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Basic concepts of organic chemistry (4.1.1)
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IUPAC is the International Union of Pure and Applied Chemistry. It sets the rules which chemists all around the world use to systematically name organic molecules.
This is commonly referred to as nomenclature.
Organic molecules are named with a stem, prefix, and a suffix.
The stem is given by the number of carbon atoms in the longest continuous chain or ring. This is often referred to as the main chain.
The prefix is used to indicate the presence of side chains or lower priority functional groups (e.g. halogens).
The suffix is used to indicate the highest priority functional groups.
Numbers are used before prefixes and suffixes to indicate where the functional group is on the main chain the additional functional groups are.
Functional groups have different priorities for naming purposes. Generally speaking oxygen-containing groups hold the highest priority.
The priority of oxygen-containing groups then increases according to their oxidation level, with alcohol being the lowest and carboxylic acids being the highest.
The simplest molecules to name are the alkanes.
The table below shows how the stem and suffix are applied.
When molecules are branched, this means there are side chains.
The molecule is named using the stem of the longest continuous chain, a prefix for the side chain, and a suffix for the functional group.
When molecules contain alicyclic rings, the prefix cylco- is also added.
Numbers are used before prefixes to indicate where on the main chain the functional group is attached.
The molecule below is called 2-methylbutane to show the methyl group is attached to the second carbon of the main chain.
When there are more than one of the same group di-, tri-, tetra-, penta-, etc., are used to show there are 2, 3, 4, or 5 of that group.
The molecule above is 2,2-dimethylpropane.
Prefixes are written in alphabetical order, but remembering to ignore di-, tri-, or tetra-.
The molecule above is 3-bromo-1,2-dichloropropane.
The numbering for the carbon-carbon double bond is given by which carbon it starts on and has the lowest possible number.
The two alkenes above are also isomers of one another. They are but-1-ene and but-2-ene, respectively.
In cyclic groups, the numbering begins at the highest priority functional group.
The molecule above is an alicyclic molecule with five carbons, so is based on cyclopentane as the parent alkane.
It has an , as this group takes priority the molecule will have the suffix -ol, and we number this carbon 1.
Its full systematic name is 2-chlorocyclopentan-1-ol.
When naming molecules containing a benzene follow the normal IUPAC rules, where prefixes are used alongside numbers and di-, tri-, etc., to indicate any low priority groups attached to the benzene ring.
Benzene can be considered a side chain/substituent. When benzene is attached to an alkyl chain with another functional group it is indicated by prefix phenyl-.
Some benzene derivatives with higher priority substituents have their own parent names that you just need to learn. They are an exception to the general rules.
These are phenol, phenylamine, benzoic acid, and benzaldehyde.
When naming primary amines where the is on the end of the carbon chain, the suffix -amine is used.
If the is in the middle of the alkyl chain, then the prefix amino- can be used.
If there are two or more different alkyl groups, then the amine is named as an N -substituted variant of the longest alkyl chain. For example, N – methyl – N -ethylpropylamine below.
Secondary amines are where two of the same alkyl group are attached to the nitrogen atom; di- can be used.
Tertiary amines are where three of the same alkyl groups are attached to the nitrogen atom, tri- can be used.
Primary amides are named using the prefix -amide. In primary amides, one carbon, the carbonyl carbon, is bonded to the amide nitrogen.
In secondary amides, two carbons are bonded to the amide nitrogen. One of these carbons is the carbonyl group.
The alkyl chain attached to the nitrogen is added at the start of the chemical name, prefixed with N.
The chain containing the carbonyl group is named according to the length of that alkyl group.
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In tertiary amides, three carbons are bonded to the amide nitrogen. One of these carbons is the carbonyl group.
The alkyl chains attached to the nitrogen are added at the start of the chemical name, prefixed with N. The chains are listed in alphabetical order. The chain containing the carbonyl group is named according to the length of that alkyl group.
The easiest way to remember how to name esters is that they are named after the alcohol and the carboxylic acid that would be combined to make them, in that order.
The parent alcohol is given by the prefix for its corresponding alkyl group.
The carboxylic acid part is given with the suffix -anoate.
Note the colour coding in the example below.
Nitriles are simple to name if the group is found on the end of an alkyl chain. The name of the parent alkane is used followed by the suffix -nitrile.
When the group is found in the middle of a chain/ring then the prefix cyano- is used.
Be careful not to confuse the nitro- ( group) prefix with the cyano- ( group) prefix.
Side chains containing only carbon and hydrogen are known as alkyl groups. The general formula for alkyl groups is .
The general formula is the simplest algebraic formula for any member of a homologous series.
You can use the general formula to generate the molecular formula of any member of that homologous series.
Displayed formulae show all the bonds and atoms present in a molecule.
One line is used to represent one covalent bond.
The displayed formula of ethanoic acid is shown below.
Structural formulae are used to convey structure within molecules in the smallest amount of detail necessary.
Work your way along the main carbon chain and summarise what is attached to each carbon.
Side chains are shown in parentheses.
Repeating elements can also be summarised in parentheses.
When working out more complex examples, it can help to draw out the displayed formula and annotate it.
The molecule below has the structural formula .
Skeletal formula represents a molecule’s structure by removing all carbon labels, as well as hydrogen bound to carbon, from a molecule to leave a zigzag-like carbon skeleton. Only heteroatoms, or functional groups, such as , , or are shown.
Key features of skeletal formula:
- Each line represents a single bond.
- The end of a line is a .
- The points at which two lines meet at an angle is a carbon atom.
- The number of hydrogens is implicit given that carbon should always have four bonds.
Examples:
Aliphatic compounds consist of carbon and hydrogen atoms arranged in straight chains, branched chains, or non-aromatic rings.
Most ‘simple organic molecules’ are aliphatic compounds.
Alicyclic compounds are a subset of aliphatic compounds that form non-aromatic rings with or without side chains.
Anything with a cycloalkane ring can be described as alicyclic as long as it does not contain a benzene ring.
Aromatic compounds contain a conjugated system of pi electrons in a ring structure.
Any compound that contains at least one benzene ring can be described as aromatic
Saturated hydrocarbons only contain single carbon-carbon bonds. They contain the maximum number of hydrogen atoms possible.
Unsaturated molecules contain at least one multiple carbon-carbon bond including , , and aromatic rings. There is the potential to add more hydrogen atoms to the compound.
A functional group is the part of a molecule that determines the chemical properties and reactions of that molecule.
A homologous series of compounds have the same functional group (and therefore similar chemical properties) but with each successive member differing by a group.
To find any member of the homologous series just substitute n for the desired number of carbons.
The sixth member of the carboxylic acid homologous series, general formula , is , or . This is hexanoic acid.
Structural isomers are molecules that have the same molecular formula but a different structural formula.
They may have a different arrangement of the carbon chain, a different functional group, or a different positioning of the same functional group.
The term ‘structural isomer’ can be used to identify all its subtypes.
Chain isomers are a type of structural isomer that have the same molecular formula but different arrangement of the carbon skeleton, hence a different structural formula. They are often described according the the amount of branching present and generally only differ in physical properties.
Methylpropane and butane are examples of chain structural isomers.
Functional group isomers have the same molecular formula but different functional groups, hence a different structural formula.
In this type of structural isomerism the reactivity differs greatly between isomers.
Positional isomers have the same molecular formula but different positions of functional groups on the carbon chain, hence a different structural formula.
This is a type of structural isomerism.
Propan-1-ol and propan-2-ol are structural isomers which exhibit differences in physical properties and reactivity.
Stereoisomers are molecules with the same structural formula but a different arrangement in space.
The two relevant types of stereoisomerism in organic chemistry are optical and E/Z.
E/Z isomerism is applicable to alkenes whereas optical isomerism applies where four different groups are bonded around a carbon.
During reaction mechanisms, electrons are rearranged. Bonds are broken and new bonds can be made.
When a bond breaks, we call this bond fission.
In homolytic bond fission, the electrons are shared equally and free radicals are formed.
This type of bond fission is typically initiated using UV radiation.
The graphic below demonstrates how the electrons (blue + pink) are distributed in homolytic bond fission.
In heterolytic bond fission, the two electrons are distributed unevenly when the bond breaks. This means that ions are formed.
The most electronegative atom in the bond will typically become the negative ion (anion).
Radicals, sometimes also called free radicals, are chemical species that exist with an unpaired electron.
Radicals are formed in the process of homolytic bond fission with UV light.
Radicals are represented using a dot. For example,
and
Radical mechanisms are shown with a sequence of equations rather than curly arrows.
Most radical reactions will happen in 3 distinct processes: initiation, propagation, and termination.
In organic chemistry, a curly arrow is used to show the movement of a pair of electrons.
Electron pairs move from an area of high electron density (negative ions, pi bonds, lone pairs) to an area of low electron density (cations or partial positively charged atoms).
Typically curly arrows show the formation of a new covalent bond or heterolytic bond fission.
In the substitution of a haloalkane with the hydroxide ion:
- The first curly arrow represents a new bond being made between oxygen and carbon.
- The second curly arrow represents the carbon-bromine bond breaking to leave a bromide ion.
The tail of the arrow always begins at the source of the electrons; a nucleophile. This could be either a lone pair of electrons on an atom or a pair of electrons in a bond.
DO NOT draw arrows starting from electrophiles.
The head of the arrow should signify where the electron pair has moved to; this should clearly point to the receiving atom.
Arrows start from the bond being broken and end at the atom receiving the electrons.
Always start the curly arrow from the middle of the bond that is being broken.
Point the arrow towards the atom receiving the electrons.
Dipoles, or , should be added to relevant groups where the polarity drives the reaction. When bonds have been broken, include any necessary charges in the products to reflect the bond cleavage.
Reactions often occur in multiple steps. Mechanisms show the movement of electrons throughout these steps.
The image below demonstrates the mechanism by showing the movement of electron pairs using curly arrows.
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- First arrow: A pair of electrons from the pi bond of the alkene are donated to the delta-positive atom of the molecule. A new sigma-bond between and is formed (the pi bond is broken).
- Second arrow: A pair of electrons from the sigma bond is donated to the delta-negative atom. The sigma bond is broken and the bromide ion is formed .
- Third arrow: The pair of electrons from the bromide ion are donated to the carbocation. A new sigma bond is formed between carbon and bromine.