Molecules and Chemical Bonds: Build One in 3D

Sharing is bonding

Atoms join because joining lowers their energy. The simplest way to join is to share. Each hydrogen atom has one electron and would like a second to fill its first shell. Two hydrogen atoms come close and share a pair of electrons that belongs to both. That shared pair is a covalent bond, drawn as one line: H–H. The result is a hydrogen molecule, H₂, in which both atoms count a full shell. In the picture, bring the two atoms together and see their electron clouds pull them in, then push back if they get too close. The balance point, about 74 picometres apart, is the bond length.

Water is bent

Oxygen needs two more electrons and each hydrogen needs one, so one oxygen shares with two hydrogens: H₂O. Oxygen also holds two pairs of electrons that are not shared, and these push the two O–H bonds closer together. The result is a bent molecule with an angle of 104.5° instead of a straight line. Oxygen pulls the shared electrons harder than hydrogen does, so the oxygen end is slightly negative and the hydrogen ends are slightly positive. That lopsided charge is why water molecules cling to each other, and why water dissolves so many things. Turn the model in the picture and read the angle.

Carbon dioxide is straight

Carbon needs four more electrons and oxygen needs two. In CO₂ the carbon atom shares two pairs with each oxygen, which is a double bond, written O=C=O. Count them: carbon has 4 bonds and each oxygen has 2, so every valence is satisfied. Carbon has no unshared pairs to push the bonds around, so the two double bonds point in opposite directions and the molecule is straight, at 180°. Each oxygen pulls equally in opposite directions, so the molecule is not lopsided at all. It is the gas you breathe out and the gas plants take in. Compare it with water in the picture: both hold oxygen, yet the shapes and the behaviour differ.

Methane and ethanol

Methane, CH₄, is one carbon with four single bonds to hydrogen. The four bonds spread as far apart as they can, towards the corners of a tetrahedron, with angles of 109.5°. It is the main part of natural gas. Ethanol, C₂H₆O, is built in the same way, only as a chain: two carbons joined together, each topped up with hydrogens to make four bonds, and a hydroxyl group –OH at the end, written CH₃CH₂OH. The same atoms in another order make a different substance, dimethyl ether, CH₃OCH₃. So a molecule is not only a list of atoms. It is a list plus a shape.

Salt has no molecules

Table salt works differently. Sodium gives its lone outer electron to chlorine, which has one place free in its outer shell. Sodium becomes the positive ion Na⁺ and chlorine becomes the negative ion Cl⁻. Opposite charges attract, and each ion ends up surrounded by six of the other kind, in a cubic lattice that repeats in every direction. There is no separate NaCl molecule, only the formula ratio 1 : 1. This is an ionic bond. Strong attraction in all directions is why salt crystals are hard and need 801 °C to melt. Rotate the crystal in the picture and count the neighbours around one ion.

Build a molecule

Time to assemble one. Under the picture you can pick carbon, hydrogen, oxygen and nitrogen atoms and join them. Each atom wants a fixed number of bonds, its valence: carbon 4, nitrogen 3, oxygen 2 and hydrogen 1. A molecule is complete when every atom has all its bonds filled. Worked example: one nitrogen and three hydrogens give NH₃, ammonia, because nitrogen's 3 bonds meet the 3 single bonds of the hydrogens. If the sandbox knows your molecule it names it, for example water, methane, carbon dioxide, ethanol or ammonia. Otherwise it shows the formula and tells you which bonds are still open.

Molecules and bonds