6.3: Distinguishing Isomers

Structural Isomers

For organic molecules with only a few carbon atoms such as CH₄, C₂H₆, and C₃H₈, there is only one possible arrangement (structural formula) that contains all of the atoms listed in the molecular formula and follows the bonding rules to make a stable structure. Remember that carbon follows the octet rule and always forms four bonds; hydrogen is an exception to the octet rule and always forms one bond.

Now consider a molecular formula with more atoms: C₅H₁₂. We can quickly tell by the ratio of carbon atoms to hydrogen atoms that this is an alkane with all single bonds. However, the molecular formula does not tell us if all of the carbon atoms are in one chain or whether there are any branches. 

Before we go farther, remember from your previous experience drawing Lewis structures that they do not accurately represent the three-dimensional structure of a molecule. This is important in distinguishing isomers because the same molecule can be drawn differently. 

Stereoisomers

Unlike structural isomers, stereoisomers have not only the same number of each type of atom, but also the same bonding pattern. Therefore, we must look a little more closely at the structures to find the differences between these isomers.

Geometric Isomers

Geometric isomers are sets of molecules with the same bonding patterns, but some restriction in rotation that makes the atoms or groups point in different directions in the different versions.

Optical Isomers (Enantiomers)

The last category of isomers that we will examine are optical isomers which are pairs of molecules called enantiomers. 

At first glance, the two models below may seem to represent the same molecule.

In fact, they do have the same molecular formula, CHBrClF. However, there is a difference between them. Enantiomers are pairs of chiral molecules (pronounced Ki-ral like in kayak). A chiral molecule has a carbon atom with four different groups or atoms attached to it such as:

      F

      |

H - C - Cl

      |
     Br

Molecules with these chiral centers, as the carbon atom in this molecule is called, have non-superimposable mirror images. The image below shows a chiral amino acid (the R group is not the same as any of the other three groups) emphasizing that the molecule has a mirror image, just like your hands. 

Just as your hands are not superimposable, neither are the two molecules in the picture above. You cannot overlap your two hands with the palms facing the same direction and have the thumbs and fingers line up. If you line up the fingers and thumbs, then your palms are facing in opposite directions. The same is true for chiral molecules. In the photo below, I am able to align the carbon, hydrogen, and bromine atoms (black, white, and orange), but when I do so, the fluorine and chlorine atoms (purple and green) do not match up. 

There is no way that I can turn the models to align all five atoms. The only way to make them the same would be two break two of the bonds and reform them in different positions. The two molecules in the photo are enantiomers. They have the same chemical formula and the same bonding pattern (in each case H, Br, Cl, and F are attached to the carbon atom with single bonds), but they are nonsuperimposable mirror images of one another. 

Enantiomers generally have the same physical and chemical properties. However, they can interact differently with enzymes in the body. There are twenty naturally occurring amino acids of which 19 are chiral. All 19 of these have the groups arranged around the chiral center in the same way which we designate L- as in L-alanine or L-leucine. Sugars are also chiral and all of the ones that humans can digest are the same form and are designated D-, such as D-glucose. Amino acids and sugars will be introduced in the next chapter, Introduction to Biochemistry, but the difference between the L- and D- designations is a topic for a more advanced course.