Biochem Func. Groups

8/14/2019 Biochem Func. Groups

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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. Thesame 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 aregenerally 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 asthe 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 ideaof different independent or semi-independent atoms or groups of atoms on the samemolecule is central to our modern understanding of organic chemistry. It is called the

concept offunctional groups. The nomenclature of organic compounds, like most of the

rest of our understanding of reactions of organic compounds, is based upon the concept offunctional 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 componentof 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. Thisprocess is called substitution of the functional group.

The principle used is that organic compounds are named and generally understood assubstituted 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

theAlkanes, followed by theAlkenes andAlkynes.

Alkane Alkene Alkyne

CH3-CH3

Ethane Ethene Ethyne


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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 apolyatomic ion or complex ion. And all of these are called radicals, by a meaning of the

term radicalthat 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 arefar 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 toany group of atoms.

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

HalogenDerivatives

Fluoro- Chloro- Bromo- Iodo-

Alcohol Aldehyde Ether Ketone
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NH2CO2H

Carboxylic

Acid

Ester Amine Amide Amino

R-N=O R-N=N-R' R-NO2 R-C N R 2C=NR'

Nitroso Azo Nitro Nitrile Imine

-O-C N O=C=N- R-N C RN=C=O ROOR'

Cyanate Isocyanide/Isonitrile Isocyanate Organic Peroxide

Thiol/MercaptansThioether/Sulfide Disulfide

Sulfenic Acid Sulfinic Acid Sulfonic Acid

RS(=O)R R-S(=O)2R

Sulfonate Ester Sulfoxide/SulfinylSulfone/Sulfonyl

PR3 R3P=O PR 5 P(OR)R2Phosphine/Phosphane Phosphine Oxide Phosphorane Phosphinite
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P(OR)2R P(OR)3 OP(OR)R2 R-P(=O)(OR)2

PhosphonitePhosphite/Phosphite

EsterPhosphinate Phosphonate

OP(OR)3 P=P P=N P(=O)(OR)3Phosphate Diphosphene Phosphazene Phosphate Ester

PC5R5Phosphorine

Haloalkanes (also known asHalogenoalkanes) 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 knownfamily 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-IHalogen

DerivativesFluoro- Chloro- Bromo- Iodo-

An Alcohol functional group is a hydroxyl group bonded to an sp 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 generallycalled a phenol rather than an alcohol. Also, if the hydroxyl group is bonded to one of the

sp 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 twononbonded electron pairs.

Alcohol Functional Group, Hydroxyl

GroupEthanol, Ethyl Alcohol, Grain Alcohol

An Aldehyde is an organic compound containing a terminal carbonyl group. Thisfunctional group, which consists of a carbon atom which is bonded to a hydrogen atomand 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 wordaldehyde seems to have arisen from alcoholdehydrogenated.
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Aldehyde Functional Group, Aldo Group Methanal, Formaldehyde

Ether is the general name for a class of chemical compounds which contain an oxygenatom 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 carboxylicacids, 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 arecalled 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 byR') replaces a hydrogen atom in the hydroxyl group of an organic acid. Organic acids aremolecules which have an -OH group from which the hydrogen (H) can dissociate as an


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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 reversereaction 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 keyatom. 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 carbonylgroup, 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:


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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.

Amide Functional Group

or

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 formulaR-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)3CNONitroso 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

Group4-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 Greeka (not) +zoe (to live).

Nitro Compounds are organic compounds that contain one or more nitro functionalgroups (-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 compoundsare trinitrophenol (picric acid) and trinitrotoluene (TNT).

R-NO2


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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 orcyano group and compoundswith 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-nitrogendouble 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 anelimination 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, bornemainly 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 thenitrogen 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).


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-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 asulfhydryl 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 etherexcept that it contains a sulfur atom in place of theoxygen. 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 andthe cofactor biotin.

In organic chemistry , "Sulfide" usually refers to the linkage C-S-C, although the termthioetheris 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 canmean CH3-SH. The preferred descriptor for such SH-containing compounds is thiolormercaptan, i.e. methanethiol or methyl mercaptan.


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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 overallconnectivity is therefore C-S-S-C. The terminology is almost exclusively used in

biochemistry, bioinorganic and bioorganic chemistry. Formally the connection is called apersulfide, 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 isnot 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 animportant 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 tothat very quickly if it were formed. Although this compound is unimportant, there are

many derived compounds, with formulaR-S(=O)2-OH for variousR. These may thenform salts or esters, calledsulfonates.

Sulfonic acids are a class of organic acids with the general formulaRSO3H, whereR isusually 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 functionalsulfonyl group in them) for this reason. They are also used as catalysts and intermediates


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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 inorganic chemistry. p-Toluenesulfonic acid is also an important reagent.

Note that thesulfonic acids andsulfonates are analogous to carboxylic acids andcarboxylates; 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 carboxylicacids, 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 acidiccation 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 asulfinylfunctional group attached to two carbon atoms.

The general structural formula is RS(=O)R where R and R' are the organic groups.

Sulfoxides can be considered as oxidized sulfides. A common sulfoxide is DMSO.

Sulfinyl Functional Group, RS(=O)RAlliin, 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


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hydrocarbon substituents. The general structural formula is RS(=O)2R where R and R'

are the organic groups. A common sulfone is sulfolane C4H8SO2.

Sulfonyl Functional Group, RS(=O)2R

Phosphine is the common name forphosphorus hydride (PH3), also known by the

IUPAC namephosphane and, occasionally,phosphamine. It is a colorless, flammablegas 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 agroup of substituted phosphines, with the structure R3P, where other functional groups

replace hydrogens. They are important in catalysts where they complex to various metalions.

Phosphine Oxide, organophosphorus compounds with the formula - OPR3. Phosphinesare 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-stablephosphoran 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 meanphosphite ester, an organophosphorus compound

with the formula P(OR)3. Thephosphite 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 orPhosphonic 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 bisphosphonateisHEDP. 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 areNTMP, EDTMPand DTPMP. These common

phosphonates are the structure analogues to the well-known aminopolycarboxylatesNTA,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


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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, ADPandATP) and inDNA andRNA and can be released by the hydrolysis ofATPorADP. Similar reactions exist for the other nucleoside diphosphates and triphosphates.

Phosphoanhydride bonds inADPandATP, or other nucleoside diphosphates andtriphosphates, 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 inorganic 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. Khler 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 kineticallystabilized 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 iscovanlently linked to a nitrogen atom by a double bond and to three other atoms or

radicals by single bonds. Two examples are hexachlorophosphazene andbis(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 calledphosphinine orphosphabenzene. Phosphorine is a planar aromatic compound with 88%

of the aromaticity of that of benzene.


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Biochem Func. Groups

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