Absolute Configuration: Rules & Example

Instructor: Kristen Procko

Kristen has taught chemistry and biochemistry at the undergraduate and Master's level and has a PhD in chemistry.

Learn the rules for assigning the absolute configuration at a chiral carbon atom in an organic molecule, as well as how to assign R and S stereochemistry. You'll also see examples that will help you approach problems involving stereochemistry.

Chiral Carbon Atoms

Carbon, when neutral, is bonded to four groups in a tetrahedral arrangement. What this means is that each group points as far away from the other in three-dimensional space as it can. Imagine carbon in the center of the tetrahedron shown below, with each of the four atoms that it is bonded to pointing in the direction of each corner. This describes the tetrahedral geometry of carbon.

Tetrahedron shape

When a molecule contains a chiral carbon atom, there are four different groups attached to the carbon. Because of the way the groups orient themselves in space, the molecule can exist in one of two configurations at that carbon, called the absolute configuration. If the molecule has just one chiral carbon, these two configurations are called enantiomers. The two possible molecules are mirror images of each other, but they are non-superimposable. Take a peek at the two organic molecules below; they are mirror images, but if you tried to lay them on top of each other, the groups would never line up perfectly. This is what is meant by 'non-superimposable.'

chirality basic example

This is a tough concept, so let's consider a real life example. Take the palms of your hands and face them toward each other. The thumbs line up, and so do your pinky fingers. The hands are mirror images. Now, try to put one hand on top of the other with the palms facing down. No matter how we position the hands, the thumbs will never line up. This is because they are non-superimposable.

You are more chiral than just your hands. In fact, 19 out of 20 of the amino acids that make up your body are chiral! The proteins that carry out your biological functions are made of these amino acids, so your proteins are chiral too. This means that they can interact with molecules containing chiral carbons distinctly. A protein may recognize one enantiomer of an organic molecule as a drug, and the enantiomer of that same organic molecule may have little to no effect.

Since chirality is so critical in biological systems, it is important to be able to assign the absolute configuration of a chiral carbon. Let's look at how this is done.

Assigning Stereochemistry at a Chiral Carbon Atom

The Rules

There are three steps to assign R or S, which is called the absolute configuration of the chiral carbon atom. Groups are first assigned a priority based on the atomic weight of the first atom bonded to the chiral carbon, which can be found on a periodic table. The higher the atomic weight, the higher priority.

  1. Point the lowest priority group away from you. This means that the low priority group needs be on the dashed wedge in the example below.
  2. Number the remaining three groups according to priority: 1 = highest priority and 3 = lowest priority.
  3. Draw a circle beginning at the group numbered 1 that ends with an arrow at group 3.

If the arrow points clockwise, the compound is R. If the arrow points in a counterclockwise direction, the chiral carbon is S.

Let's revisit our earlier example and assign stereochemistry (the three-dimensional arrangement of the atoms). Notice that the lowest priority group, the hydrogen atom, is already pointing away from you. Bromine has the highest molecular weight of the atoms, so this gets the highest priority. Chlorine is next, followed by fluorine, so we number the compounds as shown below. When we draw our arrows, we can see that the compound on the left is S and the one on the right is R.

chirality example with assignments

Assigning Chirality When the Group Contains Multiple Atoms

When the groups contain more than one atom, we may need to look beyond the first atom to assign the absolute configuration. The example on the left is fairly straightforward. The first group is CH2 in two chains, so we need to look beyond that position. As we move outward one atom, we can see that the nitrogen has higher priority than another carbon atom, which makes this compound R. In the example on the right, the groups contain only carbon and hydrogen, but they are different groups:

chirality example looking beyond the first atom

Again, the first atom is carbon in each group, so we must look beyond to assign priority. In our example, the higher priority chains contain another carbon instead of hydrogen atoms.

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