Chapter 1

Organic Chemistry II: Here We Go Again!

IN THIS CHAPTER

Reviewing the material you learned in Organic I

Previewing what you find out in Organic II

If you're looking at this chapter, it's probably because you're getting ready to take the second half of organic chemistry, are in the midst of Organic II, or you're trying to figure out what Organic II covers in time to change your major from pre-med to art history. In any respect, you probably successfully completed Organic Chemistry I. Many of the study techniques (and coping mechanisms) you learned that helped you do well in Organic I are helpful in Organic II. The two primary things to remember are

• Never get behind.
• Carbon has four bonds.

In this book we use larger, more complex molecules than you may have encountered in Organic I. We chose to do this because, firstly, that's the nature of Organic II - larger and more complex molecules. Secondly, many of you will be taking biochemistry at some point, and to succeed in that subject you need to become comfortable with large, involved molecules. (If you do take biochemistry, be sure to check out Biochemistry For Dummies by John T. Moore and Richard H. Langley [Wiley]. We understand the authors are really great guys.)

To get you started, this chapter does a quick review of the topics commonly found in Organic I, and then gives an overview of what we cover in Organic II.

While you read over what you specifically need from Organic I, make sure you note anything you feel weak about so that you can do a quick review now.

Recapping Organic Chemistry I

In Organic I you learned that organic chemistry is the study of carbon compounds. Until the mid-1800s, people believed that all carbon compounds were the result of biological processes requiring a living organism. This was called the vital force theory. The synthesis (or formation) of urea from inorganic materials showed that other paths to the production of carbon compounds are possible. Many millions of organic compounds exist because carbon atoms form stable bonds to other carbon atoms. The process of one type of atom bonding to identical atoms is catenation. Many elements can catenate, but carbon is the most effective, with apparently no limit to how many carbon atoms can link together. These linkages may be in chains, branched chains, or rings, providing a vast number of compounds.

Carbon is also capable of forming stable bonds to a number of other elements, including the biochemically important elements hydrogen, nitrogen, oxygen, and sulfur. The latter three elements form the foundation of many of the functional groups you studied in Organic I, while hydrogen is in nearly every organic compound.

Intermolecular forces

You learned about intermolecular forces in Organic I. Intermolecular forces (forces between chemical species) are extremely important in explaining the interaction between molecules. Intermolecular forces that you saw in Organic I and see again in Organic II include dipole-dipole interactions, London, hydrogen bonding, and sometimes ionic interactions.

Dipole-dipole forces exist between polar regions of different molecules. The presence of a dipole means that the molecule has a partially positive (d+) end and a partially negative (d-) end. Opposite partial charges attract each other, whereas like partial charges repel.

Hydrogen bonding, as the name implies, involves hydrogen. This hydrogen atom must be bonded to either an oxygen atom or a nitrogen atom. (In nonbiological situations, hydrogen bonding also occurs when a hydrogen atom bonds to a fluorine atom.) Hydrogen bonding is significantly stronger than a normal dipole-dipole force, and is much stronger than London dispersion forces, the forces between nonpolar molecules due to the fluctuations of the electron clouds of atoms or molecules. The hydrogen bonded to either a nitrogen or oxygen atom is strongly attracted to a different nitrogen or oxygen atom. Hydrogen bonding may be either intramolecular or intermolecular.

In organic reactions, ionic interactions may serve as intermolecular or intramolecular forces. In some cases, these may involve metal cations, such as Na+, or anions, such as Cl-. Cations may include an ammonium ion from an amino group, such as RNH3+. The anion may be a carboxylate ion, such as RCOO- from a carboxylic acid. The oppositely charged ions attract each other very strongly (stronger than the other intermolecular interactions).

Functional groups

Carbon is an extremely versatile element because it can form many different compounds. Most of the compounds you see have one or more functional groups, which contain atoms other than carbon and hydrogen and/or double or triple bonds, and define the reactivity of the organic molecule.

In Organic I you probably started with the hydrocarbons, compounds of carbon and hydrogen, including the alkenes and alkynes that contained double and single bonds, respectively. Then you probably touched on some of the more common functional groups, such as alcohols and maybe even some aromatic compounds.

Reactions

You encountered many reactions in Organic I. Every time you encountered a different functional group, you had a slew of reactions to learn. Reactions that told how the functional group could be formed, common reactions that the functional group underwent - reactions, reactions, and more reactions.

Two of the most important ones you learned were substitution and elimination reactions: SN1, SN2, E1, and E2. We hope you learned them well because you'll be seeing them again quite often.

Spectroscopy

In Organic I you probably covered different types of spectroscopy and how they're used in structure determinations. You discovered how mass spectroscopy can give you an idea about molar mass and what fragments may be present in the molecule. You found out that infrared spectroscopy can be used to identify functional groups, and you learned to look at the fingerprint region. Then finally you progressed to nuclear magnetic resonance (NMR) spectroscopy, one of the main tools of organic chemists, which can be used to interpret chemical shifts and splitting patterns to give you more clues about structure.

Isomerism and optical activity

During Organic I you were exposed to the concepts associated with isomerism and optical activity. You need to be familiar with these concepts in Organic II, so we take a few minutes here for a brief review.

Isomers are compounds that have the same molecular formula but different structural formulas. Some organic and biochemical compounds may exist in different isomeric forms, and these different isomers have different properties. Two common types of isomers in organic systems are cis-trans isomers and isomerism due to the presence of a chiral carbon.

Cis-trans isomers

The presence of carbon-carbon double bonds leads to the possibility of isomers. Double bonds are rather restrictive and limit molecular movement. Groups on the same side of the double bond tend to remain in that position (cis), while groups on opposite sides tend to remain across the bond from each other (trans). You can see an example of each in Figure 1-1. However, if the two groups attached to either of the carbon atoms of the double bond are the same, cis-trans isomers are not possible. Cis isomers are the normal form of fatty acids, but processing tends to convert some of the cis isomers to the trans isomers.

FIGURE 1-1:Cis and trans isomers.

Cis-trans isomers are also possible in nonaromatic cyclic systems. The cis form has similar groups on the same side of the ring, while the trans form has similar groups above and below the ring.

Chiral compounds

A carbon atom that has four different groups attached is chiral. A chiral carbon rotates plane-polarized light, light whose waves are all in the same plane, and has an enantiomer (non-superimposable mirror image). Rotation, which may be either to the right (dextrorotatory) or to the left (levorotatory), leads to one optical isomer being d and the other being l. Specific rotation (represented by , where a = observed rotation, T = temperature, and D = sodium D line) is a measure of the ability of a compound to rotate light. The specific rotation comes from the observed rotation (a) divided by the product of the concentration of the solution and the length of the container. Other than optical activity, the physical properties of enantiomers are the same.

A racemic mixture is a 50:50 mixture of the enantiomers.

A meso compound is a compound with chiral centers and a plane of symmetry. The plane of symmetry leads to the optical rotation of one chiral carbon cancelling the optical rotation of another.

Diastereomers are stereoisomers that aren't enantiomers.

R-S notation is a means of designating the geometry around the chiral center. This method requires the groups attached to the chiral center to be prioritized in order of decreasing atomic weight. To assign the center, place the lowest priority group (the group that has the lowest atomic weight) on the far side and count the remaining groups as...