1: Chapters

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Kirk McMichael
Washington State University

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1.1: Carbonyl Group - Notation, Structure, and Bonding
You will be learning and applying the principles which govern the structure of organic compound and relating your understanding of structure to the reactions--the changes in structure--which happen when specific portions of organic compounds interact with other chemical substances. We will spend the first several weeks of the semester looking at a group of organic compounds which share a common structural element--the carbonyl group.
1.2: Functional Groups, Hybridization, Naming
First, let's look at the various structural representations you were asked to develop for the molecules given at the end of the last lecture. Here they are:
1.3: Additions- Electrophilic and Nucleophilic
Last time we listed three reasons to expect that the carbonyl (C=O) group would be a functional group, a reactive part of the molecule. All of these reasons were connected with the way electrons are distributed in the group. Functional groups are the places where changing the location of electrons can happen fairly easily, which means that the distribution of electrons in a functional group is a key to its reactivity. We need a specific example to make these ideas useful.
1.4: Acetal Formation, Mechanism, Resonance
Last time I left you with a problem, "what is the mechanism for the base catalyzed addition of water to a carbonyl group?" Let's go through that and see how it goes.
1.5: Nitrogen Nucleophiles - Imine Formation
In many of the biological reactions of carbonyl groups the nucleophile is a nitrogen atom. The eventual outcome is different, so let's take a look at the details. The specific molecule as an example of a nitrogen nucleophile is methylamine. What happens if Nu = CH3NH2? Here's the complete mechanism.
1.6: Addition of Organometallics - Grignard
Last time we looked at a reaction in which a new carbon-carbon bond was made. Today, we'll look at another such reaction, one which is generally quite useful for synthesis, the assembly of larger carbon structures from smaller molecules.
1.7: Oxidation and Reduction, alpha-C-H acidity
Last time we saw how a nucleophilic addition of a carbon atom to the carbonyl carbon could be carried out through the use of a Grignard reagent. This time we'll look at oxidations and reductions of carbonyl groups and at the acidity of the alpha hydrogen atom
1.8: Enolates, Aldol Condensation, Synthesis
Last time we worked through the reagents which oxidize aldehydes to carboxylic acids and the reagents which reduce aldehydes to primary alcohols and ketones to secondary alcohols. We also learned how enolate ions can be formed by the removal of an alpha hydrogen atom and how these enolate ions can act as nucleophiles toward bromine.
1.9: Carboxylic Acid Derivatives- Interconversion
Today we'll look at carboxylic acid derivatives. This group of compounds also contains a carbonyl group, but now there is an electronegative atom (oxygen, nitrogen, or a halogen) attached to the carbonyl carbon. This difference in structure leads to a major change in reactivity. Here we find that the reactions of this group of compounds typically involve substitution of the electronegative atom by a nucleophile.
1.10: Carboxylic Acid Derivatives - Alpha Carbon Reactions
Last time we looked at several reactions of carboxylic acid derivatives and learned how to make esters and amides. Today we'll look at some further reactions of esters, including some which make new carbon-carbon bonds.
1.11: Fats, Fatty Acids, Detergents
Last time we looked at several reactions of carboxylic acid derivatives and learned how to make esters and amides. Today we'll look at some further reactions of esters. We'll also examine the chemistry of the ester functional group in fats.
1.12: Carboxylic Acids
Last time we looked the reactions of esters with lithium aluminum hydride and with Grignard reagents. We followed that with the chemistry of enolates formed from esters and then looked at fats and soaps. Today we'll look at the parent functional group of carboxylic acid derivatives, the carboxylic acid group itself. We'll see how we can make carboxylic acids and ask why they are acids.
1.13: Alcohols
Today, we'll examine the chemistry of alcohols. First, we'll review the reactions we've already seen which make alcohols. Then we'll look at the reactions of the alcohol functional group.
1.14: Ethers, Epoxides, Thiols
Today, we'll go on to look at the acidity of alcohols and the uses of their conjugate bases as nucleophiles. That will take us to the chemistry of ethers. We'll finish with a look at thiols, close relatives of alcohols in which a sulfur atom has replaced the oxygen.
1.15: Chirality, Three Dimensional Structure
Today we'll take a look at structure. We'll find that we have to begin to think in three dimensions to understand some structural differences between very similar compounds.
1.16: R/S Naming, Two or More Stereogenic Centers
Today, we'll look at naming compounds with stereocenters, and then we'll examine the complications which arise when a molecule has more than one stereocenter in it.
1.17: Carbohydrates- Monosaccharides
Last time we learned how a chiral compound's absolute configuration can be described by the R/S naming system. We also considered the situations which can arise when a compound has two (or more) stereogenic carbons. Our examples for that were in fact sugars; monosaccharide aldotetroses. We'll begin by making some structural sense of those terms.
1.18: Glycosides, Disaccharides, Polysaccharides
Today we'll look in more detail at the chemistry of that hemiacetal linkage. In particular, we'll recall how hemiacetals are converted to acetals. We'll find that these acetal linkages are what holds di- and polysaccharides together.
1.19: Amines- Structure and Synthesis
Last time we completed our study of carbohydrates. Now we are turning our attention to another important class of organic compounds, amines. Many important drugs are amines, the bases present in RNA and DNA are amines, and the fundamental building blocks of proteins are amino acids.
1.20: Amines- Reactions
Last time we looked at the behavior of amines as bases, at their involvement in hydrogen bonds, and at the ways they can be synthesized. This time, we'll continue our study of amines by examining some of their reactions.
1.21: Amino Acids and Peptides
Now we'll look at what happens when a carboxylic acid functional group and an amine functional group are in the same molecule. Our focus will be on the alpha amino acids, those in which the amino group is bonded to the alpha carbon -- the one next to the carbonyl group -- of the carboxylic acid. These are the basic building blocks of proteins and are the most important type of amino acid.
1.22: Proteins
Last time we looked at the structural characteristics of amino acids and the peptide bond which joins individual amino acids together to make proteins and peptides. We also learned about the sequence (order) in which amino acid units are joined in peptides. Today we'll study the ways in which the specific sequence of a peptide may be discovered and the methods which are used to synthesize such a peptide.
1.23: Nucleic Acids
Today we'll study the chemistry of the molecule which carries the information necessary for directing the biosynthesis of proteins and peptides. This is DNA, and we'll learn that the structure of DNA provides a very strong rationale for its function.
1.24: Nucleophilic Substitution, SN2, SN1
Today's topic takes us back to an important organic reaction mechanism. We've studied a few reactions which proceed by this mechanism. Now it's time to examine it in detail.
1.25: Elimination - E2 and E1
Last time we saw an overview of the nucleophilic substitution mechanisms of alkyl halides. We examined one of these, the SN2 mechanism in detail. Today we'll examine the other, the SN1 mechanism, and then go on to look at elimination reactions, the major competition for substitutions.
1.26: Alkenes and Alkyne Structure
Today we'll begin by looking at the structural characteristics of alkenes, the products of elimination reactions. Then we'll return to the topic of elimination reactions and examine their reaction mechanisms in more detail.
1.27: Electrophilic Additions
Last time we learned how the carbon-carbon double bond introduces stereochemical distinctions into alkenes, and we looked at the mechanisms of the elimination reactions which are important in making alkenes. Today we'll examine the characteristic reactions of alkenes -- additions
1.28: Polymers
Last time we examined the characteristic reactions of alkenes -- additions. Today, we'll see how reactions like these and some familiar reactions of carboxylic acid derivatives can be used to make very long chains -- polymers. We have already looked at some important polymers from biological systems; starch, cellulose, proteins, and nucleic acids.
1.29: Metabolic Organic Reactions
Today we're going to examine a selection of processes which occur in metabolism. We will focus on comparing these reactions to reactions we have already studied. In particular we will see that the reactions which break carbon-carbon bonds are just reverse versions of the aldol and Claisen condensations which we have studied earlier. Keep in mind that while we are looking for connections between these reactions and familiar organic reactions, all steps in these schemes are catalyzed by enzymes.
1.30: Aromatic Compounds
Today we'll find that resonance is very important in understanding both the structure and the reactions of aromatic compounds. First, let's take a look at the structural representations which distinguish aromatic compounds from those that aren't aromatic.
1.31: Electrophilic Substitution
Today we'll look at examples of electrophilic aromatic substitution reactions, learn what we can make with them, and see how the prior presence of a substituent on the aromatic ring influences where the attacking electrophile becomes attached.
1.32: Side Chain Oxidations, Phenols, Arylamines
Misc.
1.33: Radical Reactions
Last time we looked at how the benzene ring changes the reactivity of an atom or group to which it is directly attached. Today we'll finish presenting new material in the course by taking a brief look at reactions in which bond making and bond breaking events involve electrons moving singly rather than as pairs.