The presentation of organic chemistry in this online text is conventional; however, the use of visual aids such as three-dimensional models, animated or interactive displays and links to related material renders it much more informative than a bound paper text. An attractive feature of this text is the easy transition from an introductory discussion to a more advanced or expanded treatment of a topic. Color-shaded boxes contain links to such material, which may be consulted as often as desired, or not at all. Thus an introductory presentation of acid-base chemistry may be shifted to a more detailed treatment, including solvent effects on pKa and kinetic acidity measurements. The order in which topics are introduced may be changed. Different instructors introduce special topics, such as spectroscopy, at different stages; consequently, no specific organization has been suggested in this regard.

The main topic categories are listed on the left of the table of contents, beginning with a short introduction, which. is not an essential part of the text. Mouse clicking on a topic will display a selection of sub-menus in the space on the right. A list of specific topics covered by each sub-menu is displayed below. Special topics are listed on the lower right of the contents table, and these also display sub-menus on clicking. Interactive problem sets are incorporated at appropriate stages. The alphabetical index at the bottom includes links to the full virtual text site.

• A brief review of atomic configuration, including the Aufbau principle and the valence shell.
• Bonding models for ionic and covalent molecules are presented, based on the octet rule. Kekule/Lewis formulas are drawn and valence is defined.
• Shapes of simple covalent molecules are described, using perspective drawings. Simple VSEPR theory is formulated, and Jmol manipulatable models are presented. Some cases of hypervalent compounds involving third row elements are shown.
• Isomerism illustrates the importance of drawing structural formulas. The example of progesterone and tetrahydrocannabinol is presented as an advanced topic.
• Formula analysis demonstrates the structural information provided by a molecular formula. Examples of plausible and impossible molecular formulas are given.
• Structural equivalence of atoms and groups is explained. Primary, secondary, tertiary & quaternary carbons are defined. A recommended advanced topic, showing how the structural equivalence or non-equivalence of carbon atoms can lead to structural formulas is offered.
• Formal charge is defined. The concepts of electronegativity and polar covalent bonds are developed, and the relationship of dipole moment to molecular shape is demonstrated. More models are shown.
• The concept of resonance is introduced. Basic rules of resonance are given with examples.
• Functional groups are defined, and a table of common groups is given. The terms electrophile and nucleophile are introduced.
• Atomic and molecular orbitals are shown. Hybridization is defined, and an animation illustrating it is provided. Simple correlation diagrams are drawn. Jmol models of different carbon hybridization states and molecular orbitals are presented.

• The various components and conditions of a chemical reaction are described.
• Reactions are classified in two ways. First, in terms of structural change (addition, elimination, substitution & rearrangement). Second, by functional group reactivity.
• The concept of reaction mechanism is introduced. Curved arrow notation for electron movement is shown. Heterolysis and homolysis are defined.
• Reactive intermediates are described (carbocations, carbanions, radicals & carbenes). The terms electrophile and nucleophile are redefined.
• An extensive review of acid-base chemistry is presented. Bronsted acids and bases, and the concept of conjugate pairs are defined. General principles governing equilibria are stated, pKa and pH are defined, and the Henderson-Hasselbach equation is written. The use of pKa values for measuring basicity is explained. Lewis acid-base theory is presented and related to electrophile/nucleophile terminology. A more advanced treatment of acidity is an option.
• Examples of simple ionic reactions are shown using curved arrow symbols. Tautomerism is shown as an example of a rearrangement. Methane chlorination is presented as an example of a free radical chain reaction. An advanced topic explores the relationship of basicity and nucleophilicity.
• Energy changes in chemical reactions are described. Definitions of exothermic and endothermic reactions are given. Thermodynamic stability is discussed and illustrated by different C₆H₁₂ isomers. A table of standard bond energies is presented. A more advanced treatment of energy is offered as an option..

• Saturated hydrocarbons are defined as alkanes and cycloalkanes
• The IUPAC rules of organic chemical nomenclature are introduced. Numerous examples are provided, and molecular formula analysis is repeated. Basic types of bicycloalkanes are shown.
• Unsaturated hydrocarbons are defined as alkenes and alkynes (and cyclic analogs). IUPAC rules for the nomenclature of these hydrocarbons are presented with numerous examples. The value of formula analysis is reinforced using hydrocarbon isomers.
• Combustion of alkanes and cycloalkanes is presented as an important exothermic reaction. Heat of combustion measurements are shown to provide information about ring strain. The unusual reactivity of small rings is due to this angle strain.
• Halogenation reactions of alkanes are described. The chlorination of methane is revisited. An animation of the free radical chain mechanism is provided. Halogenation of larger alkanes is shown to give mixtures of isomeric products. The selectivity of such halogenations is discussed and interpreted using bond dissociation energies. A stability order for alkyl radicals is proposed. An advanced treatment of this subject is available as an option.

• Stereoisomerism is defined and contrasted with constitutional isomerism.
• Configurational stereoisomers of alkenes are shown. The nomenclature of such isomers is established, using both cis-trans and E-Z prefix terminology.
• Configurational stereoisomerism of disubstituted cycloalkanes is demonstrated. Examples use a cis-trans notation. An advanced nomenclature for more highly substituted rings is an option.
• Conformational structures of alkanes are shown. Conformers of ethane and butane are examined using Jmol models. Syn, anti and gauche terminology is introduced, along with the concept of torsional strain. An advanced discussion of rotamer analysis is offered as an option.
• The puckered or nonplanar shape of cycloalkanes larger than three carbons is described. Angle, torsional and crowding strain factors are noted. Conformational analysis of cycloalkanes and substituted cycloalkanes is presented, with an emphasis on cyclohexane. Chair, boat and twist conformations are shown with Jmol models. Axial and equatorial locations on the chair conformer are designated. The complex isomerism of dsubstituted cyclohexanes is analyzed with Jmol models.

• The components and conditions of a chemical reaction are recalled. Observable characteristics of a reaction are listed (e.g. intermediates, heat of reaction & reaction rate)
• The concept of an activation energy is introduced, energy diagrams are drawn, transition state is defined, and the influence of temperature on reaction rate described.
• Factors influencing reaction rates are noted. Kinetic analysis and the molecularity of a reaction are discussed.
• The operational variables in a reaction are reviewed (e.g. reactants, reagents, solvents and catalysts).
• Product selectivity in the form of regioselectivity, stereoselectivity and stereospecificity is defined.
• Electronic and steric factors that influence reaction rate are noted.
• The distinction between thermodynamic and chemical stability is made.

• An overview of an addition reaction to an alkene is shown
• The addition of strong Bronsted acids is described, and Markovnikov rule regioselectivity noted. Six self test questions are presented.
• A two-step mechanism is described, with the stability of a carbocation intermediate being a critical factor in regioselective rate differences. An advanced discussion of carbocation stability is offered.
• The possibility of carbocation rearrangement is introduced with a few examples An advanced discussion of such rearrangements is offered.
• Addition reactions initiated by electrophiles (Lewis acids), especially electrophilic halogen are described. The anti-Markovnikov addition of diborane is discussed and illustrated.
• Stereoselectivity in all the above addition reactions is described and explained.
• The catalytic addition of hydrogen to alkenes, together with heats of hydrogenation serves as an indicator of double bond stability.

• A general treatment of oxidation-reduction terminology is made. The assignment of oxidation states to carbon is an optional topic.
• The oxidative addition reactions hydroxylation and epoxidation are demonstrated..
• Oxidative cleavage of double bonds, especially by ozonolysis, is described. Several problems are given as a self-test. Further information about ozonolysis is offered as an advanced topic. Glycol cleavage reactions are also discussed.
• Free radical reactions of alkenes include addition and allylic substitution.
• Alkyne addition reactions are illustrated by catalytic hydrogenation, including the Lindlar catalyst, and by addition of electrophilic reagents such as Bronsted acids and halogens. The relative reactivity of the triple bond is discussed.
• Acid catalyzed addition of water (hydration) and hydroboration lead to enol tautomers that rapidly rearrange to their keto forms.
• Nucleophilic addition reactions and dissolving metal reduction of alkynes are shown.
• The acidity of terminal alkynes is noted, and examples of the reactivity of acetylide anions are given.

• Dienes are classified as isolated, conjugated or cumulated. Heats of hydrogenation indicate stability.
• A molecular orbital treatment of conjugated dienes is given, along with Jmol models.
• Addition of Br₂ and HBr to a conjugated diene is described. The distinction between 1,2- and 1,4-addition is made, as is which one is rate-favored versus thermodynamically favored.
• Diels-Alder cycloaddition reactions of conjugated dienes are described. The stereospecificity of the reaction is noted, and several problems are given for a self-test. Advanced treatment of [4+2]cycloaddition is offered as option. Further discussion of allenes is also an option.
• The unique character of the simple aromatic hydrocarbon benzene is presented.
• Electrophilic substitution reactions and heat of hydrogenation testify to the exceptional thermodynamic (and chemical) stability of benzene.
• A molecular orbital treatment of benzene is given, along with Jmol models.
• The nomenclature of various substituted benzene derivatives is presented.
• Fused benzene ring compounds, such as naphthalene, coronene, hexahelicene and buckeyball are shown with a collection of Jmol models.
• Other aromatic compounds are described. Factors essential for aromatic character are listed, especially the Huckel rule. Antiaromaticity is briefly described.
• A general definition of an annulene is given, along with examples of aromatic ions. Several advanced topics are offered in this respect.

• Chirality and its relationship to symmetry is defined. Examples of symmetry elements and illustrative Jmol modes are available as an option.
• Enantiomorphism is described, and Jmol models showing this stereoisomerism are available. A self-test problem for identifying chiral centers is given
• Optical activity is noted as a characteristic of a pure enantiomer, and a polarimeter is described. Racemates are 50:50 mixtures of enantiomers.
• The Cahn-Ingold-Prelog nomenclature of chiral structures is presented. Many examples are given, and an instructive tutorial using Jmol models is offered.
• The stereoisomerism of compounds having two or more chiral centers is examined. Fischer projection drawings are presented.
• Stereogenic nitrogen compounds are briefly discussed.
• Achiral stereoisomers and meso compounds are described. Jmol models illustrate this feature. Examples of other configurational drawing systems are an option.
• Methods for resolving racemates are discussed. An advanced treatment of resolution is an option.
• Conformational enantiomorphism is explored. Biphenyl enantiomorphism is shown as an option.
• The complex stereoisomerism of disubstituted cyclohexanes is treated with appropriate Jmol models. Advanced treatment of stereogenic element analysis is available as an option.
• A general summary of isomerism and molecular structure descriptors completes this chapter.

• Some general characteristics of the carbon-halogen bond are reviewed.
• Examples of nucleophilic substitution reactions are given. Reaction variables (e.g. nucleophile, solvent, alkyl group, and halide group) and observables (e.g. alkyl configuration and kinetics) are discussed.
• Two mechanisms, S_N2 and S_N1, identified by kinetic molecularity, are presented.
• An animation of the single-step S_N2 reaction, illustrating inversion of configuration may be viewed. Steric hindrance to back-side nucleophile attack is illustrated by models.
• The two-step S_N1 mechanism is separated into rate-determining and product-determining steps. An animation may be viewed. The Hammond postulate is stated and explained. The influence of electrophilic metal salts may be selected as a special topic.
• Self-test questions concerning substitution are presented. A discussion of stereoelectronic effects is offered as a special topic..
• Elimination reactions are examined in an analogous manner. E2 and E1 mechanisms are established. Animations are provided. The Zaitsev rule is defined, and the anti-stereospecificity of E2 reactions illustrated by models.
• A summary of factors influencing substitution versus elimination is presented.

• Common and IUPAC nomenclature of alcohols is presented.
• An overview of the hydroxyl group and its influence is followed by discussion of specific reactions.
• Electrophilic substitution at oxygen leads to ethers, esters and sufonates
• Nucleophilic substitution of the hydroxyl group requires initial activation. Some of these methods are discussed. Proof of inversion of configuration during the substitution is presented. Other substitution methods are presented as an optional topic.
• Elimination of water (dehydration) produces alkenes. This is compared with the hydration of alkenes.
• Oxidation of primary & secondary alcohols to aldehydes and ketones by chromic acid and PCC is discussed, Other mild oxidation techniques are given as a special topic.
• Ether nomenclature is discussed.
• The preparation of ethers, especially by the Williamson procedure, is described.
• Ether cleavage is the most general reaction of ethers.
• A brief treatment of epoxide reactions is given.
• The chemistry of thiols and sulfides is available as a special topic.

• Electrophilic substitution is the most common reaction of benzene and its derivatives. Five different examples are given, and an animation illustrating bromine substitution is provided.
• The activating or deactivating influence of substituents is described and explained in terms of inductive and resonance effects.
• The directing influence of substituents (ortho/para versus meta) is discussed and interpreted in a similar fashion. Numerous examples are provided and illustrated by reaction diagrams.
• The interplay of substituent effects in disubstituted cases is described.
• Chemical transformation of certain substituent groups themselves is discussed Combinations of all these reactions in a multistep synthesis is examined by self-test problems.
• Nucleophilic substitution, elimination & addition reactions are described. . Additional information about benzynes is a special topic. Another advanced topic is the Birch reduction.
• Phenol chemistry is presented in a separate section.
• The chief subjects are phenol acidity, electrophilic ring substitution and oxidation to quinones.

 Amines

• A treatment of amine nomenclature includes some fundamental heterocyclic systems and a collection of naturally occurring amines.
• A review of formula analysis applied to nitrogen containing compounds is provided.
• Physical properties of amines is linked to hydrogen bonding. The wide range of amine basicities is discussed in terms of resonance and aromaticity. A consideration of the acidity of amines leads to a listing of important amine derived bases.
• Reactivity of amines begins with alkylation and acylation. Preparation of primary amines.
• Reaction with benzenesulfonyl chloride (Hinsberg test); Preparation of secondary and tertiary amines.
• Reaction of amines with nitrous acid is related to the amine class. Preparation of aryl diazonium salts and their subsequent reactions is a broad topic. Self-test problems are presented.
• Elimination reactions of amines are presented. The Hofmann rule is explained.
• Oxidation states of nitrogen are listed. The Cope elimination of amine oxides is shown. Pyrolytic cis eliminations is a special topic.
• The chemistry of phosphorous compounds is a special topic.

• The nomenclature of these carbonyl compounds is discussed. Some natural compounds are shown.
• A selection of methods for preparing aldehydes and ketones is presented.
• A discussion of properties includes a comparison of addition/elimination of water to C=O and C=C.
• Addition reactions are divided into reversible (water, alcohols, amines, HCN) and irreversible (metal hydrides and organometallics). Ylide reactions are a recommended option.
• Reduction by Wolff-Kishner, Clemmensen and thioacetals, and oxidation of aldehydes to carboxylic acids are shown. Dissolving metal and hydride transfer reductions are offered as special topics.
• Conjugate addition reactions are an optional special topic.
• Reactions at the a-carbon are introduced by isotopic exchange and bromination. pKa's for a-hydrogens of different classes of compounds are listed.
• Electrophilic substitution of enolate anions is illustrated. Additional information about enolate anions is an option, as is the Haloform reaction.
• The aldol reaction is introduced. And dehydration of aldol products is discussed.
• The challenge of effecting mixed aldols is examined. Advanced methods of conducting directed aldol reactions is an optional topic.
• Irreversible electrophilic substitution of enolate anions, and their ambident nature is discussed.
• Alternatives to enolate anions (e.g. enamines) are offered as a special topic.

• The IUPAC nomenclature of carboxylic acids and the names of natural compounds are covered.
• A listing of common carboxylic derivatives and their general names is given.
• Physical properties are listed and the acidity of the carboxyl group is exemplified and explained. Vinylagous acids are a special topic.
• Methods for preparing carboxylic acids are reviewed. The Arndt-Eistert reaction is a special topic.
• Reactions of carboxylic acids include: salt formation, substitution of the hydroxyl hydrogen, substitution of the hydroxyl group and reduction.
• The mechanism of Fischer esterification is displayed and discussed.
• Decarboxylation of b-ketoacids and the Hunsdiecker reaction are presented.

• Physical properties of these derivatives are compared with other functional classes.
• The nomenclature of carboxylic derivatives is summarized.
• Acyl group substitution, or transfer is presented as a major reaction class. Mechanisms are discussed. A comparison of carbonyl reactivity with IR stretching frequency is an advanced special topic.
• Reduction by metal hydride reagents, diborane and catalytic hydrogenation is presented.
• Reactions with organometallic reagents is discussed and summarized.
• Reactions at the a-carbon are analogous to aldehydes & ketones.
• The a-carbon acidities of various mono and diactivated compounds are compared.
• The Claisen condensation is shown, and compared with the aldol reaction.
• Mixed Claisen condensations are demonstrated.
• A comprehensive discussion of synthesis begins with a review of carbon-carbon bond formation.
• Modifications of aldol and Claisen condensation products as synthetic intermediates are shown.
• Examples of multistep synthesis beginning with a condensation or alkylation are presented.
• Vinylagous reactions, such as the Michael, are presented as an advanced topic.
• Some self-test problems are given. A more extensive treatment of synthesis design, including retrosynthetic analysis, is a special topic.