You may recognize the model above as DNA, the molecule that carries the genetic instructions for making all life on earth. The helical shape of DNA was discovered in 1953, and the detailed arrangement of atoms in the DNA molecule determines whether it is a recipe for an ant, an antelope, an antirrhinum, or anthrax.

You may also have recognized this molecule as Buckminster fullerene, a soccer-ball shaped allotrope of carbon. Buckminster fullerene, named after the architect of the geodesic dome (which it resembles), was fi rst identifi ed in 1985 and earned its discoverers the Nobel Prize for chemistry in 1996.

Now, our question is this: how did you recognize these two compounds? You recognized their shapes. Molecules are not simply a jumble of atoms: they are atoms held together in a defined three-dimensional shape. A compound’s properties are determined not only by the atoms it contains, but also by the spatial arrangement of these atoms. Graphite and diamond— the two other allotropes of carbon—are both composed only of carbon atoms and yet their properties, both chemical and physical, are completely different because those carbon atoms are arranged very differently. Graphite has carbon atoms arranged in sheets of hexagons; diamond has them arranged in a tetrahedral array.

We know what shapes molecules have because we can see them—not literally of course, but by methods such as atomic force microscopy (AFM). AFM reveals the shape of pentacene, the molecule we would usually draw as the structure below, to be as shown on the left. This is the closest we can get to actually ‘seeing’ the atoms themselves.

Most analytical techniques reveal the shapes of molecules less directly. X-ray diffraction gives information about the arrangement of atoms in space, while the other spectroscopic methods you met in Chapter 3 reveal details of the composition of molecules (mass spectros copy) or the connectivity of the atoms they contain (NMR and IR). From methods such as these, we know what shapes molecules have. This is why we urged you in Chapter 2 to make your drawings of molecules realistic—we can do this because we know what is realistic and what isn’t. But now we need to tackle the question of why molecules have the shapes they do. What is it about the properties of their constituent atoms which dictates those shapes? We will find that the answer not only allows us to explain and predict structure, but also allows us to explain and predict reactivity (which forms the topic of Chapter 5). First of all, we need to consider why atoms form molecules at all. Some atoms (helium, for example) do so only with extreme reluctance, but the vast majority of atoms in the periodic table are much more stable in molecules than as free atoms. Here, for example, is methane: four hydrogen atoms arranged around a carbon in the shape of a tetrahedron.

Molecules hold together because positively charged atomic nuclei are attracted to negatively charged electrons, and this fact allows electrons to act as ‘glue’ between the nuclei. The C and H nuclei of methane are of course positively charged, but the ten electrons (a total of six from C, four from the H atoms) bind those positive charges into a molecular structure. Ammonia (NH3) and water (H2O) also have ten electrons in total, and we know that their molecular shapes are in fact just like that of methane, but with one or two hydrogen atoms removed.

This tells us something important: it is the number of electrons which determines the shape of a molecule, and not just the number of atoms (or atomic nuclei). But what determines how electrons are arranged? Why do ten electrons give rise to a tetrahedron, for example? Before we can answer this question, we need to simplify our discussion a bit and think about electrons not in molecules but in individual atoms. We can then approximate the electronic structure of molecules by considering how the component atoms combine. It is important to remember throughout this chapter, however, that molecules are only very rarely ‘made’ directly by joining atoms together. What we are going to present is an analysis of the structure of molecules, not a discussion of ways to build them (to which we will devote much of the later part of this book). Much of what we will cover was worked out in the decades around 1900, and it all came from experimental observation. Quantum theory explains the details, and you can read much more about it in a textbook of physical chemistry. Our aim here is to give you enough of an understanding of the theory to be able to use sound principles to predict and explain the structure of organic molecules.

So, fi rst, some evidence.