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to the Molecular Structure and Naming-Nomenclature of Functional Groups and Homologous Series in Organic Chemistry Following an introduction answering the question WHY is there such a range of organic molecules? there are sections of styles of representing the structure of organic molecules e.g. molecular formula and molecular structure. Then examples of functional groups, homologous series, general formula, displayed formula, graphic formula, molecular formula, skeletal formula, structural formula, empirical formula of molecules etc. are all explained with links to more examples of structure and naming and quizzes and reaction equations, reaction conditions and mechanisms. Alkanes, Alkenes, Alkynes, Aromatics-arenes, Halogenoalkanes, Alcohols (prim/sec/tert), Phenols, Ethers, Aldehydes, Ketones, Carboxylic acids, Acid/acyl chlorides, Acid Anhydrides, Acid/acyl Amides, Esters, Nitriles, Amines (prim/tert/sec), Quaternary ammonium salts, Nitroaromatics, Diazonium salts and dyes, Sulphonic (sulfonic) acids and a variety possible Aromatic Compounds and Organic Nitrogen Compounds are also included. At the end is a guide to primary, secondary and tertiary structures i.e. the CLASSIFICATION system for haloalkanes, alcohols, amines and amides. Page sub-index: INTRODUCTION * 9.1.1 Styles of structure and formula representation * 9.1.2 Alkanes, Alkenes, Alkynes,Aromatics-arenes, Halogenoalkanes, Alcohols (prim/sec/tert), Phenols, Ethers, Aldehydes, Ketones, Carboxylic acids, Acid chlorides, Acid Anhydrides, Amides, Esters, Nitriles, Amines (prim/tert/sec), Quaternary ammonium salts, Nitroaromatics,Diazonium salts and dyes, Sulphonic (sulfonic) acids, Appendix 1 Guide to primary, secondary and tertiary CLASSIFICATION. More examples, due to the variety of Aromatic Compounds and Organic Nitrogen Compounds, are on separate web pages.
BUT first ... AN INTRODUCTION TO ORGANIC CHEMISTRY i.e. WHY is there such a range of organic molecules and hence why a vast discipline of organic chemistry? o There are many possible series of organic molecules, so why such variety? Organic compounds belong to different families, though all organic compounds are based on carbon C, hydrogen
H, and other elements such as oxygen, nitrogen etc. The chemistry of the oxides of carbon and carbonates is NOT considered part of organic chemistry.
Most food is chemically organic in nature, apart from some minerals, and many drugs and plastic materials are composed of organic molecules, consequently, organic compounds and organic chemistry is rather important to us! The term organic compound comes from the fact that most of the original organic compounds studied by scientists-chemists came from plants or animals, i.e. of natural origin and contained the 'vital force' of mother nature! o o Historically, for thousands of years, many organic compounds have been used indirectly in herbal preparations for healing and alleviating symptoms and in food materials such as honey. Many natural products have proved precursors for the development of synthetic 'man-made' drugs manufactured by the pharmaceutical industry.
These days most organic compounds are produced and synthesised from raw materials, in particular the physical separation and chemical manipulation of the products of fractionally distilling crude petroleum oil. However, this description of organic chemistry and its historical origins does NOT explain the vast range of organic molecules and their complex chemistry. The principal reason why the range of organic molecules is primarily due to the fact that carbon atoms have the ability to link together by strong covalent bonds to form linear chains, branched chains and cyclic chains and with considerable numbers of rearrangements to make different molecules of the same formula (isomers). o Carbon is in Group 4 of the periodic Table with four outer electrons (2. 4 or 1s 2s 2p ) which readily pair with electrons from an atom like oxygen or nitrogen to give four stable covalent bonds (maybe 4 single bonds, 2 single and a double bond, two double bonds or a triple and a single bond), either way, the normal valency (combining power) of carbon in organic compounds is four.
2 2 2
o o
The property of forming chains is called catenation. To add to the complexity and variety of organic molecules, carbon can also form stable bonds with other elements, especially ...
oxygen as in alcohols like ethanol acids to make esters used in flavourings and perfumes.
nitrogen and oxygen in amino acids like aminoethanoic acid amino acids in proteins.
halogens as in bromoethane
synthesis of more complex organic compounds. and sulfur & phosphorus etc. by substituting a hydrogen atom with another element or group of atoms compared to alkanes like butane o which only consists of carbon and hydrogen atoms.
So, this leads to even more possible 'families' of organic compounds and many more individual different molecules.
There is no limit to the number of different organic molecules that can be made, though only a small percentage of them would be useful. The molecular formula represents a summary of all the atoms in the molecule and a general formula sums up the formulae a series of compounds e.g. a homologous series of chemically similar compounds. More on these terms later, but you need their basic definition to appreciate the next point I'm making.
Just to give you an idea of the limitlessness of organic chemistry, using some simple molecular formulae and general formulae, consider the table below of the number of molecules which can theoretically exist for a given molecular formula e.g. if n = 5 for the number of carbon atoms in the molecular formula you get ... alkanes of molecular formula C5H12 alkenes/cycloalkanes of formula C5H10 alcohols/ethers of formula C5H12O and amines of formula C5H13N Some of these numbers have been worked out using a computer program i.e. an algorithm to compute possible numbers of molecules of a given general formula given a set of rules based on valencies.
Number of carbon atoms n in the general formula below CnH2n+2 CnH2n CnH2n+2O CnH2n+3N
10
11
12
examples of homologous series with this general formula alkanes alkenes, cycloalkanes alcohols, ethers amines
2 3
3 5
18 66
35 153
75 377 989
159 ~915
355 ~2300
13 27
7 14 32 72 171 405
o o o
As the number of carbon atoms increases the number of possible arrangement of the atoms increases
dramatically even for molecules just containing carbon and hydrogen. Once you substitute a hydrogen atom for another element or group of atoms, there is a bewildering number of
possibility of molecular structures. The fact that life, as far as we know it, is based on carbon chemistry, and we do not know of another element from which the same huge variety of stable molecules can be me made. Even unstable organic molecules can be synthesised and manipulated in the laboratory and biochemistry is based on the thousands of molecules that exist in living systems e.g. sugars, proteins (tissue, enzymes etc.), RNA, DNA, fats like lipids etc. etc. etc.!!!. In one of the simplest living cells like an E coli cell, there may be 5000 different compounds, most of them organic molecules! (e.g. as many as 3000 proteins and 1000 nucleic acids i.e. RNA/DNA molecules) The compounds in each family have a similar chemical structure and a similar chemical formula and each family of organic compounds forms what is called ahomologous series. o o As pointed out, different families arise because carbon atoms readily join together in chains (catenation) and strongly bond with other atoms such as hydrogen, oxygen and nitrogen. The result is a huge variety of 'organic compounds' which can be classified into groups of similar compounds i.e. these different homologous series. A homologous series is a family of compounds which have a general formula* and have similar chemical properties because they have the same functional group of atoms o o o o e.g. C=C alkene, C-OH alcohol or -COOH carboxylic acid etc. A functional group is an atom or combination of atoms which gives an organic molecule its distinctive and characteristic chemistry. The term 'functional' group is linked to the concept of a homologous series. A homologous series is a group of molecules with the same general formula and the same functional group.
They have similar physical and chemical properties such as appearance, melting/boiling points, solubility etc (albeit with trends e.g. increasing boiling point with increasing carbon chain length i.e. increase in molecular mass). The terms higher/lower refer to a larger/smaller or longer/shorter carbon chains.
The molecular formula represents a summary of all the atoms in the molecule e.g. butane is C4H10 and can be derived from a general formula - which is explained in the next section 9.1.1
An empirical formula is the simplest whole number ratio of the atoms in a compound as found by experiment i.e. chemical analysis. It gives no structural information and may or may not be the same as the molecular formula e.g. CH 4 is both the empirical formula and the molecular formula of methane. However, the molecular formula of the butane molecule is C4H10 but its empirical formula is C2H5. The molecular formula of a glucose sugar molecule is C6H12O6 but its empirical formula is only CH2O !
A molecular formula e.g. C3H6O2, gives a summary of all the atoms in the molecule, but gives no information on structure.
or
unambiguous in terms of interpreting ALL atom-atom links and no/some individual bonds may be shown.
However it can be acceptable to show some side-chain groups in an abbreviated form e.g. methylpropane
where the side-chain methyl group may be written in the abbreviated form, but take car in exams!
bond angles (in this case all are 109 ). The 'dotted line' bond is behind the plane of the screen/paper/page and the 'wedge' bond is towards you. The other two thin line bonds are in the plane of the screen/paper/page etc. This gives a good impression of the real shape of the molecule in terms of the directional covalent bonds and all bond angles here are ~109 .
o
in which none of the H atoms bonded to carbon atoms are shown. The lines represent either carbon-carbon
bonds (single, double or triple), but other lines are needed to show bonds to other atoms which are NOT carbon or hydrogen e.g. C-Cl in
and hydrogen atoms are shown if they are bonded to non-carbon atoms e.g. the C-OH in
A general formula sums up the formulae a series of compounds e.g. a homologous series of chemically similar compounds with closely related formulae e.g. the only difference may be more/less -CH2- groupings in the carbon longest chain. There are many examples quoted throughout the rest of this page in the style CxHyOz etc. where x, y and z are integer variables like 1, 2, 3 etc. but they related for a particular homologous series e.g. for saturated non cyclo alkanes the general formula is CnH2n+2 for alkanes, so that n=1 generates the formula for methane CH4 and n=5 generates the formula for pentane C5H12 etc. and ..... CnH2n+1COOH is the general formula for monocarboxylic acids, so that n=0 generates the formula for methanoic acid HCOOH and n=4 generates the formula for pentanoic acid CH3CH2CH2CH2COOH (so do not assume n always indicates the total carbon atoms in a molecule!). However in all cases, the IUPAC systematic name is derived from the longest carbon chain, so both meth... (for one carbon) and pent... (for five carbons) occur in the names of the examples above.
FUNCTIONAL GROUPS and HOMOLOGOUS SERIES Summary of nomenclature, structure and representation in pictures-graphics
9.1.2 ALKANES or cycloalkanes HYDROCARBONS (saturated) ANE, e.g. ALKANES, saturated hydrocarbons i.e. no double or triple bonds. They can be linear, branched, cyclo, substituted etc. (see later - haloalkanes etc.)
butane,
pentylcyclohexane,
cyclopropane
2,2-dimethylpropane,
2,2,3-trimethylbutane
Exemplar homologous series: CnH2n+2 for non-cyclo alkanes (n=1,2,3 etc.) and CnH2n for cycloalkanes (n=3,4,5 etc.) isomeric with non-cyclo alkenes
further
Notes on selected reactions of alkanes from a mechanistic point of view but giving general equations and reaction conditions too
9.1.3 ALKENE HYDROCARBONS (unsaturated) ENE, ALKENES, unsaturated hydrocarbons with a carbon=carbon C=C double bond functional group (ene) They can have more than one C=C, be linear, branched, cyclo
pent-1-ene,
3-ethylpent-1-ene,
cyclobuta-1,3-diene
or
buta-1,3-diene,
cyclohexene
further
Type in an alkene name short answer QUIZ Exemplar homologous series: CnH2n for non-cyclo alkenes (n=2,3 etc. with one C=C bond) isomeric with cycloalkanes and CnH2n-2 for cycloalkenes (n=3,4,5 etc., and with one C=C bond)
Notes on selected reactions of alkenes from a mechanistic point of view but giving general equations and reaction conditions too
9.1.4 ALKYNE HYDROCARBONS (unsaturated) YNE e.g. ALKYNES, unsaturated hydrocarbons with a C C triple bond functional group (yne) e.g.
ethyne, and
propyne
Exemplar homologous series: CnH2n-2 for non-cyclo alkynes (with one triple bond)
9.1.5 AROMATIC HYDROCARBONS (unsaturated) 'ARENES' are aromatic hydrocarbons with at least one benzene ring functional group e.g.
or
benzene,
or
methylbenzene
further
further
Notes on selected reactions of aromatic compounds (arenes) from a mechanistic point of view but giving general equations and reaction conditions too
9.1.6 aliphatic/aromatic HALOGEN COMPOUNDS Aliphatic: HALO e.g. HALOGENOALKANES (HALOALKANES) C-X halogen functional group where X = F fluoro, Cl chloro.., Br bromo or I iodo X is named as a prefix substituent in any type of organic molecule from alkanes to carboxylic acids.
chloromethane,
bromoethane,
dichlorodifluoromethane
1-bromo-1-chlorobutane,
iodocyclohexane
1,2-dibromocyclopentane,
chloromethylbenzene
or phenylchloromethane, which can also be classified as an aromatic compound BUT the halogen is not attached directly to the benzene ring so it is not an aryl halide) Exemplar homologous series: CnH2n+1X for non-cyclo saturated halogenoalkanes (X=F,Cl,Br,I and n=1,2,3 etc.) and CnH2n-1X for saturated cyclohalogenoalkanes (n=3,4,5 etc. with one C-X bond) A sub-CLASSIFICATION based on structural differences, which can have chemical consequences on e.g. rate of reaction or products formed in a reaction. o o Halogenoalkanes are classified according to the atoms/groups attached to the carbon of the halogen atom X. Primary halogenoalkanes have the structure R-CH2-X, R = H, alkyl, aryl etc. i.e. apart from chloromethane they have one alkyl/aryl group attached to the C of the C-X group. e.g. chloroethane CH3CH2Cl
Secondary halogenoalkanes have the structure R2CH-X, R = alkyl or aryl etc. i.e. they have two alkyl/aryl groups attached to the C of the C-X group. e.g. 2-bromobutane CH3CHBrCH2CH3
Tertiary halogenoalkanes have the structure R3C-X, R = alkyl or aryl etc. i.e. they have three alkyl/aryl groups attached to the C of the C-X group. e.g. 2-iodo-2-methylpropane (CH3)3CI
further
Notes and examples of the structure, classification and nomenclature of primary, secondary and tertiary haloalkanes - 3 linked pages
Notes on selected reactions of halogenoalkanes (haloalkanes) from a mechanistic point of view but giving general equations and reaction conditions too NOTE: Aromatic HALO ... ARENES (aromatic halogen compounds) have the halogen atom directly attached to the benzene ring.
chlorobenzene,
1,4-dichlorobenzene,
chloro-2-methylbenzene
9.1.7 ALCOHOLS (aliphatic, alkanols) and PHENOLS (aromatic) Aliphatic OH hydroxy functional group (ol) e.g. ALIPHATIC ALCOHOLS. Aliphatic alcohols are classified as primary, secondary and tertiary. You can have diols, triols etc, with 2,3 etc, OH groups. If there is a 'higher ranking' functional group in the molecule the substituent OH is called by the prefix 'hydroxy' see * examples. Primary aliphatic alcohols R-OH where R is alkyl
ethanol,
ethan-1,2-diol
or
3-methylbutan-1-ol
4-hydroxybutanoic acid*
Secondary aliphatic alcohols R-CH(OH)-R' where R or R' are both alkyl (or aryl):
propan-2-ol,
butan-2-ol,
cyclohexanol,
pentan-3-ol
cyclopentanol,
2-hydroxybutanoic acid*
Tertiary aliphatic alcohols RR'R"C-OH where R,R' or R" are all alkyl (or aryl):
or
2-methylpropan-2-ol,
2-methylbutan-2-ol
or
3-methylpentan-1-ol
Exemplar homologous series: CnH2n+1OH for saturated non-cyclic aliphatic alcohols (n=1,2,3 etc.)
or the less informative CnH2n+2O isomeric with aliphatic non-cyclo ethers and CnH2n-1OH for cycloalcohols (n=3,4,5 etc. with one C-OH)
Notes on selected reactions of alcohols from a mechanistic point of view but giving general equations and reaction conditions too AROMATIC PHENOLS ROH, R=aryl only, when the -OH functional group is attached directly to a benzene ring the molecule is called a phenol. If there is a 'higher ranking' functional group in the molecule the substituent OH is called by the prefix 'hydroxy' see * example.
or
or
phenol,
2-chlorophenol,
3-methylphenol
2,5-dichloro-4-methylphenol,
3-hydroxybenzoic acid*
9.1.8 ETHERS Alkyl/arylOXYalkane/arene e.g. ETHERS which have the C-O-C linkage. The smaller carbon chain with the oxygen atom, is given the prefix in the name alkyl/aryl..oxyane (alkyl-O- groups like CH3-O- are called alkoxy groups).
methoxymethane,
methoxyethane,
2-ethoxypropane
ethoxyethane,
2-methoxypropane,
Exemplar homologous series: CxH2x+1-O-CyH2y+1 for saturated non-cyclo ethers (x or y =1,2,3 etc.) or the less informative CnH2n+2O (n=2,3,4 etc.) isomeric with non-cyclo aliphatic alcohols or CnH2nO for cycloethers (n=2,3,4 etc. with one C-O-C linkage, non shown at the moment)
further
9.1.9 ALDEHYDES and KETONES (a group of carbonyl compounds) AL e.g. ALDEHYDES have the -CHO functional group at the end of a carbon chain e.g.
ethanal,
propanal,
or
2-methylpropanal
butanal,
pentanal,
2-methylbutanal
Exemplar homologous series: CnH2n+1CHO for aliphatic aldehydes (n=0,1,2 etc.) or the less in formative CmH2mO (m=1,2,3 etc.) isomeric with ketones and saturated cyclic aliphatic ethers
further
Notes on selected reactions of aldehydes/ketones from a mechanistic point of view but giving general equations and reaction conditions too ONE e.g. KETONES have the C-CO-C functional group linkage within the carbon chain:
propanone,
or
butanone,
pentan-2-one
or
pentan-3-one
Exemplar homologous series: CxHxn+1-CO-CyH2y+1 for aliphatic ketones (x or y = 1,2,3, etc.) or the less informative CnH2nO (n=3,4,5 etc.) isomeric with aldehydes and saturated cyclic aliphatic ethers
further
Notes on selected reactions of aldehydes/ketones from a mechanistic point of view but giving general equations and reaction conditions too
9.1.10 CARBOXYLIC ACIDS OIC ACID e.g. CARBOXYLIC ACIDS with the -COOH functional group, substituents quoted as prefixes (dioic if 2 -COOH groups) e.g. aliphatic carboxylic acids
methanoic acid,
propanoic acid,
*aminoethanoic acid
2-methylpropanoic acid,
*2-hydroxybutanoic acid
* ethanedioic acid
If there is a 'higher ranking' functional group in the molecule the substituent OH/NH2 is called by the prefix 'hydroxy/amino see * examples. Exemplar homologous series: CnH2n+1COOH for saturated aliphatic mono carboxylic acids (n=0,1,2,3 etc.) or the less informative CnH2nO2 (n=1,2,3,4 etc.) isomeric with aliphatic esters aromatic carboxylic acids (-COOH directly attached to the ring)
* 3-hydroxybenzoic acid,
2-chlorobenzoic acid,
* benzene-1,2-dicarboxylic acid
(sometimes carboxylic rather than oic is used e.g. the dicarboxylic acids of benzene)
further
Notes and examples of the structure and nomenclature of carboxylic acids and their derivatives
9.1.11 ACID ANHYDRIDES OIC ANHYDRIDE e.g. CARBOXYLIC ACID ANHYDRIDES with the RCO-O-RCO linkage e.g.
or
ethanoic anhydride
or
pentanoic anhydride
Exemplar homologous series: (CnH2n+1CO)2O derived from aliphatic mono carboxylic acids (n=2,3 etc.)
further
Notes and examples of the structure and nomenclature of carboxylic acids and their derivatives
9.1.12 ACID or ACYL CHLORIDES OYL CHLORIDE e.g. CARBOXYLIC ACID or ACYL CHLORIDES with the -COCl functional group e.g.
or
propanoyl chloride,
butanoyl chloride
or
pentanoyl chloride,
benzoyl chloride
Exemplar homologous series: CnH2n+1COCl derived from aliphatic mono carboxylic acid chlorides (n=1,2,3 etc.)
further
Notes and examples of the structure and nomenclature of carboxylic acids and their derivatives
Notes on selected reactions of acid/acyl chlorides from a mechanistic point of view but giving general equations and reaction conditions too
9.1.13 ACID AMIDES AMIDE e.g. CARBOXYLIC ACID AMIDES with the -CONH2 functional group e.g.
or
ethanamide,
propanamide
butanamide,
pentanamide,
benzamide
Exemplar homologous series: CnH2n+1CONH2 derived from aliphatic mono carboxylic acid amides (n=0,1,2,3 etc.)
further
Notes and examples of the structure and nomenclature of carboxylic acids and their derivatives
9.1.14 ESTERS alkyl/aryl OATE e.g. ESTERS of CARBOXYLIC ACIDS derived from ALCOHOLS or PHENOLS. Esters have the -COOC- linkage:
methyl methanoate,
propyl propanoate
ethyl propanoate,
ethyl benzoate
Exemplar homologous series: CxH2x+1-COO-CyH2y+1 simple saturated aliphatic esters (x=0,1,2, etc. and y=1,2,3 etc.) or the less informative CnH2nO2 (n=2,3,4 etc.) isomeric with carboxylic acids
further
Notes and examples of the structure and nomenclature of carboxylic acids and their derivatives
9.1.15 NITRILES The nitrile functional group consists of a carbon to nitrogen triple bond.
The name is based on the longest carbon chain, including the C of the nitrile group e.g.
methanenitrile,
ethanenitrile,
propanenitrile,
Exemplar homologous series: CnH2n+1CN derived from aliphatic mono carboxylic acid chlorides (n=0,1,2,3 etc.)
further
Notes and examples of the structure and nomenclature of carboxylic acids and their derivatives
9.1.16 AMINES
PRIMARY AMINES have two hydrogen atoms and one alkyl or aryl group attached to the nitrogen to form the amine or amino group NH2.
ethylamine (aminoethane),
Exemplar homologous series: CnH2n+1NH2 for saturated mono primary amines (n=1,2,3 etc.) SECONDARY AMINES have one hydrogen atom and two alkyl or aryl groups attached to the nitrogen
ALIPHATIC: dimethylamine,
ethylmethylamine,
diethylamine,
TERTIARY AMINES have no hydrogen atom and three alkyl or aryl groups attached to the nitrogen
ALIPHATIC: trimethylamine,
ethyldimethylamine,
diethylmethylamine,
9.1.17 QUATERNARY AMMONIUM SALTS If all for hydrogens of an ammonium ion are replaced with alkyl or aryl groups then an ionic quaternary salt is formed. e.g. the simplest is tetramethylammonium chloride, (CH3)4N Cl
+ -
9.1.18 NITRO-AROMATIC COMPOUNDS These have the nitro -NO2 group directly attached to the ring e.g.
nitrobenzene,
; 1,3-dinitrobenzene,
2-methylnitrobenzene or 1-methyl-2-nitrobenzene,
9.1.19 DIAZONIUM SALTS and AZO DYES Diazonium salts are formed when primary aromatic amines reaction with nitrous acid The diazonium cation has a nitrogen - nitrogen triple bond system directly attached to the benzene ring e.g.
(1)
from phenylamine+
(2)
from 4-methylphenylamine
In alkaline solution these diazonium salts couple with phenols and aromatic amines to form azo dyes which have benzene rings linked with an azo -N=N- bond systeme.g.
9.1.20 SULPHONIC ACIDS These molecules have a strongly mono-basic acidic group -SO2OH directly attached to the benzene ring e.g.
benzenesulphonic acid,
APPENDIX 1 A guide to primary, secondary and tertiary structures The CLASSIFICATION system for haloalkanes, alcohols, amines and amides
PRIMARY
SECONDARY
TERTIARY
HALOALKANES (halogenoalkanes)
affect both the rate (reactivity) and mode (substitution or elimination) of the reaction
bromoethane
Phenols are NOT classified in this way. The ease of oxidation ALCOHOLS and nature of product is affected by the class of the alcohol
examples of alcohols
There are prim/sec/tert aliphatic AMINES (alkyl) or aromatic (aryl) amines. See also Note 3. below the table.
diphenylamine
The amide group comprises an amine group attached to the C acyl or acid AMIDES of a C=O carbonyl group, which gives it its own unique chemistry i.e. its neither an amine or an aldehyde or ketone!
examples of amides
*************************************** *
NOTES
1. 2.
Abbreviations commonly used: prim or 1 (primary), sec or 2 (secondary) and tert or 3 (tertiary) R and R' do not have to be the same i.e. -R2 could mean -RR' and -R3 could mean -RR'R"
3.
o
amines can form a quaternary ammonium ion e.g. in the salt tetramethylammonium chloride, (CH3)4N Cl
+ -
4.