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A short summary of each chapter, then the key terms that chapter names. Each chapter link opens that chapter in the OpenStax book.
Open the bookChapter 1
The purpose of this chapter has been to get you up to speed—to review some ideas about atoms, bonds, and molecular geometry. As we’ve seen, organic chemistry is the study of carbon compounds. Although a division into organic and inorganic chemistry occurred historically, there is no scientific reason for the division An atom consists of a positively charged nucleus surrounded by one or more negatively charged electrons.
Chapter 2
A carbon-oxygen bond is polar, for example, because oxygen attracts the shared electrons more strongly than carbon does. Many molecules as a whole are also polar, owing to the presence of individual polar bonds and electron lone pairs. The polarity of a molecule is measured by its dipole moment , μ Understanding organic chemistry means knowing not just what happens but also why and how it happens at the molecular level.
Chapter 3
A functional group is a group of atoms within a larger molecule that has a characteristic chemical reactivity. Because functional groups behave in approximately the same way in all molecules where they occur, the chemical reactions of an organic molecule are largely determined by its functional groups They contain no functional groups, are relatively inert, and can be either straight-chain ( normal ) or branched . Alkanes are relatively unreactive and rarely involved in chemical reactions, but they nevertheless provide a useful vehicle for introducing some important general ideas.
Chapter 4
Cyclic molecules are so commonly encountered throughout organic and biological chemistry that it’s important to understand the consequences of their cyclic structures. Thus, we’ve taken a close look at cyclic structures in this chapter Cycloalkanes are saturated cyclic hydrocarbons with the general formula C n H 2 n . In contrast to open-chain alkanes, where nearly free rotation occurs around C-C bonds, rotation is greatly reduced in cycloalkanes.
Chapter 5
An object or molecule that is not superimposable on its mirror image is said to be chiral , meaning “handed.” A chiral molecule is one that does not have a plane of symmetry cutting through it so that one half is a… In this chapter, we’ve looked at some of the causes and consequences of molecular handedness—a topic of particular importance in understanding biological chemistry. The subject can be a bit complex but is so important that it’s worthwhile spending time to become familiar with it The most common cause of chirality in organic molecules is the presence of a tetrahedral, sp 3 -hybridized carbon atom bonded to four different groups—a so-called chirality center .
Chapter 6
A bond is formed in a polar reaction when the nucleophile donates an electron pair to the electrophile. All chemical reactions, whether in the laboratory or in living organisms, follow the same chemical rules. To understand both organic and biological chemistry, it’s necessary to know not just what occurs but also why and how chemical reactions take place. In this chapter, we’ve taken a brief look at the fundamental kinds of organic reactions, we’ve seen why reactions occur, and we’ve seen how reactions can be described
Chapter 7
In this chapter, we’ve looked at some consequences of alkene stereoisomerism and at the details of the broadest class of alkene reactions—the electrophilic addition reaction An alkene is a hydrocarbon that contains a carbon-carbon double bond. Because they contain fewer hydrogens than alkanes with the same number of carbons, alkenes are said to be unsaturated Because rotation around the double bond can’t occur, substituted alkenes can exist as cis-trans stereoisomers.
Chapter 8
The converse of this elimination reaction is the addition of various substances to the alkene double bond to give saturated products With the background needed to understand organic reactions now covered, this chapter has begun the systematic description of major functional groups Alkenes are generally prepared by an elimination reaction, such as dehydrohalogenation, the elimination of HX from an alkyl halide, or dehydration, the elimination of water from an alcohol. HCl, HBr, and HI add to alkenes by a two-step electrophilic addition mechanism.
Chapter 9
The real importance of this chapter is that alkyne chemistry is a useful vehicle for looking at the general strategies used in organic synthesis—the construction of complex molecules in the laboratory The chemistry of alkynes is dominated by electrophilic addition reactions, similar to those of alkenes. Alkynes are less common than alkenes, both in the laboratory and in living organisms, so we haven’t covered them in great detail. An alkyne is a hydrocarbon that contains a carbon-carbon triple bond.
Chapter 10
Alkyl halides are not often found in terrestrial organisms, but the kinds of reactions they undergo are among the most important and well-studied reaction types in organic chemistry. In this chapter, we saw how to name and prepare alkyl halides, and we’ll soon make a detailed study of their substitution and elimination reactions Simple alkyl halides can be prepared by radical halogenation of alkanes, but mixtures of products usually result. The reactivity order of alkanes toward halogenation is identical to the stability order of radicals: R 3 C · > R 2 CH · > RCH 2 · .
Chapter 11
The reaction of an alkyl halide or tosylate with a nucleophile/base results either in substitution or in elimination. The resultant nucleophilic substitution and base-induced elimination reactions are two of the most widely occurring and versatile reaction types in organic chemistry, both in the laboratory and in biological pathways Nucleophilic substitutions are of two types: S N 2 reactions and S N 1 reactions . In the S N 2 reaction, the entering nucleophile approaches the halide from a direction 180° away from the leaving group, resulting in an umbrella-like inversion of configuration at the carbon atom.
Chapter 12
The structure of an organic molecule is usually determined using spectroscopic methods, including mass spectrometry and infrared spectroscopy. The ionized sample molecule is called the molecular ion, M + , and measurement of its mass gives the molecular weight of the sample. Finding the structure of a new molecule, whether a small one synthesized in the laboratory or a large protein found in living organisms, is central to the progression of chemistry and biochemistry. Mass spectrometry (MS) tells the molecular weight and formula of a molecule; infrared (IR) spectroscopy identifies the functional groups present in the molecule
Chapter 13
The exact position of each peak is called the chemical shift . Nuclear magnetic resonance spectroscopy , or NMR , is the most valuable of the numerous spectroscopic techniques used for structure determination. Although we focused in this chapter on NMR applications with small molecules, more advanced NMR techniques are also used in biological chemistry to study protein structure and folding When magnetic nuclei, such as 1 H and 13 C, are placed in a strong magnetic field, their spins orient either with or against the field.
Chapter 14
A conjugated diene or other compound is one that contains alternating double and single bonds. Only the two bonding orbitals are occupied; the two antibonding orbitals are unoccupied. The unsaturated compounds we’ve looked at previously have had only one double bond, but many compounds have numerous sites of unsaturation, which gives them some distinctive properties. Many such compounds are common in nature, including pigments and hormones
Chapter 15
The word aromatic is used for historical reasons to refer to the class of compounds related structurally to benzene. Aromatic rings are a common part of many biological structures and are particularly important in nucleic acid chemistry and in the chemistry of several amino acids. In this chapter, we’ve seen how and why aromatic compounds are different from such apparently related compounds as cycloalkenes Aromatic compounds are systematically named according to IUPAC rules, but many common names are also used.
Chapter 16
We’ve continued the coverage of aromatic molecules in this chapter, shifting focus to concentrate on reactions. In particular, we’ve looked at the relationship between aromatic structure and reactivity, a relationship critical to understanding how numerous biological molecules and pharmaceutical agents are synthesized and why… An electrophilic aromatic substitution reaction takes place in two steps—initial reaction of an electrophile, E + , with the aromatic ring, followed by loss of H + from the resonance-stabilized carbocation intermediate… Many variations of the reaction can be carried out, including halogenation, nitration, and sulfonation.
Chapter 17
In previous chapters, we focused on developing general ideas of organic reactivity, looking at the chemistry of hydrocarbons and alkyl halides and seeing some of the tools used in structural studies. With that accomplished, we have now begun to study the oxygen-containing functional groups that lie at the heart of organic and biological chemistry Alcohols are among the most versatile of all organic compounds. They occur widely in nature, are important industrially, and have an unusually rich chemistry.
Chapter 18
Ethers are compounds that have two organic groups bonded to the same oxygen atom, ROR′. The organic groups can be alkyl, vinylic, or aryl, and the oxygen atom can be in a ring or in an open chain. Ethers are prepared by either Williamson ether synthesis, which involves S N 2 reaction of an alkoxide ion with a primary alkyl halide, or the alkoxymercuration reaction, which involves Markovnikov addition of an…
Chapter 19
The nucleophilic addition reaction is the most common general reaction type for aldehydes and ketones. Aldehydes and ketones are among the most important of all functional groups, both in the chemical industry and in biological pathways. In this chapter, we’ve looked at some of their typical reactions. Aldehydes are normally prepared in the laboratory by oxidation of primary alcohols or by partial reduction of esters.
Chapter 20
Like aldehydes and ketones, the carbonyl carbon atom is sp 2 -hybridized; like alcohols, carboxylic acids are associated through hydrogen-bonding and therefore have high boiling points Although weaker than mineral acids such as HCl, carboxylic acids dissociate much more readily than alcohols because the resultant carboxylate ions are stabilized by resonance between two equivalent forms Carboxylic acids are among the most useful building blocks for synthesizing other molecules, both in nature and in the laboratory. Thus, an understanding of their properties and reactions is fundamental to understanding biological chemistry.
Chapter 21
Acid halides, acid anhydrides, esters, and amides are the most common such derivatives in the laboratory; thioesters and acyl phosphates are common in biological molecules The chemistry of carboxylic acid derivatives is dominated by the nucleophilic acyl substitution reaction . The reactivity order is acid halide > acid anhydride > thioester > ester > amide Carboxylic acid derivatives —compounds in which the -OH group of a carboxylic acid has been replaced by another substituent—are among the most widely occurring of all molecules and are involved in almost all biological…
Chapter 22
An example is the α halogenation of ketones on treatment with Cl 2 , Br 2 , or I 2 in acid solution. The α -substitution reaction of a carbonyl compound through either an enol or enolate ion intermediate is one of the four fundamental reaction types in carbonyl-group chemistry Alpha bromination of carboxylic acids can be similarly accomplished by the Hell-Volhard-Zelinskii (HVZ) reaction, in which an acid is treated with Br 2 and PBr 3 . Alpha hydrogen atoms of carbonyl compounds are weakly acidic and can be removed by strong bases, such as lithium diisopropylamide (LDA), to yield nucleophilic enolate ions.
Chapter 23
The aldol reaction is a carbonyl condensation that occurs between two aldehyde or ketone molecules. Aldol reactions are reversible, leading first to β -hydroxy aldehydes/ketones and then to α , β -unsaturated products after dehydration. A mixed reaction can be successful, however, if one of the two partners is an unusually good donor (ethyl acetoacetate, for instance) or if it can act only as an acceptor (formaldehyde and benzaldehyde, for instance). In this chapter, we’ve discussed the fourth and last of the common carbonyl-group reactions—the carbonyl condensation.
Chapter 24
The chemistry of amines is dominated by the lone-pair electrons on nitrogen, which makes amines both basic and nucleophilic. The basicity of arylamines is generally lower than that of alkylamines because the nitrogen lone-pair electrons are delocalized by interaction with the aromatic π system. We’ve now seen all the common functional groups that occur in organic and biological chemistry. Of those groups, amines are among the most abundant and have among the richest chemistry.
Chapter 25
Now that we’ve now seen all the common functional groups and reaction types, our focus has changed to looking at the major classes of biological molecules. Carbohydrates are polyhydroxy aldehydes and ketones. They are classified according to the number of carbon atoms and the kind of carbonyl group they contain. Glucose, for example, is an aldohexose, a six-carbon aldehydo sugar.
Chapter 26
Proteins and peptides are large biomolecules made of α -amino acid residues linked together by amide, or peptide, bonds. Determining the structure of a peptide or protein begins with amino acid analysis. The peptide is hydrolyzed to its constituent α -amino acids, which are separated and identified. Edman degradation by treatment with phenyl isothiocyanate (PITC) cleaves one residue from the N terminus of the peptide and forms an easily identifiable phenylthiohydantoin (PTH) derivative of the N-terminal amino acid .
Chapter 27
Lipids are the naturally occurring materials isolated from plants and animals by extraction with a nonpolar organic solvent. Animal fats and vegetable oils are the most widely occurring lipids. Both are triacylglycerols —triesters of glycerol with long-chain fatty acids . Animal fats are usually saturated, whereas vegetable oils usually have unsaturated fatty acid residues
Chapter 28
Enzyme-catalyzed hydrolysis of nucleic acids yields nucleotides , the monomer units from which RNA and DNA are constructed. Further enzyme-catalyzed hydrolysis of the nucleotides yields nucleosides plus phosphate. The nucleotides are joined by phosphate links between the 5′ phosphate of one nucleotide and the 3′ hydroxyl on the sugar of another nucleotide DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are biological polymers that act as chemical carriers of an organism’s genetic information.
Chapter 29
Although the details of specific biochemical pathways are sometimes complex, all the reactions that occur follow the normal rules of organic chemical reactivity The catabolism of fats begins with digestion, in which ester bonds are hydrolyzed to give glycerol and fatty acids. The fatty acids are degraded in the four-step β -oxidation pathway by removal of two carbons at a time, yielding acetyl CoA. Metabolism is the sum of all chemical reactions in the body.
Chapter 30
The stereochemistry of these reactions is controlled by the symmetry of the orbitals involved in bond reorganization Highest occupied molecular orbital (HOMO) Lowest unoccupied molecular orbital (LUMO) A pericyclic reaction takes place in a single step through a cyclic transition state without intermediates.
Chapter 31
Synthetic polymers can be classified as either chain-growth or step-growth. Chain-growth polymers are prepared by chain-reaction polymerization of vinyl monomers in the presence of a radical, an anion, or a cation initiator. Radical polymerization is sometimes used, but alkenes such as 2-methylpropene that have electron-donating substituents on the double bond polymerize easily by a cationic route through carbocation intermediates. Similarly, monomers such as methyl α -cyanoacrylate that have electron-withdrawing substituents on the double bond polymerize by an anionic, conjugate addition pathway
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