6.4: Distinguishing Isomers
- Page ID
- 288507
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)- To view two or more chemical structures and determine if they represent the same compound or isomers
- To distinguish between structural isomers, geometric isomers, and optical isomers
Isomers
For organic molecules with only a few carbon atoms such as CH4, C2H6, and C3H8, there is only one possible arrangement that contains all of the atoms listed in the molecular formula and follows the bonding rules to make a stable structure.
Now consider a molecular formula with more atoms: C5H12. 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. 
Figure \(\PageIndex{1}\): Three isomers of C5H12.
The three compounds above are isomers. The prefix "iso" means "same". Isomers are two or more compounds that have the same atoms, but arranged in a different way. The different arrangements can affect properties such as melting point, boiling point, and which bonds are most likely to change in chemical reactions.
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.
| Structure 1 | Structure 2 | Relationship |
|---|---|---|
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Isomers because the branching CH3 group is bonded in a different location. |
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Not isomers. These are the same, just flipped |
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Not isomers. Single bonds can rotate, so it does not matter whether the CH3 groups are shown pointing up or down. |
Structural Isomers
Structural isomers have atoms bonded in a different order. For instance, there may be branches in different places such as in Figure \(\PageIndex{1}\).
| Structure 1 | Structure 2 | Relationship |
|---|---|---|
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Structural Isomers. They are both C4H10O, but the atoms are bonded in different places. As a result Structure 1 is an ether and Structure 2 is an alcohol. |
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Structural Isomers. They are both C4H10O, but the atoms are bonded in different places. Both Structure 1 and Structure 2 are alcohols, but the reactions they can undergo are different because of the different arrangement of the carbon atoms. Note: Structure 1 in this row is also an isomer of Structure 1 in row 1. There can be many isomers of a compound. |
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Structural Isomers. Both are C4H8 but Structure 1 has the double bond at the end of the carbon chain whereas for Structure 2 it is in the middle. Note: The difference may be easier to see using Condensed Structural Formulas. Structure 1, CH3-CH2-CH=CH2, has one CH3 group and one CH group whereas Structure 2, CH3-CH=CH-CH3, has two CH3 groups and two CH groups. |
Stereoisomers
Not all isomers are structural isomers. Unlike structural isomers, stereoisomers have the same number of each type of atom and the atoms are bonded in the same order. The difference between stereoisomers their 3D arrangement. Geometric isomers and optical isomers are subcategories of stereoisomers.
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. In other words, geometric isomers have a different 3D arrangement around a bond that cannot rotate.
Just like in a model kit, double bonds in molecules cannot rotate. Therefore the two molecules below are isomers, not the same compound.
Figure \(\PageIndex{2}\): The two geometric isomers of C4H8. The structure on the left is the trans isomer and the structure on the right is the cis isomer.
The structure on the left in Figure \(\PageIndex{2}\) has one end of the carbon chain pointing up from the double bond and the other pointing down from the double bond in a zigzag shape. This is called the trans isomer. "Trans" means across and the carbon chain is going across the double bond: up on one side and down on the other. Because the double bond cannot rotate, this compound cannot flip or rotate to get the same 3D arrangement as the structure on the right.
The structure on the right in Figure \(\PageIndex{2}\) has both ends of the carbon chain pointing up. This is the cis isomer. "Cis" means same and both ends of the carbon chain are pointing up (or down, depending on your perspective) relative to the double bond.
| Structure 1 | Structure 2 | Relationship |
|---|---|---|
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Geometric isomers. In this case we compare the 3D arrangement of the chlorine atoms rather than carbon chains. Structure 1 is the cis isomer and Structure 2 is the trans isomers. Geometric always come in pairs: one cis isomer and one trans isomer with everything else the same. |
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Geometric isomers. It does not matter that the length of the chain is different on the left and right of the double bond. Structure 1 is the trans isomer and Structure 2 is the trans isomer. |
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Not isomers. These two structures have a different number of atoms. |
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Structural isomers. Both of these structures are C4H8, but the atoms are bonded in a different order. In Structure 1 the double bond is on the end of the chain. It is neither a cis nor trans isomer because the carbon chain goes neither up nor down on the left (and it goes both up and down on the right). Note: Geometric isomers must have atoms bonded in the same order. Everything must be the same except that one isomer is the cis configuration and the other is trans. |
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:
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.
Summary
- There is not one correct way to represent a chemical structure on paper. Images of the same compound may appear flipped or rotated. Also remember that single bonds can rotate and that 2D representations of structures usually do not show the correct bond angles.
- Isomer means "same parts". Structures are isomers of one another if they have the same number of atoms of each element, but arranged in a different way.
- In structural isomers, atoms are bonded in a different order. For example, one isomer may have six carbon atoms in a single chain whereas another may have five carbon atoms in a chain with a sixth branching off of that chain. The location of double bonds may also be different in structural isomers. For instance, one isomer may have a double bond between the first and second carbons while a structural isomer may have the double bond between the second and third carbons.
- Stereoisomers have all of the same atoms bonded in the same order, but with a different 3D arrangement. In geometric isomers, there is a different 3D arrangement around a double bond. One isomer has a cis configuration and the other one is trans. Optical isomers have a different 3D arrangement around a chiral center which is a carbon atom bonded to four different atoms or groups.