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Medicinal Chemistry of Functional Groups

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May 28th, 2019 Medicinal Chemistry (https://pharmafactz.com/category-medicinal-chemistry/)

(https://pharmafactz.com/medicinal-chemistry-and-pharmacology-functional-groups/)

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 (https://pharmafactz.com/medicinal-chemistry-glossary/)
is crucial. Functional groups are speci c 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 Pre x Suf x Example Example of Functionality Found in a Drug Molecule

Alkane
Alkyl Alkyl- -ane
R(CH2)nH

Alkene
Alkenyl Alkenyl- -ene
R2C=CR2

Alkyne
Alkynyl Alkynyl- -yne
RC≡CR’
 Benzene
Phenyl Phenyl- -benzene
RC6H5RPh

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

Chemical Class Group Pre x Suf x Example Example of Functionality Found in a Drug Molecule

Fluoroalkane
Fluoro Fluoro- Alkyl uoride
RF

Chloroalkane
Chloro Chloro- Alkylchloride
RCl

Bromoalkane
Bromo Bromo- Alkylbromide
RBr

Iodoalkane
Iodo Iodo- Alkyliodide
RI

Oxygen-containing Functional Groups

Chemical Example of Functionality Found in a Drug

Group Pre x Suf x Example
Class Molecule

Alcohol
Hydroxyl Hydroxyl- -ol
ROH
 Ether
Ether Alkoxy- Alkyl ether
ROR’

Aldehyde Formyl- or
Aldehyde -al
RCHO oxo-

Ketone
Carbonyl Oxo- or –oyl- -one
RCOR’

Carboxylic
Acid Carboxyl Carboxy- -oic acid
RCOOH

alkanoyloxy-
Ester Alkyl
Carboalkoxy or
RCOOR’ alkanoate
alkoxycarbonyl

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 Pre x Suf x Example Example of Functionality Found in a Drug Molecule
 Amine
RNH2;
R2NH; Amine Amino- -amine
R3N;
R4N+

Imine
RC(=NH)R’;
RC(=NR’’)R’; Imine Imino- -imine
RC(=NH)H;
RC(=NR’)H

-nitrile
Nitrile
Nitrile Cyano- or
RCN
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

Example of
Chemical Functionality
Group Pre x Suf x Example
Class Found in a Drug
Molecule

carboxamido-
Amide
Carboxamide or -amide
RCONR2
carbamoyl-

Nitro
Nitro Nitro-  
RNO2

Carbamate (- -
Carbamate
RO(C=O)NR2 carbamoyl)oxy- carbamate

Urea
Urea    
R2N(C=O)NR2
Sulfur-containing Functional Groups

Chemical Example of Functionality

Group Pre x Suf x Example
Class Found in a Drug Molecule

Thiol
Sulfhydryl sulfanyl- -thiol
RSH

Thioether
substituent (substituent)
(sul de) Sul de
sulfanyl- sul de
RSR’

Sulfoxide (substituent)
Sul nyl -sul nyl-
RSOR’ sulfoxide

Sulfone (substituent)
Sulfonyl -sulfonyl-
RSO2R’ 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.
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