7: Reaction Mechanisms Continued
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- 7.0: Prelude to Nucleophilic Substitution Reactions
- Dr. Tim Spector, Professor of Genetic Epidemiology at Kings College in London, knows a thing or two about twins. He should: as head of the Department of Twin Research at Kings College, Spector works with about 3500 pairs of identical twins, researching the influence of a person's genetic blueprint on everything from how likely they are to be obese, to whether or not they hold religious beliefs, to what kind of person they fall in love with.
- 7.1: Two Mechanistic Models for Nucleophilic Substitution
- As we begin our study of nucleophilic substitution reactions, we will focus at first on simple alkyl halide compounds. While the specific reactions we'll initially consider do not occur in living things, it is nonetheless useful to start with alkyl halides as a model to illustrate some fundamental ideas that we must cover. Later, we will move on to apply what we have earned about alkyl halides to the larger and more complex biomolecules that are undergoing nucleophilic substitution in cells.
- 7.2: Nucleophiles
- A nucleophile is an atom or functional group with a pair of electrons (usually a non-bonding, or lone pair) that can be shared. The same, however, can be said about a base: in fact, bases can act as nucleophiles, and nucleophiles can act as bases. What, then, is the difference between a base and a nucleophile?
- 7.3: Electrophiles
- Next, we turn to electrophiles. In the vast majority of the nucleophilic substitution reactions you will see in this and other organic chemistry texts, the electrophilic atom is a carbon bonded to an electronegative atom, usually oxygen, nitrogen, sulfur, or a halogen.
- 7.4: Leaving Groups
- In our general discussion of nucleophilic substitution reactions, we have until now been using chloride ion as our common leaving group. Alkyl chlorides are indeed common reactants in laboratory nucleophilic substitution reactions, as are alkyl bromides and alkyl iodides.
- 7.5: Prelude to Nucleophilic Carbonyl Addition Reactions
- Acetals are derived from aldehydes. The reactions that occur at the carbonyl carbon of aldehydes and ketones is absolutely central to the chemistry of carbohydrates such as starch and cellulose, and it is this chemistry that is the subject of the chapter we are about to begin.
- 7.6: Nucleophilic Additions to Aldehydes and Ketones - An Overview
- Recall from chapter 1 that the ketone functional group is made up of a carbonyl bonded to two carbons, while in an aldehyde one (or both) of the neighboring atoms is a hydrogen.
- 7.7: Hemiacetals, Hemiketals, and Hydrates
- One of the most important examples of a nucleophilic addition reaction in biochemistry, and in carbohydrate chemistry in particular, is the addition of an alcohol to a ketone or aldehyde. When an alcohol adds to an aldehyde, the result is called a hemiacetal; when an alcohol adds to a ketone the resulting product is a hemiketal.
- 7.8: Acetals and Ketals
- Hemiacetals and hemiketals can react with a second alcohol nucleophile to form an acetal or ketal. The second alcohol may be the same as the first (ie. if R2=R3 in the scheme below), or different.
- 7.9: Prelude to Nucleophilic Acyl Substitution Reactions
- Understanding the reactivity of carboxylic acid derivative groups will allow us to appreciate why penicillin is so prone to degradation, and why - very significantly for all of us - the era of not having to worry about bacterial infections may be near an end, as common toxic bacterial species such as Staphylococcus develop increasingly robust resistance to antibiotics.
- 7.10: Carboxylic Acid Derivatives
- The functional groups at the heart of this chapter are called carboxylic acid derivatives: they include carboxylic acids themselves, carboxylates (deprotonated carboxylic acids), amides, esters, thioesters, and acyl phosphates.
- 7.11: The Nucleophilic Acyl Substitution Mechanism
- The fact that one of the atoms adjacent to the carbonyl carbon in carboxylic acid derivatives is an electronegative heteroatom – rather than a carbon like in ketones or a hydrogen like in aldehydes - is critical to understanding the reactivity of carboxylic acid derivatives.
- 7.12: Hydrolysis of Thioesters, Esters, and Amides
- So far we have been looking at the formation of thioesters, carboxylic esters, and amides, starting from carboxylates. In hydrolytic acyl substitution reactions, nucleophilic water is the incoming nucleophile and a carboxylate group is the final product. Because carboxylates are the least reactive among the carboxylic acid derivatives, these hydrolysis reactions are thermodynamically favorable, with thioester hydrolysis the most favorable of the three.