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Depending on the atoms making up the molecule, different shapes may come into play that are a factor in dictating the molecules physical and chemical properties. Take any of the hydrocarbons, for example. Carbon has the interesting property of catenation, which means carbon atoms can keep hooking together to make long chains of carbon molecules. Hydrocarbons have only hydrogen and carbon in their molecular makeup, and since both atoms are about the same elctronegativity, there is no polarity existing in the molecule. This is not the case with water. Water consists of two hydrogen atoms and one oxygen atom. The oxygen atom is very electronegative, so there is a polarity established within the structure of the water molecule, negative around the oxygen atom and positive around the hydrogen atoms. As a result of this, water, known as the "universal solvent" since it dissolves so many substances, will not mix with a hydrocarbon. This is where the old saying "Oil and water won't mix" probably came from. The oil (hydrocarbon) is less dense than the water, so the oil layer separates and floats on top of the more dense water layer.
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