16.30 Molecules

Before you read this post, I suggest you read posts 16.27 and 16.29

In post 16.29, we saw that electrons occupy atomic energy levels to minimise their overall energy. However, some electron configurations are more stable (they have a lower overall energy) than others. The evidence for this statement is that some atoms are much less likely to form molecules or ions in chemical reactions (subjects of this and planned later posts) than others.

Atoms in which there are no energy levels with less than two electrons are more stable. This statement needs some further explanation. Because the 2px, 2py and 2pz levels all have the same energy, the most stable situation is when they are all filled with electrons.

So, the atoms we met in post 16.29 would be more stable if they have the electron configurations of helium or neon.

How can they achieve these electron configurations? By sharing electrons with other atoms!

So the hydrogen atom would like to have two electrons in its 1s energy level. It can achieve this goal by sharing its single electron with another hydrogen atom. The shared pair of electrons is called a covalent bond because sharing electrons keeps the two hydrogen nuclei close to each other. Because a hydrogen atom has only one electron to share it can form one covalent bond H-; then two hydrogen atoms join together to form a hydrogen molecule H-H or H2. A molecule is simply two or more atoms that share electrons; to explain this another way, a molecule is two or more atoms joined by one or more covalent bonds.

According to post 16.29, an oxygen atom needs two extra electrons to attain the electron configuration of neon. It can achieve this by sharing two pairs of electrons (in its 2py and 2pz energy levels). So, oxygen can form two covalent bonds, -O-. Two oxygen atoms can then be held together by two chemical bonds to form an oxygen molecule O=O or O2.

Similarly, according to post 16.29, a nitrogen atom needs to share three of its electrons (in the 2px, 2py and 2pz levels) to attain the electron configuration of neon. So it can form three covalent bonds. Two nitrogen atoms can then be held together by three covalent bonds to form the nitrogen molecule N2.

The same reasoning should lead you to the conclusion that fluorine can form one covalent bond and can form a fluorine molecule F2.

An oxygen atom can form two bonds and a hydrogen atom can form one bond; so one oxygen atom can form bonds with two hydrogen atoms to form a water molecule H-O-H or H2O. Oxygen and hydrogen are both gases at room temperature but water is a liquid. So the result of bond formation is to form stuff that is completely different to the original elements. Water is called a compound because, unlike an element, it contains more than one type of atom. A compound is not the same as a mixture of oxygen and hydrogen; if we could prevent this mixture from exploding, it would be a mixture of two gases. In the water molecule oxygen and hydrogen atoms are held together by covalent bonds.

The formation of chemical bonds by a carbon atom is a bit more difficult to understand. It is worthwhile for carbon to absorb energy to promote one of the two electrons in its 2s level into the   level. It then has one electron in each of four energy levels (2s, 2px, 2py and 2pz). These electrons can each be shared with another electron from another atom to form four covalent bonds. For example it can form carbon dioxide O=C=O or CO2, with two oxygen atoms, or methane CH4 with four hydrogen atoms.

We can use these ideas to explain the shapes of molecules. Each of the four covalent bonds in methane is a shared pair of electrons. Since electrons all have a negative charge, the four bonds will tend to repel each other to move as far apart as possible (see post 16.25), while still joining the carbon atom to four hydrogen atoms. In a three-dimensional space, they do this by pointing towards the four corners of a regular tetrahedron, so they make an angle of 109.5o with each other. This tetrahedron has the carbon atom at its centre and the four oxygen atoms at its corners, as shown by the molecular model below.

CH4 methane molecul

Why have I neglected the electrons in the 1s level? Their atomic orbitals are spherical and closer to the nucleus, so don’t interact in the same way with the electrons in the higher energy levels.

An alternative type of model for the methane molecule, called a spacefilling model, because it attempts to show the space occupied by the atoms is shown below.

Methane molecule isolated on white

Similarly, the water molecule has two bonds and two pairs of electrons in its 2s and 2px levels. These four pairs of electrons tend to repel each other in the same way. As a result a water molecule has the bent shape shown in the picture below.

H2O Wasser Molekl

But covalent bonds can’t explain all the molecules that exist. We might expect that nitrogen atoms would combine with oxygen atoms to form the O=N-N=O or N2O2 molecule. But it also forms NO and NO2, as well as other oxides. People who are interested in pollution from diesel engines sometimes refer to mixture sof NO and NO2 as NOx.

In order to explain the formation of many of these other molecules, we need to consider a pair of electrons shared between two atoms where one of the atoms contributes both of the electrons in the pair. A bond of this kind is called a coordination bond.

So atoms can be held together by shared pairs of electrons to form molecules. In a planned future post, on molecular orbitals, we shall see that this idea, called the valence bond theory, can’t explain some properties of molecules very satisfactorily. But the valance bond theory is a fairly simple idea that explains many of the properties of molecules.


Related post

16.29 Electrons in atoms
16.27 Atoms

Follow-up posts

16.31 Electrons in molecules
16.33 Chemical reactions
16.37 Solids, liquids and gases
16.40 Complicated ions
16.45 Water
16.47 Fats
16.48 How does soap work?
17.48 Moles
17.49 Acids
17.50 Alkalis
20.7 Polymers
20.27 Chirality
20.32 Isomerism





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