Chemical Structures and SMILES

Introduction

Organic chemists use structural drawings to communicate. There are numerous structural drawing programs available that chemists use to create these drawings. While structural drawings are essential to organic chemists, it is often necessary to represent such drawings in an equivalent format. For example, the structure shown below is called toluene. Another alternative representation of this structure is Cc1ccccc1, which is called a SMILES.

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Exercise 2 Draw complete Lewis structures for each of the following formulas. Indicate whether or not geometic isomers are possible.

	Yes	No
	Yes	No
	Yes	No
	Yes	No
	Yes	No
	Yes	No

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Designating Diastereomers

It's not always the case that there are two identical groups attached to the doubly bonded carbon atoms. In such instances the meaning of cis and trans becomes murky if not meaningless. In order to identify diastereomeric alkenes unambiguously, chemists have devised a convention based upon the Cahn-Ingold-Prelog rules. The convention works as follows:

1. Prioritize the two groups attached to one of the doubly bonded carbon atoms according to the Cahn-Ingold-Prelog rules.
2. Prioritize the two groups attached to the other doubly bonded carbon atom according to the Cahn-Ingold-Prelog rules.
3. The stereoisomer in which the two groups with the same priority are on the same side of the double bond is designated with the prefix "Z".
4. The stereoisomer in which the two groups with the same priority are on the opposite sides of the double bond is designated with the prefix "E".

Figure 3 demonstrates the application of these rules to specify the two diastereomers of 1-fluoro-2-chloropropene.

Figure 3

More Rules

E Z	E Z	E Z
E Z	E Z	E Z

Some Relevant Examples

An interesting example of the importance of geometric isomerism is found in the structures of fats and oils. Unsaturated fats and oils contain double bonds. Figure 4 shows the structure of a typical "polyunsaturated" fat that might be obtained from an oil such as corn oil. The word polyunsaturated simply means that the fat or oil contains more than one double bond. What's interesting about this structure is that all the double bonds have the Z-configuration. This bit of information offers some insight into the nature of fatty acid biosynthesis since the Z-configuration is inherently less stable than the E arrangement.

Figure 4

Now You're Cookin'

In contrast to the structure shown in Figure 4, most of the double bonds in vitamin A have the E-configuration as shown in Figure 5.

Figure 5

Your RDA of Vitamin A

Isomerization of Alkenes

Although the pi bond prevents rotation about a double bond, it is possible to interconvert cis and trans isomers photochemically. To understand how this happens, consider the changes in the molecular orbital diagram of the pi bond of an alkene shown in Figure 6.

Figure 6

A Pi Bond: HOMO and LUMO

Irradiation of a cis-alkene with light of the appropriate wavelength excites an electron from the p to the p* orbital. This breaks the pi bond. If rotation around the sigma bond occurs very fast, the substituent attached to one of the carbons will end up on the opposite side of the pi bond when the excited electron returns to its lower energy state and the pi bond is reformed. The formation of the trans-isomer is favored because it is more stable.

The photochemical isomerization of cis alkenes to their trans diastereomers plays an important role in the chemistry of vision. Figure 7 summarizes the essential transformations that are involved.

Figure 7

Oh Say Can You See

The key point of interest in terms of this discussion is the photochemical isomerization a specific double bond in a molecule called 11-cis-retinal. This reaction occurs in your eye under the control of an enzyme called opsin.

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