Displaying Molecular Formulae

There are several methods for displaying molecular structures. The most detailed is a displayed structure:

All the atoms and all the bonds are shown.

A skeletal formula reduces the structure to a simple outline.

Hydrogen atoms bonded to carbon atoms are not shown, not even their bonds. Carbon atoms are not shown, but bonds between carbon atoms show where they must be located.

A shortened formula gives each carbon atom in turn, but does not include bonds.

Propanone's shortened formula is CH₃COCH₃.

The molecular formula simply lists the atoms in a molecule.

Propanone's molecular formula is C₃H₆O.

The empirical formula only gives the proportions of the elements in a molecule.

Propanone's empirical formula is the same as its molecular formula: C₃H₆O.

Lactic acid:

Lactic acid's shortened formula is CH₃CHOHCOOH. The molecular formula is C₃H₆O₃ and the empirical formula is CH₂O.

Naming Organic Molecules

NB: It is helpful to add Capital Letters to long scientific words. It helps to see how the word is made up. Example: ChloroFluoroCarbon. This unusual format is known as "CamelCase".

Rules for naming organic molecules:

Find the longest carbon chain and the alkane it corresponds to (methane, ethane, propane, butane, pentane, etc).

The prefixes that represent the different numbers of atoms
Number of carbon atoms	Prefix	Number of carbon atoms	Prefix
1	meth-	6	hex-
2	eth-	7	hept-
3	prop-	8	oct-
4	but-	9	non-
5	pent-	10	dec-

Take care here! A compound should be displayed with the longest chain written horizontally, but in an exam this is not the case. At first sight, the molecule might be seen to have a longest chain from one side to another, but in fact the longest straight chain incorporates carbon atoms that are above or below the horizontal, so the chain is longer than you think.

Any branching chains are named using the same system: methyl, ethyl, propyl, etc.
1. Use numbers if necessary to say where the branch is attached e.g. 2-MethylPentane and 3-MethylPentane are isomers. 4-MethylPentane is the same as 2-MethylPentane with the atoms counted from the other end of the pentane chain. Use the lower number.
2. Use “di”, “tri”, “tetra” etc if several identical branches are attached e.g. DiMethylPropane, TetraMethylButane. Add numbers if necessary e.g the isomers 2,2-DiMethylPentane, 2,3 DiMethylPentane, 2,4-DiMethylPentane and 3,3-DiMethylPentane are isomers of EthylPentane.
3. When incorporating the branch names, keep them in alphabetical order, i.e., ethyl comes before methyl.

EthylPentane

Above: Skeletal formula of EthylPentane; CH₃CH₂CH(CH₃CH₂)CH₂CH₃ (shortened), C₇H₁₆ (molecular / empirical).

3D model of EthylPentane.

Halogen atoms are named like methyl branches e.g. 1,1,1-TriChloroEthane, DiChloroDiFluoroMethane

Above: Displayed formula of 1,1,1,-TriChloroEthane; CH₃CCl₃ (shortened), C₂H₃Cl₃ (molecular / empirical).

Alkenes (with a C=C bond) alter the end of the alkane name. Similar rules for multiple C=C bonds and positions apply: e.g. Ethene, Propene, But-1-Ene (CH₂=CHCH₂CH₃), Buta-1,3-DiEne (CH₂=CHCH=CH₂).

Carboxylic acids alter the ending too: Ethanoic Acid, Butanoic Acid, etc. The -COOH group can only be at the end of a carbon chain so numbers are rarely needed. HOOC-COOH is EthaneDioic Acid, HOOC CH=CHCOOH is ButeneDioic Acid.
Alcohols add "-ol" to the end of the name, or sometimes "hydroxy-" to the beginning if another ending is required. E.g. Ethanol, Propan-1-ol, Propane-1,2,3-Triol, 2-HydroxyPropanoic Acid

Example: Propane-1,2,3-Triol (Glycerol); CH₂OHCHOHCH₂OH (shortened), C₃H₈O₃ (molecular/empirical).

Displayed formula
Skeletal formula

Isomers

Definition: Isomers are different chemical compounds which have the same molecular formula. (Do not confuse isomers (different molecules) with isotopes, which are different atoms. Isotopes are atoms with different mass numbers which have the same atomic number.)

C₄H₁₀ has two isomers; Butane CH₃CH₂CH₂CH₃ and MethylPropane CH₃CH(CH₃)CH₃

Butane
MethylPropane

These are a type of structural isomer called chain isomers. Structural isomers have different patterns of bonds ("conformations"). Chain isomers have different arrangements of the main carbon chain.

C₃H₈O has three isomers; Propan-1-ol, CH₃CH₂CH₂OH, Propan-2-ol, CH₃CHOHCH₃, and MethoxyEthane, CH₃CH₂OCH₃.

Propan-1-ol
Propan-2-ol
MethoxyEthane

These three are also structural isomers. Propan-1-ol and propan-2-ol are positional isomers; The difference is where the -OH group is attached. MethoxyEthane (not a type of compound you need to know) is not an alcohol, which makes it a functional group isomer of the other two isomers.

If two molecules have the same conformation (the same atoms are bonded in the same pattern) then they are stereoisomers. Stereoisomers have different 3D arrangements of their atoms. In Topic 4.1 (Year 2) we look at isomers which are mirror images of one another, which are called enantiomers or optical isomers. Stereoisomers which are not mirror images of one another are called diastereomers or geometric isomers. We will look at one example, E-Z or cis-trans isomers, in Topic 2.5.

Types of Reaction

There are three types of reactant you need to know about, and two types of bond fission.

Reactants

Radicals

Radicals are chemicals which one (or more) unpaired electrons. Most radicals are very reactive, and many radicals are simply free atoms such as Cl^·. The radical electron is shown as a dot - Cl^· for example.

Nucleophiles

Nucleophiles have a lone pair of electrons and are often negatively charged. They react by forming a new covalent bond using their lone electron pair. Examples include :NH₃, :OH^-, N≡C:^-.

Electrophiles

Electrophiles have missing electrons - they are at least partially electron deficient. O=N⁺=O is an example.

Bond fission

Bond fission is simply the braking of a covalent bond. There are only two ways this can happen. Either both electrons in the bond go to one atom, or each atom gets one electron each.

Homolytic fission

If one electron goes to each atom when the bond breaks, the process is symmetrical and is called homolytic fission. The two atoms both become radicals, with an unpaired electron each. The movement of the single electrons is shown with curly, single-headed arrows (often described as "fish-hooks"). You are not required to know how to draw this form of bond breaking, but need to recognise the process and its role in radical reactions.

Homolytic fission of a generalised bond between atoms A and B.

Heterolytic fission

If a bond breaks and both electrons go to one atom (the more electronegative one, usually) then we call this asymmetrical process heterolytic fission. One atom gains a negative charge and the other gains a positive charge. The movement of the electron pair is shown with a curly, double-headed arrow.