The Concept of Functional Groups

James Richard Fromm

In organic chemistry , functional groups are specific groups of atoms within molecules,
that are responsible for the characteristic chemical reactions of those molecules. The
same functional group will undergo the same or similar chemical reaction(s) regardless of
the size of the molecule it is a part of.

In organic molecules, the atoms are linked by covalent bonds. Organic molecules are
generally large and may be complex, involving many such bonds. Inorganic compounds
have considerably simpler structure in terms of number, but not necessarily type, of
bonds. In organic molecules, to a first approximation, we may say that one bond does not
affect another. Thus an atom such as a chlorine atom, -Cl, or a group of atoms such as
the alcohol group, -OH, on one end of a molecule will behave chemically in the same
way almost without regard to the molecule to which it is covalently attached. The idea
of different independent or semi-independent atoms or groups of atoms on the same
molecule is central to our modern understanding of organic chemistry. It is called the
concept of functional groups. The nomenclature of organic compounds, like most of the
rest of our understanding of reactions of organic compounds, is based upon the concept of
functional groups.

Functional groups consist of one or more atoms, and they can be atoms of identical or
different elements. The simplest organic molecule is one carbon bonded covalently to
four hydrogens, CH4. This compound, a gas, is called methane and is a major component
of natural gas. For any other functional group to attach itself to methane, one hydrogen
must be removed and the other functional group must be attached in its place. This
process is called substitution of the functional group.

The principle used is that organic compounds are named and generally understood as
substituted compounds of carbon and hydrogen, the substitution being that of a functional
group for one or more hydrogens. The simplest compounds of carbon and hydrogen are
the Alkanes, followed by the Alkenes and Alkynes.

Alkane Alkene Alkyne

CH3-CH3

Ethane Ethene Ethyne

If a chlorine atom is substituted onto methane, the compound produced is chloromethane.

CH3Cl

Combining the names of functional groups with the names of the parent alkanes
generates a powerful systematic nomenclature for naming organic compounds. The non-
hydrogen atoms of functional groups are always associated with each other and with the
rest of the molecule by covalent bonds. When the group of atoms is associated with the
rest of the molecule primarily by ionic forces, the group is referred to more properly as a
polyatomic ion or complex ion. And all of these are called radicals, by a meaning of the
term radical that predates the free radical.

The first carbon after the carbon that attaches to the functional group is called the alpha
carbon.

Functional groups are attached to the carbon backbone of organic molecules. They
determine the characteristics and chemical reactivity of molecules. Functional groups are
far less stable than the carbon backbone and are likely to participate in chemical
reactions. Six common biological functional groups are hydrogen, hydroxyl, carboxyl,
amino, phosphate, and methyl.

-H NH2CO2H OP(OR)3 -CH3

Hydrogen Hydroxyl Carboxyl Amino Phosphate Methyl

The following is a list of common functional groups. In the formulas, the symbols R and
R' usually denotes a hydrocarbon side chain of any length, but may sometimes refer to
any group of atoms.

R-X R-F R-Cl R-Br R-I

Halogen
Fluoro- Chloro- Bromo- Iodo-
Derivatives

Alcohol Aldehyde Ether Ketone

 NH2CO2H

Carboxylic
Ester Amine Amide Amino
Acid

R-N=O R-N=N-R' R-NO2 R-C N R2C=NR'

Nitroso Azo Nitro Nitrile Imine

-
O-C N O=C=N- R-N C R–N=C=O ROOR'
Cyanate Isocyanide/Isonitrile Isocyanate Organic Peroxide

Thiol/MercaptansThioether/Sulfide Disulfide

Sulfenic Acid Sulfinic Acid Sulfonic Acid

R−S(=O)−R′ R-S(=O)2−R′

Sulfonate Ester Sulfoxide/Sulfinyl Sulfone/Sulfonyl

PR3 R3P=O PR5 P(OR)R2

Phosphine/Phosphane Phosphine Oxide Phosphorane Phosphinite
 P(OR)2R P(OR)3 OP(OR)R2 R-P(=O)(OR)2
Phosphite/Phosphite
Phosphonite Phosphinate Phosphonate
Ester

OP(OR)3 P=P P=N P(=O)(OR)3

Phosphate Diphosphene Phosphazene Phosphate Ester

PC5R5
Phosphorine

Haloalkanes (also known as Halogenoalkanes) are a group of chemical compounds,

consisting of alkanes, such as methane or ethane, with one or more halogens linked,
fluorine, chlorine, bromine or iodine, forming an organic halide. The most widely known
family within this group are the chlorofluorocarbons (CFCs). The haloalkanes have the
general formula R-X where R- represents some alkyl or aryl group and -X represents one
of the members of the halogen family: fluorine, chlorine, bromine and/or iodine.

R-X R-F R-Cl R-Br R-I

Halogen
Fluoro- Chloro- Bromo- Iodo-
Derivatives

An Alcohol functional group is a hydroxyl group bonded to an sp³ hybridized carbon. It

can be regarded as a derivative of water, with an alkyl group replacing one of the
hydrogens. If an aryl group is present rather than an alkyl, the compound is generally
called a phenol rather than an alcohol. Also, if the hydroxyl group is bonded to one of the
sp² hybridized carbons of an alkenyl group, the compound is referred to as an enol. The
oxygen in an alcohol has a bond angle of around 109° (c.f. 104.5° in water), and two
nonbonded electron pairs.

Alcohol Functional Group, Hydroxyl

Ethanol, Ethyl Alcohol, Grain Alcohol
Group

An Aldehyde is an organic compound containing a terminal carbonyl group. This

functional group, which consists of a carbon atom which is bonded to a hydrogen atom
and double-bonded to an oxygen atom (chemical formula O=CH-), is called the aldehyde
group. The aldehyde group is also called the aldo, formyl or methanoyl group. The word
aldehyde seems to have arisen from alcohol dehydrogenated.
 Aldehyde Functional Group, Aldo Group Methanal, Formaldehyde

Ether is the general name for a class of chemical compounds which contain an oxygen
atom connected to two (substituted) alkyl groups. A typical example is the solvent and
anesthetic, diethyl ether, commonly referred to simply as "ether", (ethoxyethane, CH3-
CH2-O-CH2-CH3).

Ether Functional Group Ethoxyethane, Diethyl Ether

Ketones are either the functional group characterized by a carbonyl group (O=C) linked
to two other carbon atoms or a compound that contains this functional group. A ketone
can be generally represented by the formula: R1(CO)R2.

A carbonyl carbon bonded to two carbon atoms distinguishes ketones from carboxylic
acids, aldehydes, esters, amides, and other oxygen -containing compounds. The double-
bond of the carbonyl group distinguishes ketones from alcohols and ethers. The simplest
ketone is acetone, dimethyl ketone or propanone.

Ketone Functional Group, Keto Group Propanone, Dimethyl Ketone, Acetone

Carboxylic Acids are organic acids characterized by the presence of a carboxyl group,
which has the formula -C(=O)OH, usually written -COOH or -CO2H. Carboxylic acids
are Bronsted Acids — they are proton donors. Salts and anions of carboxylic acids are
called carboxylates.

The simplest series of carboxylic acids are the alkanoic acids, R-COOH, where R is a
hydrogen or an alkyl group. Compounds may also have two or more carboxylic acid
groups per molecule.

Carboxyl Functional Group Ethanoic Acid, Acetic Acid

Esters are organic compounds in which an organic group from an alcohol (symbolized by
R') replaces a hydrogen atom in the hydroxyl group of an organic acid. Organic acids are
molecules which have an -OH group from which the hydrogen (H) can dissociate as an
H+ ion. The most common esters are the carboxylate esters, where the acid in question is
a carboxylic acid.

Ester Functional Group Isoamyl Ethanoate, Flavor of Banana

Esters are produced by a reversible reaction between an alcohol and a carboxylic acid
which causes loss of water and the formation of an ester:

Alcohol + Carboxylic Acid Ester + Water

R'OH + RCOOH RCOOR' + H2O

Esters are named as derivatives of the carboxylic acid from which they are formed.
Condensation of ethanoic acid with methanol will produce methyl ethanoate. The
esterification reactions are generally easily reversible by addition of water; the reverse
reaction is called the hydrolysis of the ester and proceeds in the presence of aqueous base.

condensation reaction to form an ester is called esterification. Esterification can be

catalysed by the presence of H+ ions. Sulfuric acid is often used as a catalyst for this
reaction.

Amines are organic compounds whose functional group contains nitrogen as the key
atom. Structurally amines resemble ammonia, wherein one or more hydrogen atoms are
replaced by organic substituents such as alkyl and aryls groups. An important exception
to this rule is that compounds of the type RC(O)NR2, where the C(O) refers to a carbonyl
group, are called amides rather than amines. Amides and amines have different structures
and properties, so the distinction is chemically important. Somewhat confusing is the
fact that amines in which an N-H group has been replaced by an N-M group (M = metal)
are also called amides. Thus (CH3)2NLi is lithium dimethylamide.

Amine Functional Group Methamphetamine

An Amide is one of two kinds of compounds:

 • a carbonyl group (C=O) linked to a nitrogen atom (N), or a compound that
contains this functional group; or
• a particular kind of nitrogen anion.

Amides are the most stable of all the carbonyl functional groups.

or
Amide Functional Group
Amide Functional Group

An Amino is represented by both an NH2 and a Carboxyl (COOH)

Nitroso refers to a functional group in organic chemistry which has the general formula
R-N=O. Nitroso compounds can be prepared by the reduction of nitro compounds or by
the oxidation of hydroxylamines. A good example is (CH3)3CNO, known formally as 2-
methyl-2-nitrosopropane.

R-N=O (CH3)3CNO
Nitroso Functional Group 2-methyl-2-nitrosopropane

Azo Compounds refer to chemical compounds bearing the functional group R-N=N-R',
in which R and R' can be either alkyl or aryl. The N=N group is called an azo or
diimide.

R-N=N-R'

Azo Functional
4-hydroxyphenylazobenzene
Group

Many of the more stable derivatives contain two aryl groups due to the electron
delocalization. The name azo comes from azote, an old name of nitrogen that originates
in French and is derived from the Greek a (not) + zoe (to live).

Nitro Compounds are organic compounds that contain one or more nitro functional
groups (-NO2). They are often highly explosive; various impurities or improper handling
can easily trigger a violent exothermic decomposition.

Aromatic nitro compounds are typically synthesized by the action of a mixture of nitric
and sulfuric acids on a suitable organic molecule. Some examples of such compounds
are trinitrophenol (picric acid) and trinitrotoluene (TNT).

R-NO2
 Nitro Functional Group

A Nitrile is any organic compound which has a -C N functional group. In the -C N

group, the carbon atom and the nitrogen atom are triple bonded together. The prefix
cyano- is used in chemical nomenclature to indicate the presence of a nitrile group in a
molecule. A cyanide ion is a negative ion with the formula CN-. The -CN group is
sometimes, less properly, referred to as a cyanide group or cyano group and compounds
with them are sometimes referred to as cyanides. Nitriles sometimes release the highly
toxic CN- cyanide ion.

R-C N

Nitrile Functional Group

An Imine is a functional group or chemical compound containing a carbon-nitrogen

double bond. Imines, due to their diverse reactivity, are common substrates in a wide
variety of transformations. An imine can be synthesised by the nucleophilic addition of
an amine to a ketone or aldehyde giving a hemiaminal -C(OH)(NHR)- followed by an
elimination of water to yield the imine.

R2C=NR'

Imine Functional Group

The Cyanate ion is an anion consisting of one oxygen atom, one carbon atom, and one
nitrogen atom, [OCN]-, in that order, and possesses 1 unit of negative charge, borne
mainly by the nitrogen atom. The structure of cyanate can be considered to resonate.

Cyanate Functional Group

An Isocyanide (also called an Isonitrile is an organic compound with the functional

group R-N C. The C N functionality is connected to the organic fragment via the
nitrogen atom, not via carbon as is found in the isomeric nitriles, which have the
connectivity R-CN. Hence the prefix iso. Nitrogen and carbon are connected through a
triple bond with a positive charge on nitrogen and a negative charge on carbon.

Isocyanide/Isonitrile Functional Group

Isocyanate is the functional group of atoms –N=C=O (1 nitrogen, 1 carbon, 1 oxygen),

not to be confused with the cyanate functional group (see above).
 -N=C=O

Isocyanate Functional Group

Organic Peroxides are organic compounds containing the peroxide functional group
(ROOR'). If the R' is hydrogen, the compound is called an organic hydroperoxide.
Peresters have general structure RC(O)OOR.

The O-O bond easily breaks and forms free radicals of the form RO-. This makes organic
peroxides useful as catalysts for some types of polymerization.

R-O-O-R'

Organic Peroxide Functional Group

A Thiol/Mercaptan is a compound that contains the functional group composed of a

sulfur atom and a hydrogen atom (-SH). Being the sulfur analogue of an alcohol group
(-OH), this functional group is referred to either as a thiol group or a sulfhydryl group.
Thiolate ions have the form R-S-. Such anions arise upon treatment of thiols with base.

Thiol or Mercaptan Functional Group

A Thioether/Sulfide is a functional group that has the structure R1-S-R2. Like many
other sulfur-containing compounds, volatile thioethers characteristically have foul odors.

A thioether is similar to an ether except that it contains a sulfur atom in place of the
oxygen. Because oxygen and sulfur belong to the chalcogens group in the periodic table,
the chemical properties of ethers and thioethers share some commonalities. This
functional group is important in biology, most notably in the amino acid methionine and
the cofactor biotin.

In organic chemistry , "Sulfide" usually refers to the linkage C-S-C, although the term
thioether is less ambiguous. For example, the thioether dimethyl sulfide is CH3-S-CH3.
Polyphenylene sulfide has the empirical formula C6H4S. Occasionally, the term sulfide
refers to molecules containing the -SH functional group. For example, methyl sulfide can
mean CH3-SH. The preferred descriptor for such SH-containing compounds is thiol or
mercaptan, i.e. methanethiol or methyl mercaptan.
 Thioether/Sulfide Functional Group

Disulfides - A disulfide bond is a single covalent bond derived from the coupling of thiol
groups. The linkage is also called an SS-bond or disulfide bridge. The overall
connectivity is therefore C-S-S-C. The terminology is almost exclusively used in
biochemistry, bioinorganic and bioorganic chemistry. Formally the connection is called a
persulfide, in analogy to a peroxide (R-O-O-R), but this terminology is rare.

Three sulfur atoms singly bonded in a sequence are sometimes called a trisulfide bond,
although there are in fact two S-S bonds. Disulfide bonds are usually formed from the
oxidation of sulfhydryl (-SH) groups.

Disulfide Functional Group

Sulfenic Acids are organosulfur oxyacids having the general structure RSOH, where R is
not a hydrogen. Until recently, sulfenic acids were considered too unstable to exist as
anything but intermediate transition states of biomolecular reactions. Research has
shown, however, that certain proteins rely upon these sulfenate mechanisms to play an
important regulatory role in the structure and function of these proteins.

Sulfenic Acid Functional Group

Sulfinic Acids are oxoacids of sulfur with the structure RSO(OH).

Sulfinic Acid Functional Group

Sulfonic Acid is an hypothetical acid with formula H-S(=O)2-OH. This compound is a

tautomer of sulfurous acid HO-S(=O)-OH, but less stable, and would likely convert to
that very quickly if it were formed. Although this compound is unimportant, there are
many derived compounds, with formula R-S(=O)2-OH for various R. These may then
form salts or esters, called sulfonates.

Sulfonic acids are a class of organic acids with the general formula RSO3H, where R is
usually a hydrocarbon side chain. Sulfonic acids are typically much stronger acids than
their carboxylic equivalents, and have the unique tendency to bind to proteins and
carbohydrates tightly; most "washable" dyes are sulfonic acids (or have the functional
sulfonyl group in them) for this reason. They are also used as catalysts and intermediates
for a number of different products. Sulfonic acid salts (sulfonates) are important as
detergents, and the antibacterial sulfa drugs are also sulfonic acid derivatives. The
simplest example is methanesulfonic acid, CH3SO2OH, a reagent regularly used in
organic chemistry. p-Toluenesulfonic acid is also an important reagent.

Note that the sulfonic acids and sulfonates are analogous to carboxylic acids and
carboxylates; in both cases, -C(=O)- is replaced by -S(=O)2-. Chemical properties are
similar as well, although sulfonic acids are often even stronger acids than carboxylic
acids, the hydrogen being easier to leave than in most compounds, and they readily form
esters.

The sulfonic acid and sulfonate functional groups, -SO2OH and -SO2O-, are found in
many chemical compounds, e.g. certain detergents and dyes as well as in strongly acidic
cation exchange resins.

Sulfonic Acid Functional Group

Sulfonate Ester - an ester similar to an ester formed from a carboxylic acid except the
carbon (C) of the carboxyl group (COO) is replaced by a sulfur (S) atom.

Sulfonate Ester Functional Group

A Sulfoxide/Sulfinyl contains a sulfinyl functional group attached to two carbon atoms.

The general structural formula is R−S(=O)−R′ where R and R' are the organic groups.
Sulfoxides can be considered as oxidized sulfides. A common sulfoxide is DMSO.

Alliin, an example of a sulfoxide occurring

Sulfinyl Functional Group, R−S(=O)−R′
in nature.

A Sulfone/Sulfonyl contains a sulfonyl functional group attached to two carbon atoms.

The central sulfur atom is twice double bonded to oxygen and has two further
hydrocarbon substituents. The general structural formula is R−S(=O)2−R′ where R and R'
are the organic groups. A common sulfone is sulfolane C4H8SO2.

Sulfonyl Functional Group, R−S(=O)2−R′

Phosphine is the common name for phosphorus hydride (PH3), also known by the
IUPAC name phosphane and, occasionally, phosphamine. It is a colorless, flammable
gas with a boiling point of -88 °C at standard pressure. Pure phosphine is odorless, but
"technical grade" phosphine has a highly unpleasant odor like garlic or rotting fish, due to
the presence of substituted phosphine and diphosphine (P2H4). Phosphines are also a
group of substituted phosphines, with the structure R3P, where other functional groups
replace hydrogens. They are important in catalysts where they complex to various metal
ions.

Phosphine Oxide, organophosphorus compounds with the formula - OPR3. Phosphines

are often air-sensitive, and are often oxidized to phosphine oxides on prolonged storage.

Phosphoranes are functional groups in chemistry with pentavalent phosphorus. It has

the general structure PR5. The parent compound is the non-stable phosphoran PH5.

Phosphinite, an organophosphorus compounds with the formula P(OR)R2.

Phosphonite, organophosphorus compounds with the formula P(OR)2R.

Phosphite is sometimes used to mean phosphite ester, an organophosphorus compound

with the formula P(OR)3. The phosphite ion (PO33-) is a polyatomic ion with a
phosphorus central atom. Its geometry is trigonal pyramidal. Many phosphite salts,
such as ammonium phosphite, are highly water soluble.

Phosphinate, organophosphorus compounds with the formula OP(OR)R2.

Phosphonates or Phosphonic Acids are organic compounds containing one or more C-

PO(OH)2 or C-PO(OR)2 (with R=alkyl, aryl) groups. Biphosphonates were first
synthesized in 1897 by Von Baeyer and Hofmann. An example of such a bisphosphonate
is HEDP. Since the work of Schwarzenbach in 1949, phosphonic acids are known as
effective chelating agents. The introduction of an amine group into the molecule to
obtain -NH2-C-PO(OH)2 increases the metal binding abilities of the phosphonate.
Examples for such compounds are NTMP, EDTMP and DTPMP. These common
phosphonates are the structure analogues to the well-known aminopolycarboxylates NTA,
EDTA and DTPA. The stability of the metal complexes increases with increasing number
of phosphonic acid groups. Phosphonates are highly water-soluble while the phosphonic
acids are only sparingly soluble. Phosphonates are not volatile and poorly soluble in
organic solvents.

Phosphate is also an organophosphorus compounds with the formula OP(OR)3.

Organophosphates are most commonly found in the form of adenosine phosphates,
(AMP, ADP and ATP) and in DNA and RNA and can be released by the hydrolysis of ATP
or ADP. Similar reactions exist for the other nucleoside diphosphates and triphosphates.
Phosphoanhydride bonds in ADP and ATP, or other nucleoside diphosphates and
triphosphates, contain high amounts of energy which give them their vital role in all
living organisms. They are generally referred to as high energy phosphate, as are the
phosphagens in muscle tissue. Compounds such as substituted phosphines, have uses in
organic chemistry but do not seem to have any natural counterparts. In organic
chemistry, a phosphate, or organophosphate, is an ester of phosphoric acid.

Diphosphene is a molecule that has a phosphorus-phosphorus double bond, indicated by

R-P=P-R'. Diphosphenes are heavier analogues of Azo Compounds.

In 1877, H. Köhler and A. Michaelis reported the isolation of a compound that was
thought to be the phosphorus analogue of azobenzene, "Ph-P=P-Ph", but it later turned
out to be wrong.

In 1981, Masaaki Yoshifuji reported the first stable diphosphene, which is kinetically
stabilized by very bulky two substituents attached to the phosphorus atoms. Numerous
other diphosphenes with a variety of substituents have been synthesized and structurally
characterized. In addition, there are several transition metal complexes where the
diphosphene behaves as an end-on donor through one or both phosphorus atoms.

Phosphazenes are any of a class of chemical compounds in which a phosphorus atom is

covanlently linked to a nitrogen atom by a double bond and to three other atoms or
radicals by single bonds. Two examples are hexachlorophosphazene and
bis(triphenylphosphine)iminium chloride.

Phosphate Esters have the general formula P(=O)(OR)3. In organic chemistry, a

phosphate, or organophosphate, is an ester of phosphoric acid.

Phosphorine is a heavy benzene containing a phosphorus atom instead of a CH in its

ring, so it is considered to be a heavier element anolog of pyridine. It is also called
phosphinine or phosphabenzene. Phosphorine is a planar aromatic compound with 88%
of the aromaticity of that of benzene.