As chemists, we often need to talk about chemicals with other people (both scientists and non-scientists). To help us unambiguously communicate the composition and structure of a molecule, an international standard naming system (IUPAC nomenclature) was developed – but, like many systems, it isn’t perfect. Firstly, there are many historic or alternative names for certain structures that are still widely used and not necessarily known by everyone (especially in other countries). Secondly, the list of standard names is very long and we cannot always assume that the other person will be familiar with it (especially if s/he works in a different field).
We therefore need a simple way to communicate the composition and structure of a molecule – what elements are present, in what quantities and in what arrangement. This primer will introduce us to the standard non-nomenclature systems used to exchange information about molecules.
When we want to represent the composition of some substance, we simply write down the individual elements that make up the molecule along with the number of atoms.
A molecule of water is made up of an atom of oxygen (O) and two atoms of hydrogen (H). We would write this as H2O – by convention (known as the Hill system), carbon is listed first, then hydrogen, then other elements in alphabetical order (unless the molecule has no carbon, in which case all elements are listed alphabetically). If we wanted to indicate that two molecules of water were involved in a reaction, we would write 2H2O.
This principle applies to any molecule we can think of. Although caffeine (a stimulant found in coffee and tea) is a relatively complicated molecule, it’s only eight atoms of carbon, ten of hydrogen, four of nitrogen and two of oxygen – C8H10N4O2.
This kind of representation is called a molecular formula – it tells us what kind of atoms we have, and how many of each. We can simplify this further into an empirical formula, which only tells us the relative amounts of each atom. The empirical formula for water is still H2O, but caffeine would be C4H5N2O – there is twice as much nitrogen as oxygen, five times as much hydrogen and four times as much carbon.
More common in general chemistry is the structural formula, which gives us information about how the atoms are arranged in the molecule. Butanoic acid (a smelly compound found in vomit, body odour and Parmesan cheese) may be written as C4H8O2, but we can deliver more information by writing it as CH3CH2CH2COOH – this tells us where each atom is located.
We can simplify long repeating units by using brackets, so butanoic acid could also be written as CH3(CH2)2COOH to indicate that there are two -CH2– groups. This is generally only convenient for three or more repeating units though.
Structural formulae take a little getting used to, but are the best way to communicate how the atoms are arranged if we are limited to letters and numbers. If drawing is an option, chemists will often use skeletal formulae for maximum clarity
In a skeletal formula, straight lines are drawn at an approximate angle of 109°, which is close to the actual angle between bonds in real molecules. Each corner represents a carbon atom with the maximum number of hydrogen atoms possible attached. Carbon and hydrogen are so common in organic chemistry that it would take too long to draw them every time, so we just leave them out. All other atoms (O, N etc.) are drawn with their hydrogen atoms (if they have them) attached.
At this point, it’s worth taking a look at how many bonds atoms tend to form. In general, hydrogen must form one bond, oxygen two, nitrogen three and carbon four. If we can see that a carbon atom is connected to two others, the remaining two bonds must be taken up with hydrogen. Double bonds count as two, so the carbon in the -COOH group still has four bonds even though it has no hydrogen.
If we take a look at our molecule of butanoic acid again, we can now see how the skeletal formula works. The expanded (or Lewis) structure also shows how our atoms are arranged, but takes more time to draw and can be cluttered.
When drawing skeletal formulae, we are trying to represent a three-dimensional molecule with a two-dimensional medium. As carbon’s bond angles are around 109°, its four bonds will form a tetrahedron (triangular pyramid) and only two of the bonds can be in the same plane. To show this, we may use wedged lines to represent bonds coming towards us (in front of the 2D medium), and dashed lines to represent bonds going away (behind the 2D medium).
By convention, skeletal formulae are drawn so that the carbon skeleton is in the plane of the medium (hence in a -CH2– group the two hydrogen atoms will be in front of and behind the plane). To save time, we normally only draw wedged or dashed lines when we need to show the correct position of an important group.