There’s two situations where you’ll encounter the terms “cis” and “trans”.
The first is in alkenes. Remember that we can’t rotate Pi bonds? This means that a molecule like 2-butene will have two possible isomers; the isomer where the two methyl groups are on the same side of the double bond is called “cis”, and the isomer where the two methyl groups are on the opposite side are called “trans”. A more generalized system for double bonds involves the Z – E system.
- Cis – Same – “Zame”
- Trans – Opposite – “Epposite”
The second place where you encounter cis/trans is in cyclic alkanes.
When a molecule forms a ring, that “locks” it to a certain extent. Think of a belt (or better yet, a dog collar). Before you fasten it together, you can twist it as much as you want. But once you fasten it, there are practical limits to how much you can turn it inside-out. If the radius is too small (or the material too stiff!), it becomes “locked”. You can’t turn it inside out anymore. That describes the situation with the cyclic alkanes we’ll encounter the most here.
So if two groups are on the same side of a ring, we use the same word : cis to describe it. And if they’re on the opposite side, we use the word “trans” to describe it.
To show this though we’ll need new visual terminology to depict how these molecules appear in 3D.
- To show a group pointing OUT of the page, we use a dark line “Wedge”.
- To show a group pointing IN to the page, we use a dashed line “Dash”.
So for 1,2-dimethyl cyclohexane, we can show the following two possibilities.
These two molecules are isomers of each other. We call them “stereoisomers” because they have the same connectivity but differ in the arrangement of their arrangement in space.
Thanks for reading! James
P.S. Subtle extra point. There’s a lot of confusion between the terms “cis” and “syn” and “trans” and “anti”. The difference is subtle: “cis” and “trans” implies that the orientation of the two groups is locked; you can’t convert cis to trans through rotation. The terms “syn” and “anti” imply similar relationships to “cis” and “trans”, but can also be applied to systems which are not locked. For example in certain Newman projections we can convert a “syn” relationship to an “anti” one through bond rotation.