A lot of drugs in the market are small organic molecules and as a student of medicinal chemistry, biochemistry, pharmacy, pharmacology or medicine, knowledge of the different functional groups is crucial. Functional groups are specific substituents or moieties, composed of an atom or a group of atoms, within molecules that possess similar chemical properties whenever it occurs in different compounds. Functional groups determine the characteristic physical, chemical and biological properties of a molecule.

Implicit and Explicit Atoms

When hydrogens attached to carbons are shown in the skeletal formulas of organic compounds, the hydrogens are said to be explicitly shown. However, the hydrogens bonded to carbons are often not shown as it is tedious to do so and the omission makes structures look neater. A shorthand notation, where the hydrogens bonded to carbons aren’t shown in drawings but are assumed to be present, is preferred. In such cases, the hydrogens are said to be implicit. In a similar fashion, the symbol “C” for carbon is often not drawn in skeletal formulas of organic compounds (i.e. implicit carbons).Non-carbon and non-hydrogen atoms are shown in the shorthand notation. Examples:

Functional groups commonly encountered in drugs

Note that in organic chemistry, the R group is a generic placeholder for other groups such as aliphatic groups.

Hydrocarbons

• Hydrocarbyl functional groups are ones that contain only carbon and hydrogen.

Chemical Class	Group	Prefix	Suffix	Example	Example of Functionality Found in a Drug Molecule
Alkane R(CH2)nH	Alkyl	Alkyl-	-ane
Alkene R2C=CR2	Alkenyl	Alkenyl-	-ene
Alkyne RC≡CR’	Alkynyl	Alkynyl-	-yne
Benzene RC6H5RPh	Phenyl	Phenyl-	-benzene

Alkyl Halides

Alkyl halides, which contain carbon-halogen bonds, are sometimes referred to as haloalkanes or halogenoalkanes.

Chemical Class	Group	Prefix	Suffix	Example	Example of Functionality Found in a Drug Molecule
Fluoroalkane RF	Fluoro	Fluoro-	Alkyl fluoride
Chloroalkane RCl	Chloro	Chloro-	Alkylchloride
Bromoalkane RBr	Bromo	Bromo-	Alkylbromide
Iodoalkane RI	Iodo	Iodo-	Alkyliodide

Oxygen-containing Functional Groups

Chemical Class	Group	Prefix	Suffix	Example	Example of Functionality Found in a Drug Molecule
Alcohol ROH	Hydroxyl	Hydroxyl-	-ol
Ether ROR’	Ether	Alkoxy-	Alkyl ether
Aldehyde RCHO	Aldehyde	Formyl- or oxo-	-al
Ketone RCOR’	Carbonyl	Oxo- or –oyl-	-one
Carboxylic Acid RCOOH	Carboxyl	Carboxy-	-oic acid
Ester RCOOR’	Carboalkoxy	alkanoyloxy- or alkoxycarbonyl	Alkyl alkanoate

Notes:

• Under relatively basic conditions in the body, the deprotonated, anionic form of carboxylic acids (carboxylates) are predominant.
• Alcohols may be primary, secondary or tertiary, which is dependent on the number of carbon atoms attached to the carbon bonded to the hydroxyl group:

Nitrogen-containing Functional Groups

Chemical Class	Group	Prefix	Suffix	Example	Example of Functionality Found in a Drug Molecule
Amine RNH2; R2NH; R3N; R4N+	Amine	Amino-	-amine
Imine RC(=NH)R’; RC(=NR’’)R’; RC(=NH)H; RC(=NR’)H	Imine	Imino-	-imine
Nitrile RCN	Nitrile	Cyano-	-nitrile or alkyl cyanide

• Amines may be primary, secondary, tertiary or quaternary, which is dependent on the number of carbon atoms attached to nitrogen:

Functional Groups that contain both Nitrogen and Oxygen

Chemical Class	Group	Prefix	Suffix	Example	Example of Functionality Found in a Drug Molecule
Amide RCONR2	Carboxamide	carboxamido- or carbamoyl-	-amide
Nitro RNO2	Nitro	Nitro-
Carbamate RO(C=O)NR2	Carbamate	(-carbamoyl)oxy-	-carbamate
Urea R2N(C=O)NR2	Urea

Sulfur-containing Functional Groups

Chemical Class	Group	Prefix	Suffix	Example	Example of Functionality Found in a Drug Molecule
Thiol RSH	Sulfhydryl	sulfanyl-	-thiol
Thioether (sulfide) RSR’	Sulfide	substituent sulfanyl-	(substituent) sulfide
Sulfoxide RSOR’	Sulfinyl	-sulfinyl-	(substituent) sulfoxide
Sulfone RSO2R’	Sulfonyl	-sulfonyl-	(substituent) sulfone

The number of names functional groups and moieties is far greater than what is listed here. A more comprehensive list can be found in this article.