The prefix cis- and trans- in chemical nomenclature are part of geometric isomerism. Isomers are molecules that have the same chemical formula but the individual atoms are arranged differently in space. Geometric isomerism concerns the type of isomer where the individual atoms are in the same order, but manage to arrange themselves different spatially.
Geometric isomers occur when atoms are restricted from rotating around a bond.
This molecule is 1,2-dichloroethane (C2H4Cl2). The green balls represent the chlorine atoms in the molecule. The second model can be formed by twisting the molecule around the central carbon-carbon single bond. Both models represent the same molecule and are not isomers.
Double Bonds restrict free rotation.
These molecules are 1,2-dichloroethene (C2H2Cl2). The difference between these and 1,2-dichloroethane is the two hydrogen atoms are replaced by an additional bond between the two carbon atoms. Double bonds are formed when p orbitals between two atoms overlap. If the atom were twisted, these orbitals would no longer overlap and the bond would be broken. The double carbon-carbon bond prevents the free rotation of atoms in the molecules. These two molecules have the same atoms, but are different molecules. They are geometric isomers of each other.
The cis- prefix means "on this side".
In gemetrical isomer nomenclature, the prefix cis- and trans- are used to identify which side of the double bond the similar atoms are found. The cis- prefix is from the Latin meaning "on this side". In this case, the chlorine atoms are on the same side of the carbon-carbon double bond. This isomer is called cis-1,2-dichloroethene.
The trans- prefix means "across".
The trans- prefix is from the Latin meaning "across". In this case, the chlorine atoms are across the double bond from each other. This isomer is called trans-1,2-dichloroethene.
Geometric Isomerism and Alicyclic Compounds
Alicyclic compounds are non-aromatic ring molecules. When two substituent atoms or groups bend in the same direction, the molecule is prefixed by cis-. This molecule is cis-1,2-dichlorocyclohexane.
This molecule has the substituent chlorine atoms bending in opposite directions or across the plane of the carbon-carbon bond. This is trans-1,2-dichlorocyclohexane.