Polarity
When a pair of atoms is attached through a covalent chemical bond, they are essentially sharing a pair of electrons. Some atoms have more of an affinity toward the electrons than others -- a property measured by the atom's electronegativity. If the two atoms have similar electronegativities, the bond will be non-polar, but if one atom has a larger electronegativity, the bond will be polar. Water is a polar molecule, because the electronegativity of oxygen is much greater than that of hydrogen. One end of the water molecule is electrostatically positive and the other negative. Oils are composed primarily of hydrogen-carbon bonds, which are non-polar, because both have similar electronegativities. This is why oil and water do not mix.
Melting and Boiling Points
Polarity affects melting and boiling points, as does the size of the molecule. Polar molecules attract one another and so will tend to have higher boiling and melting points. Large hydrocarbons are often a gas at room temperature because there is limited attraction between the molecules. But as the hydrocarbon molecules get larger, they tend to be a liquid at room temperature. The boiling point is higher because even non-polar molecules have some attraction for one another (known as van der Waals attraction), which increase as the molecules get larger.
Chemical Reactivity
The atoms that compose a molecule will dictate its reactions with other molecules. For example, a molecule containing carbon and hydrogen will most likely, under the right conditions, combine with oxygen to form carbon dioxide and water. A molecule containing double-bonded carbon atoms can break one of those bonds to combine with the two hydrogen atoms in a hydrogen molecule. Knowing the structure of a molecule allows scientists to make predictions about its potential reactivity with other molecules, but the extent and speed of reactions are ultimately quantified through experiment.
Molecular Structure
Two molecules could be composed of the same type and number of atoms and yet still have different properties. These are isomers, which have the same chemical formula, but the individual atoms are arranged differently. Take, for example, propyl-alcohol, which has three carbons, one oxygen and eight hydrogen atoms. The carbon atoms might be arranged (CH3)2-CHOH or they might be arranged CH3-CH2-CH2OH. In the first, the OH group is attached to the central carbon, in a molecule called iso-propyl alcohol. In the second, the OH is attached to one of the end carbons, a molecule called n-propyl alcohol. These two molecules have similar but not identical properties.