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.gif (626 bytes) alkene.gif (569 bytes) alkyne.gif (484 bytes)
Alkane Alkene Alkyne
CH3-CH3 ethene.gif (891 bytes) ethyne.gif (645 bytes)
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 alcohol.gif (353 bytes) carbox.gif (624 bytes) 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 Derivatives Fluoro- Chloro- Bromo- Iodo-

 

alcohol.gif (353 bytes) aldehyde.gif (599 bytes) ether.gif (515 bytes) ketone.gif (673 bytes)
Alcohol Aldehyde Ether Ketone

 

carbox.gif (624 bytes) ester.gif (708 bytes) amine.gif (600 bytes) amide.gif (604 bytes) NH2CO2H
Carboxylic Acid Ester Amine Amide Amino

 

R-N=O R-N=N-R' R-NO2 R-Cequiv.gif (82 bytes)N R2C=NR'
Nitroso Azo Nitro Nitrile Imine

 

-O-Cequiv.gif (82 bytes)N eqarrow.gif (846 bytes) O=C=N- R-Nequiv.gif (82 bytes)C R–N=C=O ROOR'
Cyanate Isocyanide/Isonitrile Isocyanate Organic Peroxide

 

thiol.gif (1028 bytes) sulfide.gif (1092 bytes) disulfide.gif (1134 bytes)
Thiol/Mercaptans Thioether/Sulfide Disulfide

 

rsoh.gif (950 bytes) rso2h.gif (1015 bytes) rso3h.gif (1062 bytes)
Sulfenic Acid Sulfinic Acid Sulfonic Acid

 

rso3r.gif (1119 bytes) 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
Phosphonite Phosphite/Phosphite Ester Phosphinate Phosphonate

 

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 Derivatives Fluoro- Chloro- Bromo- Iodo-

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.gif (353 bytes) ethanol.gif (621 bytes)
Alcohol Functional Group, Hydroxyl Group Ethanol, Ethyl Alcohol, Grain Alcohol

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.gif (599 bytes) methanal.gif (681 bytes)
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.gif (515 bytes) diethylether.gif (742 bytes)
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.gif (673 bytes) propanone.gif (767 bytes)
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.

carbox.gif (624 bytes) ethanoicacid.gif (749 bytes)
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.gif (708 bytes) isoamylethanoate.gif (1485 bytes)
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 eqarrow.gif (846 bytes) Ester + Water

R'OH + RCOOH eqarrow.gif (846 bytes) 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.gif (600 bytes) methamphetamine.gif (1198 bytes)
Amine Functional Group Methamphetamine

An Amide is one of two kinds of compounds:

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

amide.gif (604 bytes)  

or

amidegroup.gif (1048 bytes)
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' 4-hydroxyphenylazobenzene.jpg (4544 bytes)
Azo Functional Group 4-hydroxyphenylazobenzene

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 -Cequiv.gif (82 bytes)N functional group.  In the -Cequiv.gif (82 bytes)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-Cequiv.gif (82 bytes)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-ion.jpg (3598 bytes)

Cyanate Functional Group

An Isocyanide (also called an Isonitrile is an organic compound with the functional group R-Nequiv.gif (82 bytes)C.  The Cequiv.gif (82 bytes)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.jpg (2501 bytes)
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.gif (1028 bytes)

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.

sulfide.gif (1092 bytes)

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.gif (1134 bytes)

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.

rsoh.gif (950 bytes)

Sulfenic Acid Functional Group

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

rso2h.gif (1015 bytes)

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.

rso3h.gif (1062 bytes)

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.

rso3r.gif (1119 bytes)

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.

dimethylsulfoxide.jpg (2270 bytes) alliin.jpg (6046 bytes)
Sulfinyl Functional Group, R-S(=O)-R¢ Alliin, an example of a sulfoxide occurring 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.

dimethylsulfone.jpg (2381 bytes)

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.

phosphorine.jpg (1912 bytes)

Phosphorine


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Copyright 1997 James R. Fromm