is a carbonyl bonded to an alcohol. Thioesters are similar to esters, except a sulfur is in place of the oxygen.
In an acyl phosphate, the carbonyl carbon is bonded to the oxygen of a phosphate, and in an acid chloride, the carbonyl carbon is bonded to a chlorine.
Finally, in a nitrile group, a carbon is triple-bonded to a nitrogen. Nitriles are also often referred to as cyano groups.
A single compound often contains several functional groups. The six-carbon sugar molecules glucose and fructose, for example, contain aldehyde and ketone groups, respectively, and both contain five alcohol groups (a compound with several alcohol groups is often referred to as a ‘polyol’).
Capsaicin, the compound responsible for the heat in hot peppers, contains phenol, ether, amide, and alkene functional groups.
The male sex hormone testosterone contains ketone, alkene, and secondary alcohol groups, while acetylsalicylic acid (aspirin) contains aromatic, carboxylic acid, and ester groups.
While not in any way a complete list, this section has covered most of the important functional groups that we will encounter in biological and laboratory organic chemistry. The table on the inside back cover provides a summary of all of the groups listed in this section, plus a few more that will be introduced later in the text.
Exercise 1.13: Identify the functional groups in the following organic compounds. State whether alcohols and amines are primary, secondary, or tertiary.
Exercise 1.14: Draw one example each (there are many possible correct answers) of compounds fitting the descriptions below, using line structures. Be sure to designate the location of all non-zero formal charges. All atoms should have complete octets (phosphorus may exceed the octet rule).
a) a compound with molecular formula C6H11NO that includes alkene, secondary amine, and primary alcohol functional groups
b) an ion with molecular formula C3H5O6P 2- that includes aldehyde, secondary alcohol, and phosphate functional groups.
c) A compound with molecular formula C6H9NO that has an amide functional group, and does not have an alkene group.
1.4B: Naming organic compounds
A system has been devised by the International Union of Pure and Applied Chemistry (IUPAC, usually pronounced eye-you-pack) for naming organic compounds. While the IUPAC system is convenient for naming relatively small, simple organic compounds, it is not terribly useful for the larger, more complex molecules involved in biological organic chemistry, and thus is not generally used in this context. It is, however, a good idea to become familiar with the basic structure of the IUPAC system.
We’ll start with the simplest alkane structures. As we already know, CH4 is called methane, and C2H6 ethane. Moving to larger molecule one carbon at a time, we have propane (3 carbons), butane (4 carbons), pentane (5 carbons) and hexane (6 carbons), followed by heptane (7), octane (8), nonane (9), and decane (10).
Substituents branching from the main ‘parent’ chain are located by a carbon number, with the lowest possible number being used.
When they are substituents branching from a parent chain, we refer to small alkyl groups with the terms methyl, ethyl, and propyl.
Notice in the example below, the ‘ethyl group’ is not treated as a substituent, rather it is included as part of the parent chain, and instead the methyl group is treated as a substituent. The IUPAC name for straight-chain hydrocarbons is always based in the longest possible parent chain.
Cyclic structures are called cyclopropane, cyclobutane, cyclopentane, cyclohexane, and so on.
In the case of multiple substituents, the prefixes di, tri, and tetra are used.
Functional groups have characteristic suffixes. Alcohols, for example, have ‘ol’ appended to the parent chain name, along with a number designating the location of the hydroxyl group. Ketones are designated by ‘one’, and thiols by ‘thiol’.
Alkenes are designated with an 'ene' ending. Geometry about the double bond is specified using the terms cis and trans (as we will see in section 1.5C, there is no rotation possible about carbon-carbon double bonds, so the two structures below actually represent different molecules). In a trans alkene, the alkyl groups are on opposite sides of the double bond, whereas in a cis alkene, they are on the same side.
We will learn more details about how to specify the arrangement of groups about double bonds in section 3.7C.
Some groups can only be present on a terminal carbon, and thus a number is not necessary: aldehydes end in ‘al’, carboxylic acids in ‘oic acid’, and carboxylates in ‘oate’.
Ethers and sulfides are designated by naming the two groups on either side of the oxygen or sulfur.
If an amide has an unsubstituted –NH2 group, the suffix is simply ‘amide’. In the case of a substituted amide, the group attached to the amide nitrogen is named first, along with the letter ‘N’ to clarify where this group is located.
For esters, the group attached to the oxygen is named first, followed by the name of the remaining carboxylate group.
There are of course many more rules in the IUPAC system, and as you can imagine, the IUPAC naming of larger molecules with multiple functional groups and substituents can get very unwieldy very quickly. The illicit drug cocaine, for example, has the IUPAC name 'methyl (1R,2R,3S,5S)-3-(benzoyloxy)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate' (this name includes designations for stereochemistry, which is a structural issue that we will not tackle until chapter 3).
This is exactly why the IUPAC system is not used for biological organic chemistry - the molecules are just too big. A further complication is that, even outside of a biological context, many simple, common organic molecules are known almost universally by their ‘common’, rather than IUPAC names: acetic acid, chloroform, and acetone are only a few examples.
Exercise 1.15: Give IUPAC names for acetic acid, chloroform, and acetone.
Exercise 1.16: Draw line structures of the following compounds.
c) 2-methyl-2-butene (why is a cis/trans designation not necessary?)
f) trans-3-penteneoic acid
In biochemistry, multiple naming systems are used, depending on whether we are talking about sugars, fats, proteins, or other common biochemical families. Often, nomenclature systems evolve and change as new compound families are discovered. We will not focus very closely in this text on the IUPAC or any other nomenclature system, but if you undertake more advanced study in organic or biological chemistry you may well be expected to learn one or more different systems in some detail.
1.4C: Abbreviated organic structures
Often when drawing organic structures, chemists find it convenient to use the letter 'R' to designate part of a molecule. If we just want to refer in general to a functional group without drawing a specific molecule, for example, we can use 'R groups' to focus attention on the group of interest:
The R group is also a convenient way to abbreviate the structures of large biological molecules, especially when we are interested in something that is occurring specifically at one location on the molecule.
As an alternative, we can use a 'break' symbol to indicate that we are looking at a small piece of a larger molecule. This is used most commonly with in the context of drawing groups on large polymers such as proteins or DNA.
Finally, R groups can be used to concisely illustrate a series of related compounds.