Molecular Models, Structural Formulas and Ionic Crystals

Seeing molecules in 3-D

In 1953, James Watson and Francis Crick worked out the structure of DNA partly by building a large physical model out of metal plates and rods, guided by X-ray images made by Rosalind Franklin and Maurice Wilkins. Chemists still build models, now often on computers, because a molecule's shape controls how it behaves: how it smells, whether it dissolves, how a medicine fits into a protein.

A chemical formula such as C₂H₄ tells you which atoms are present, but not how they are connected. In this lesson you will use structural formulas and molecular models to show the connections and the shapes of molecules, and you will see why an ionic compound such as sodium chloride is built completely differently.

Ways to represent a molecule

• Molecular formula: the number of each kind of atom in one molecule: H₂O, CO₂, C₂H₄.
• Lewis structure: all valence electrons, with lines for bonds and dots for lone pairs (Lesson 9).
• Structural formula: lines for bonds between atom symbols, without lone pairs. It shows which atoms are joined and whether bonds are single, double or triple: H–O–H, O=C=O.
• Condensed structural formula: a shorthand that groups atoms around each carbon, such as CH₂=CH₂ for ethene or CH₃CH₂OH for ethanol.
• Ball-and-stick model: balls for atoms and sticks for bonds (two sticks for a double bond). It shows the angles between bonds clearly.
• Space-filling model: atoms drawn as overlapping spheres at their relative sizes. It shows the overall shape and size of the molecule best, but hides the bonds.

Model kits use standard colours so everyone reads them the same way: carbon is usually black, hydrogen white, oxygen red, nitrogen blue and chlorine green.

Shapes of some simple molecules

The shape of a molecule comes from the fact that electron pairs around a central atom repel each other and spread out as far apart as possible. (This idea is called VSEPR theory; you will use it fully in Grade 12 Chemistry, SCH4U.) For now, learn these common shapes:

• CO₂: linear (180°). Carbon has two double bonds and no lone pairs, so the two oxygens sit on opposite sides.
• H₂O: bent (about 104.5°). Oxygen has two bonds and two lone pairs; the lone pairs push the hydrogens closer together.
• CH₄: tetrahedral (109.5°). Four bonds spread out in three dimensions, like the corners of a triangular pyramid.
• NH₃: trigonal pyramidal (about 107°). Three bonds and one lone pair on nitrogen.
• C₂H₄: planar (about 120°). All six atoms lie in one flat plane around the C=C double bond.
• N₂, O₂, HCl, HCN: linear. Any molecule of two atoms is linear, and HCN's carbon has no lone pairs.

Ionic compounds: crystal lattices, not molecules

Ionic compounds do not form molecules, so they are modelled differently. In a crystal of sodium chloride, Na⁺ and Cl⁻ ions alternate in all three directions to form a cubic lattice.

• Each Na⁺ ion is surrounded by 6 Cl⁻ ions (above, below, left, right, in front, behind).
• Each Cl⁻ ion is surrounded by 6 Na⁺ ions.
• Overall the ratio is 1 : 1, which is why the formula is NaCl.

The cubic arrangement of ions is why salt crystals are tiny cubes; look at grains of table salt with a magnifying glass and you will see them. Other ionic compounds have different lattice arrangements, but all are repeating three-dimensional patterns of oppositely charged ions.