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.