In today’s lesson, we will be discussing the following topics:
1. What are Isomers? What are Geometric Isomers?
2. Using Cis/Trans/E/Z to name Alkenes
When we draw organic compounds on paper, it is really only half the story – we haven’t taken into account their 3D structure at all! The direction of bonds within two compounds with the SAME chemical formula, can have completely different effects on their reactivities! So when we jump into isomers, this will lead onto stereochemistry (in later chapters), and it all boils down to what our 3D molecules look like in real life, as opposed to a 2D sheet of paper.
Isomers
Two compounds can be called Isomers of one another if they have the same chemical formula, but are connected in different ways. For example, we see these two compounds, which both have the chemical formula C5H12
There are many different types of isomers, and the ones we will dicsuss today are Geometric Isomers. These are isomers that differ in their geometry – they cannot be interchanged by rotation about a carbon bond, like this picture below shows – these are two different configurations of 2-butene, and even though they have the same chemical formula, they are not the same shape. These rigid bonds usually happens with alkenes and rings (cyclic compounds), where the bonds do not have free rotation, and are “locked” in place.
Although we can’t rotate alkenes like I showed above, if we did the same rotation to an alkane, we’d end up getting the same compound even if the bonds pointed in a different direction, like this:
So how do we know which version of 2-butene we are referring to in a chemical name, if there are different ways of drawing it? We use a naming system that includes the prefixes Cis, Trans, E, or Z.
How do we use them? We use a priority naming system called the Cahn-Ingold-Prelog system (CIP), and I will explain the rules below. We will place either an E/Z/cis/trans before the name of the compound to signify the direction of the double bond. Cis and trans are more general and won’t work in every scenario, E/Z works every time. I recommend to use E/Z if you are not sure which one to go with. If you haven’t learned E/Z yet, then stick with cis/trans.
Notes:
(a) When finding priority of a group, a double bond is considered higher priority than a single bond, and a triple bond is even higher priority. This is because for example, with a double bond, a double bond means there are two bonds to carbon versus only one bond to carbon. This makes the atomic number higher overall.
(b) If there is more than one double bond in the shape, a number has to be placed with the E/Z/cis/trans to indicate which double bond has which direction (you might have one bond being a Z, and another an E in the same shape)
(c) If a double bond is at the end of a shape, we do not need to use E/Z/cis/trans with that double bond. (There is no priority group on one side if this is the case)
When do we use them? When we are naming an alkene (double bond). Cis and trans can be used in many cases, but we usually use E/Z rather than cis/trans when the carbons in the double bond are substituted with more than just single bonded hydrogens and carbons, like below where I show a compound that is not substituted with four different bonds that are not hydrogen on the carbon (tetra substituted, on the left), compared to the tetra substituted one that is on the right:
Cis/trans is usually used with simpler shapes, so when in doubt use E/Z!
Rules for naming Cis/Trans or E/Z
The Cahn-Ingold-Prelog naming priority system gives us rules for naming E/Z compounds, but we can use these rules with cis/trans as well?
Let’s try the following example:
1. Cut the double bond of our shape in half, perpendicular to the bond.
2. Going atom by atom, determine which groups have higher priority on either side of the double bond. Priority is based on atomic number. If there is a tie in priority, then continue onto the next bond until the tie is broken. On the left of the red dotted line, the group with the chlorine on the top is higher priority. This is because both groups branching out of our C1 are directly connected to a carbon, but the top group is further connected to the chlorine, whereas the bottom group is again connected to another carbon. On the right side of the dotted line, we have two carbon groups branching out of C2, but the top carbon is further connected to a carbon, whereas the bottom carbon branches out into two carbons together, so it is higher priority.
3. I have circled the two highest priority groups on each side. Compare these two groups – if they are going in opposite directions they will be trans or E, in the same direction and they will be cis or Z. These are going in opposite directions, so it will be an E – I didn’t use trans because we have a tetra substituted shape.
4. To name the compound, we put an “E” in front of the name, then write out the rest of the name as we normally do (eg. E – 2 – methylpentene, for example). I won’t go through naming this shape (click here for my blog post on naming general alkenes), but you can watch the video above for more examples!