Functional groups

It is important to be able to identify functional groups in organic molecules, since they are the entities that have function and undergo chemical change. There are around 15 important functions to be memorized over the two semesters, many of them used later in biochemistry and polymer chemistry.

First-semester groupsSecond-semester groupsAll sixteen at a glanceQuiz

First-semester groups

01Alkyl halides

sp³ C bonded to F, Cl, Br or I · example: 1-chlorobutane

Alkyl halides, in which sp³ carbon is bonded to fluorine, chlorine, bromine, or iodine, are generally quite dangerous compounds to work with; however, they find many uses in organic synthesis and polymer chemistry. Simple alkyl halides are used in substitution and elimination reactions, in which the polarized C–X bond makes them electrophilic and the halogen serves as a leaving group.

Alkyl halide polymers include polyvinyl chloride (PVC), used in house siding and plumbing pipes, as well as the perfluorinated Teflon that is used as a non-stick coating on cooking equipment and water-sealed plumbing tape.

02Alkenes

C=C — one σ, one π · example: cyclohexene

Alkenes are organic molecules with a double bond between two adjacent carbons. A strong sigma bond between the two atoms is joined by a weaker pi bond above and below. They will be trigonal planar in shape around the functional group and serve as important nucleophiles in organic synthesis.

They are typically made by elimination reactions in the first semester, and then by methods such as the Wittig reaction later on. The substitution pattern of the alkene plays a role in its stability and reactivity, with more attached alkyl groups stabilizing the alkene carbons through electron donation.

03Alkynes

C≡C — one σ, two π · example: 1-hexyne

Alkynes are unsaturated organic molecules featuring a triple bond between two adjacent carbons, made up of a strong sigma bond and two weaker pi bonds that occupy space away from the sigma bond axis. The sp hybrid carbons involved make attached protons on terminal alkynes slightly acidic, so strong bases may deprotonate them to produce acetylide nucleophiles. The linear shape makes alkynes suitable for directing attached groups into opposite directions in space.

Alkynes are produced by sequential elimination reactions from dihalides using strong bases like sodium amide.

04Alcohols

R–OH · example: cyclopentanol

Alcohols are readily available feedstock organic molecules containing the polar OH functional group. Depending on the nature of the alkyl group attached, these compounds may be soluble in water due to the OH group’s ability to hydrogen bond. Alcohols are weakly acidic (pKa in the 16–18 region), so they may be deprotonated by strong bases to give alkoxide nucleophiles, which are then useful for making ethers.

Primary alcohols are oxidized to aldehydes and then carboxylic acids, whereas secondary alcohols give ketones. Tertiary alcohols are typically not oxidized under standard conditions. This can serve as a useful test for differentiating alcohol type.

05Ethers

R–O–R′ · example: diethyl ether

Ethers are organic molecules in which a central oxygen is bonded to two individual carbon atoms. These molecules are inherently stable, serve as important solvents, and find applications in medicinal chemistry and areas such as anesthesiology. Many examples occur in Nature, and the functional group is synthesized by such reliable reactions as the Williamson ether synthesis.

The ether linkage is known to be robust and is generally stable in basic media. In acidic environments, protonation of the oxygen sets up a good leaving group, so substitution chemistry is possible.

06Thiols

R–SH · example: butanethiol

Thiols are the sulfur equivalent of alcohols, in which SH has replaced the OH group. The greater size and lower electronegativity of sulfur make thiols more acidic (pKa around 10) than alcohols, so they may be deprotonated by weaker bases. The lower electronegativity means S may be oxidized from 2 to 4 and then 6, in compounds such as sulfonic acids.

This also makes thiol derivatives such as acetyl-CoA important in biochemistry, as the S makes a better leaving group than its oxygen cousin. Butanethiol has an unpleasant odour and is added to the odourless natural gas supply to serve as an indicator.

07Sulfides

R–S–R′ · example: tetrahydrothiophene

Sulfides, related to thiols, are the sulfur equivalent of ethers, where the connecting sulfur has replaced the ether oxygen. The greater size and lower electronegativity of sulfur once again make sulfides more chemically flexible than their oxygen counterparts. The lower electronegativity of S means it may be oxidized from 2 to 4 and then 6, in compounds such as sulfoxides and sulfones, which themselves have broad use in organic synthesis.

Sulfides occur in Nature, for example in the key biochemical cofactor S-adenosylmethionine (SAM), which is involved in biological alkylation reactions.

Second-semester groups

08Aromatics

Planar, cyclic, 4n + 2 π electrons · example: benzene

Aromatic compounds are a class of organic molecules that contain one or more benzene-like rings, which consist of atoms arranged in a planar, cyclic structure with alternating pi bonds. This arrangement creates a conjugated π-electron system that fits Hückel’s rule (4n + 2 π electrons, conjugated and planar), giving aromatic systems exceptional stability. They exhibit unique chemical reactivity, such as undergoing substitution reactions rather than addition, to preserve their aromatic stability.

Common examples include benzene, toluene, and naphthalene. Such compounds find wide use in organic synthesis.

09Aldehydes

R–CHO · example: butyraldehyde

Aldehydes are organic compounds characterized by the presence of a carbonyl group (C=O) bonded to a hydrogen atom and an alkyl or aryl group. The general formula is R–CHO, where R represents an attached organic residue. Aldehydes are typically formed by oxidation of primary alcohols and are highly reactive due to the polar nature of the carbonyl group.

They play an important role in organic synthesis, serving as intermediates in the production of alcohols, carboxylic acids, and other useful compounds. Aldehydes may exhibit distinctive odours, for example butyraldehyde, which has the smell of rancid butter.

10Ketones

R–CO–R′ · example: cyclohexanone

A ketone is an organic compound that features the carbonyl group (C=O) bonded to two alkyl or aryl groups. The general formula for ketones is R–CO–R′, where R and R′ represent carbon residues. Unlike aldehydes, ketones do not have a hydrogen atom attached to the carbonyl carbon, which influences their reactivity. Ketones are commonly formed by the oxidation of secondary alcohols and are relatively stable compared to aldehydes.

They play important roles as electrophiles in organic synthesis as well as in biological processes, for example in metabolism. Ketones are widely used as solvents, as well as synthetic intermediates.

11Carboxylic acids

R–COOH · example: benzoic acid

Carboxylic acids are organic materials that contain the carboxyl group (–COOH), which consists of a carbonyl (C=O) and a hydroxyl (–OH) group bonded to the same carbon atom. Their general formula is R–COOH, where R represents an alkyl or aryl residue. Carboxylic acids are generally formed by the oxidation of primary alcohols or aldehydes.

They are weakly acidic, with pKa around 5, due to the electron-withdrawing carbonyl group, which also effectively stabilizes the anionic conjugate base. Carboxylic acids are widely used in food preservation, medicinal chemistry, polymers, and as intermediates in organic synthesis.

12Acid (acyl) halides

R–COX · example: propionyl chloride

Acyl halides are reactive organic compounds derived from carboxylic acids by replacing the hydroxyl group (–OH) with a halogen atom, most often Cl or Br. Their generic formula is R–COX, where R is an alkyl or aryl group and X is a halogen. The carbonyl group (C=O) in acyl halides is polarized, making them excellent electrophiles in many nucleophilic acyl substitution reactions.

They are commonly used as intermediates in organic synthesis for producing esters, amides, and anhydrides. Due to their reactivity, acyl halides are not found in Nature and must be handled carefully, as they can hydrolyze rapidly in the presence of water.

13Acid anhydrides

(RCO)₂O · example: acetic anhydride

Related to acid halides, acid anhydrides are organic intermediates derived from carboxylic acids by removing water between two COOH groups, forming a structure with two acyl groups bonded to the same oxygen atom. Their general formula is (RCO)₂O, where R represents alkyl or aryl groups. Acid anhydrides are highly reactive due to the presence of two electron-withdrawing carbonyl groups, making them useful electrophiles in nucleophilic acyl substitution reactions.

They are used in organic synthesis to give esters and amides. Anhydrides readily hydrolyze in the presence of water to regenerate carboxylic acids.

14Esters

R–COOR′ · example: ethyl acetate

Esters are formed by the reaction between a carboxylic acid and an alcohol, often with acid catalysis, and with the elimination of water in a condensation process. They contain the general structure –COOR. The ester motif includes a carbonyl (C=O) bonded to an oxygen atom that is then attached to a carbon chain or ring. Esters are generally much less reactive than acyl halides or anhydrides, since they are less electrophilic and OR is a worse leaving group.

They do undergo hydrolysis in acidic or basic conditions to regenerate the parent acid and alcohol. Esters are used in fragrances, flavourings, as solvents, and as synthetic intermediates.

15Amides

R–CONR₂ · example: N,N-dimethylformamide (DMF)

Amides are derived from carboxylic acids by replacing the hydroxyl (–OH) with an amino group (–NH₂, –NHR, or –NR₂). The general formula is R′–CONR₂, where R′ represents an alkyl or aryl group. The structure includes a carbonyl (C=O) bonded to N, which allows for significant resonance stabilization, reducing C=O reactivity compared to acyl halides or anhydrides.

Amides are important in both synthetic and biological chemistry, forming the primary backbone of proteins as peptide bonds. They are highly stable linkages, making them suitable for connecting monomers in polymers and useful motifs in drug and materials synthesis.

16Amines

R–NH₂, R₂NH, R₃N · example: triethylamine

Amines are compounds derived from ammonia (NH₃) by replacing hydrogen atoms with alkyl or aryl groups. They may be primary (–NH₂), secondary (–NHR), or tertiary (–NR₂) based on the number of substituents attached to nitrogen. Amines act as bases due to the lone pair of electrons on nitrogen, making them important as proton sponges. They also serve as good nucleophiles in processes such as nucleophilic acyl substitution and reductive amination.

Amines play important roles in biological systems such as amino acids, neurotransmitters, and various pharmaceuticals. Amines are used in dyes, polymers, and various materials.

All sixteen at a glance

The general structure to recognize, and the example for each.

Six questions before you move on

Work out an answer on paper, then reveal to check. If your reason is right but the answer is wrong, you are closer than you think.