Naming and representing organic molecules

Six ways to write one molecule

Rancid butter smells of butanoic acid. A chemist writing about it might put C₄H₈O₂ on one line, CH₃CH₂CH₂COOH on the next and a short zigzag ending in a C=O on the third, and all three mean the same molecule. Each formula answers a different question: what the ratio of atoms is, how many of each there are, what is joined to what, and what the molecule looks like when drawn quickly.

Describe the drawing

Six boxes describing butanoic acid. The top row gives the empirical formula C₂H₄O, the molecular formula C₄H₈O₂ and the general formula CₙH₂ₙ₊₁COOH with n equal to three. The bottom row gives the structural formula CH₃CH₂CH₂COOH; a displayed formula with four carbons in a row, seven C–H bonds, a C=O double bond and an O–H at the end; and a skeletal zigzag of three lines ending in a double bond to O and a single bond to OH.

The molecular formula, C₄H₈O₂, gives the actual number of atoms of each element in one molecule. Dividing through by the highest common factor gives the empirical formula, C₂H₄O, the simplest whole-number ratio. Ethyl ethanoate, the solvent in nail-varnish remover, is also C₄H₈O₂ and also C₂H₄O, so neither formula separates it from butanoic acid. Organic chemistry needs the other four for that reason.

A general formula is the algebraic formula that fits every member of a series. The carboxylic acids are CₙH₂ₙ₊₁COOH, so butanoic acid has n = 3. The alkanes are CₙH₂ₙ₊₂, the alkenes CₙH₂ₙ and the alcohols CₙH₂ₙ₊₁OH. A general formula gives the molecular formula of any member once n is chosen, and says nothing about how the atoms are arranged.

A structural formula shows, with the minimum of detail, the arrangement of atoms carbon by carbon: CH₃CH₂CH₂COOH. CH₃(CH₂)₂COOH is the same formula with the repeated unit bracketed. A group hanging off the chain goes in brackets after the carbon it is joined to, so propan-2-ol is CH₃CH(OH)CH₃. A structural formula fits one compound only, which C₄H₈O₂ does not.

A displayed formula shows every atom and every bond as a line: all four carbons, all eight hydrogens, the C=O as a double line and the O–H as a single line. Writing OH at the end of a bond is a structural shorthand, and where a question asks for the displayed formula the O–H bond has to be drawn. Bond angles are not required, so a flat drawing with right angles is accepted.

A skeletal formula reduces the drawing to the carbon skeleton. Each line is a C–C bond, each end and each corner is a carbon atom, and the hydrogens on carbon are left out: every carbon makes four bonds, and the bonds not drawn are to hydrogen. Atoms other than carbon and hydrogen are written in, with any hydrogen attached to them, so the acid group appears as a line to a double-bonded O and a line to OH. Benzene is drawn as a hexagon with a circle inside it.

The command decides which formula to write. 'Give the molecular formula' wants C₄H₈O₂. 'Draw the structure' accepts a structural, displayed or skeletal formula, provided it is unambiguous, while 'draw the displayed formula' accepts only that. In a mechanism the bonds the arrows touch are drawn displayed and the rest of the molecule can be written structurally.

Empirical formula

The simplest whole-number ratio of atoms of each element in a compound.

Molecular formula

The actual number of atoms of each element in one molecule of a compound.

General formula

An algebraic formula that can describe any member of a homologous series, such as CₙH₂ₙ₊₂ for the alkanes.

Structural formula

The minimal detail that shows the arrangement of atoms in a molecule, such as CH₃CH₂CH₂COOH.

Displayed formula

A formula showing the relative positioning of all the atoms in a molecule and every bond between them.

Skeletal formula

A simplified formula showing the carbon skeleton as lines, with hydrogen atoms on carbon removed and functional groups shown.

Homologous series and functional groups

Methane, ethane, propane and butane burn with the same clean blue flame, and none of them reacts with acid, alkali or bromine water in the dark. Their boiling points climb steadily, from −162 °C for methane to about −1 °C for butane. They are four members of one homologous series: they share a general formula, each differs from the next by CH₂, and they react in the same way because they have the same functional group.

The functional group is the atom or group of atoms that decides how a molecule reacts. In ethanol it is the OH. Ethanol and propan-1-ol both react with sodium, both burn, and both oxidise first to an aldehyde and then to a carboxylic acid, because the reactions happen at the OH and the carbon it is joined to; the length of the chain behind them makes little difference. Physical properties do change along a series. Each extra CH₂ adds electrons, so the van der Waals forces between molecules are stronger and the boiling point is higher.

Describe the drawing

Thirteen tiles, one for each homologous series, each showing its functional group drawn with bonds and the rest of the molecule as R, then the series name, its name ending or prefix and a three-carbon example. The alkane, alkene, halogenoalkane, alcohol, ketone, ester, amine and arene tiles come first; the aldehyde, carboxylic acid, acyl chloride, amide and nitrile tiles sit together on an amber band headed only at the end of a chain.

An alkyl group is an alkane with one hydrogen removed, and R stands for one in a general formula: methyl, CH₃, ethyl, C₂H₅, propyl, C₃H₇. A compound is saturated if it has only single bonds between its carbon atoms and unsaturated if it has at least one C=C or C≡C. Bromine water tells the two apart: an unsaturated compound turns it from orange to colourless, and a saturated one leaves it orange.

A definition of a homologous series needs all three of its parts: the same functional group, the same general formula, and each member differing from the next by CH₂. 'A family of similar compounds' names none of them. A functional group is defined by what it does, the part of the molecule responsible for its characteristic reactions, not by where it sits in the chain.

Homologous series

A series of organic compounds with the same functional group and general formula, in which each member differs from the next by CH₂.

Functional group

An atom or group of atoms in a molecule that is responsible for its characteristic chemical reactions.

Hydrocarbon

A compound containing carbon and hydrogen only.

Saturated

Containing only single bonds between carbon atoms.

Unsaturated

Containing at least one carbon–carbon double or triple bond.

Chains, rings and the shape around each carbon

Alkanes, alkenes and cycloalkanes are hydrocarbons, compounds of carbon and hydrogen only, and their skeletons come in three forms. In a straight-chained molecule such as pentane each carbon is joined to no more than two others. In a branched one, such as 2-methylbutane, at least one carbon is joined to three or four. In a cyclic one, such as cyclohexane, the carbons close into a ring. Straight describes the connections, not the shape: the bonds round each carbon of pentane are at 109.5°, so the chain is a zigzag, as the skeletal formula draws it.

The shape round each carbon follows from the number of regions of electron density. Four single bonds point to the corners of a tetrahedron, 109.5° apart. A carbon in a C=C has three regions, the double bond counting as one, and is trigonal planar at 120°. A carbon in a C≡C or C≡N has two and is linear, 180°. One molecule can hold all three. In but-3-enenitrile, CH₂=CHCH₂CN, carbon 1, the nitrile carbon, is linear, carbon 2 is tetrahedral, and carbons 3 and 4 are trigonal planar.

A skeletal formula draws these shapes without saying so. The zigzag of a chain is the 109.5° angle drawn flat, and benzene's hexagon is flat because each of its carbons is trigonal planar. Count the regions round a carbon, not the atoms joined to it: the carbon of a C=O is joined to three atoms and has three regions, and a double bond counts once.

Building a name

Every IUPAC name is built from three parts. The stem counts the carbons in the longest chain that contains the functional group. The suffix names the main functional group. Prefixes name the branches and any group that is not the suffix, each with a number, its locant, giving the carbon it is attached to.

Describe the drawing

A flow chart of five boxes joined by downward arrows: identify the functional groups and take the suffix from the most senior; find the longest chain containing it for the stem; number from the end that gives the suffix group the lowest locant; name branches as prefixes with locants; assemble the name. Above it the skeletal formula of 3-methylpentan-2-ol is drawn with its carbons numbered one to five from the OH end, and beside each box is the result of that step: -ol, pentan, OH on C2, 3-methyl, and finally 3-methylpentan-2-ol.

Start with the longest continuous chain of carbon atoms that contains the functional group. It need not run straight across the page. CH₃CH(CH₂CH₃)CH₃ looks like a three-carbon chain with an ethyl branch on the middle carbon, but the branch continues the chain: the longest run is four carbons, so the compound is a butane with a methyl group on carbon 2, 2-methylbutane.

Number the chain from the end that gives the suffix group the lowest number. Where no suffix group settles it, number from the end nearer the first branch or halogen. The general rule is the lowest set of locants at the first point of difference: 2,2,4 beats 2,4,4, since at the second number 2 is lower than 4. If the two ends still tie, the prefix that comes first in the alphabet takes the lower number, so CH₃CHBrCH(CH₃)CH₃ is 2-bromo-3-methylbutane.

Write the prefixes in alphabetical order. Two identical groups take di and three take tri, each with its own locant, and di and tri are ignored when alphabetising. Numbers are separated from each other by commas and from letters by hyphens, and the whole name is one word: 3-ethyl-2,2-dimethylpentane, with ethyl filed under e and dimethyl under m.

The suffix carries the functional group, with its locant immediately in front of it: propan-2-ol, pent-1-ene, pentan-3-one. Some groups never need a number. An aldehyde, carboxylic acid, acyl chloride, amide or nitrile can only sit at the end of a chain, so its carbon is always carbon 1: butanal, butanoic acid. In a nitrile the carbon of the C≡N counts in the stem, so CH₃CH₂CN is propanenitrile. Propanone and butanone need no number either, because the C=O has nowhere else to go without becoming an aldehyde.

A ring takes the prefix cyclo- on the stem for its number of carbons: cyclohexane, C₆H₁₂, drawn skeletally as a plain hexagon. Every carbon of a ring is equivalent, so one group needs no number: methylcyclohexane, chlorocyclohexane, cyclohexanol. The carbon carrying the suffix group is carbon 1, and in cyclohexene the two carbons of the C=C are 1 and 2. Numbering then runs round the ring in the direction that gives the next group the lower number, so a methyl group on a C=C carbon gives 1-methylcyclohexene and one on the carbon beside the double bond gives 3-methylcyclohexene.

The e at the end of the stem is dropped before a suffix beginning with a vowel and kept before a consonant: propan-1-ol and propanal, but propanenitrile. A molecule with two C=C bonds is a diene, and an a is added to the stem so the name can be said: buta-1,3-diene.

Where a molecule carries two functional groups, the more senior one takes the suffix and the other becomes a prefix. A carboxylic acid outranks an aldehyde, an aldehyde outranks a ketone, and a ketone outranks an alcohol, so lactic acid, CH₃CH(OH)COOH, is 2-hydroxypropanoic acid. Halogens and alkyl groups are only ever prefixes. A C=C stays in the stem as -en- whatever else the molecule carries.

Esters are named in two words from the alcohol and the acid they are made from: the alkyl group of the alcohol first, then the acid with -oic acid changed to -oate. CH₃COOCH₂CH₃ is ethyl ethanoate. The carbon chain that contains the C=O gives the second word. Primary amines are named from the alkyl group joined to the nitrogen: CH₃CH₂NH₂ is ethylamine and CH₃CH₂CH₂NH₂ is propylamine.

Reading a name back into a structure

Questions ask for the reverse as often: draw the skeletal formula of 2-methylbutan-2-ol. Work from the end of the name. The stem but gives a chain of four carbons, -an-2-ol puts an OH on carbon 2, and 2-methyl puts a CH₃ on carbon 2 as well. Draw the chain, add the groups, then fill every carbon to four bonds with hydrogen. The structural formula is CH₃C(OH)(CH₃)CH₂CH₃, and the molecular formula, C₅H₁₂O, is a check that nothing has been dropped.

Drawing out a name is also how a wrong name is caught. '2-ethylbutane' sounds possible, but drawn out it is CH₃CH(CH₂CH₃)CH₂CH₃, whose longest chain runs through the ethyl group: five carbons with a methyl on the middle one, 3-methylpentane. An ethyl group on carbon 2, or a methyl group on carbon 1, always means the longest chain was missed. '1-methylpropane' is butane, and 'pentan-4-ol' is pentan-2-ol numbered from the wrong end.

Names matter because formulae repeat. Pentan-1-ol, pentan-2-ol, pentan-3-ol and 2-methylbutan-2-ol are all C₅H₁₂O, and they differ in boiling point, in smell and in what acidified dichromate(VI) does to them. The name is the shortest exact way to say which of them is in the bottle.

Other boards: hybridisation, skeleton words and amine names

Cambridge explains the shape round each carbon by hybridisation, and its papers ask for it by name. The 2s orbital of carbon mixes with one, two or three 2p orbitals to give equivalent hybrid orbitals, each of which forms a σ bond by end-on overlap. Mixing 2s with all three 2p orbitals gives four sp³ orbitals at 109.5°. Mixing it with two gives three sp² orbitals in a plane at 120°, and the p orbital left over, at right angles to that plane, overlaps sideways with its neighbour to form the π bond of a C=C. Mixing it with one gives two sp orbitals at 180°, and the two p orbitals left over form the two π bonds of a triple bond.

Each carbon of benzene is sp², σ-bonded to two carbons and one hydrogen at 120°, so the ring is a flat hexagon. The six leftover p orbitals overlap all round the ring into one delocalised π system, the circle in the skeletal formula. In but-3-enenitrile, CH₂=CHCH₂CN, the nitrile carbon is sp, carbon 2 is sp³, and carbons 3 and 4 are sp².

OCR uses three words for the shape of a skeleton: aliphatic for straight and branched chains, alicyclic for rings that are not aromatic, such as cyclohexane, and aromatic for compounds with a benzene ring. OCR also calls the halogenoalkanes haloalkanes; the series and its naming are the same, so 1-bromopropane is a haloalkane on an OCR paper.

Amines have two naming styles in print. The alkyl-group names, ethylamine and propylamine, are the ones taught here. The systematic IUPAC forms put the chain in the stem and -amine as the suffix, with a locant where one is needed: ethanamine, propan-1-amine and propan-2-amine. Textbooks and question papers use both styles, and Edexcel's specification itself writes butylamine, so either form should be read back into a structure without hesitation.