Web LinksThese web links, organized by chapter, provide more information about topics covered in the text and will help in your study of organic chemistry.Chapter 1What constitutes Organic Chemistry? Brief overview of the main concerns of organic chemistry. Nature of the Ionic Bond Characteristics of ionic bonds. The Nature of the Co-Valent Bond Single, double, triple bonds and covalent bond polarity. What are Lewis dot notation and how is it used? How to read and write Lewis structures. Questions On Chemical Bonding Questions (with answers) on chemical bonding. Exceptions To The Octet Rule Two ways in which some atoms violate the Octet Rule. Atomic Orbital Approach To Bonding An introduction to hybridization. The Octet Rule A humorous song about the Octet Rule. Molecular Geometry and Bonding Many online quizes on the Octet Rule, bonding and Lewis structures. Top of page Chapter 2Hydrocarbons Illustrated overview of hydrocarbons. Alkanes Naming, physical and chemical properties of alkanes. Alkenes and Alkynes Naming, addition and hydrogenation reactions of alkenes. Aromatic Hydrocarbons Benzene as a representitive aromatic hydrocarbon. Alcohols and Ethers, Organic Derivatives of Water Nomenclature and major reactions of alcohols and ethers. Organic Chemistry II Adobe Acrobat files describing carboxylic acids, amines, phenols, and carbanions. Amines Nomenclature, chemical and physical properties of these derivatives of ammonia. Alkyl Halides Nucleophilic substitution reactions of alkyl halides. Designer Drugs Amine derivatives with psychological effects. Ketones and Aldehydes Quiz Self-assessment quiz on aldhehyde and ketone reactions. Synthesis of Aldehydes and Ketones Synthetic reactions of aldehydes and ketones, with links to information on specific catalysts. Top of page Chapter 3Acid And Base pH Tutorial All aspects of pH, with topical and cumulative quizzes. Acid-Base FAQ's Answers to frequently asked questions regarding pH. Carboxylic Acids and Phenols Slide show on structure, nomenclature, reactions and properties of carboxylic acids and phenols. Acids and Derivatives with Chime! Structures and typical reactions of carboxylic acids (requires Chime plugin). Carboxylic Acids Thorough review of nomenclature, properties and reactions of carboxylic acids. Buffers for pH Control Web-based form for designing buffer solutions. Acid-Base Equilibria Tutorial Web-based form that demonstrates the effects of pH, temperature and volume on the acid-base equilibrium of bromoacetic acid. Top of page Chapter 4The Alkanes Structures of several alkanes (requires Chime). The Alkanes - Self Study Questions Self-evaluation questions on alkanes. Synthesis of Alkanes Synthetic reactions of alkanes, with links to information on specific catalysts. Reactions of Alkanes Reactions of alkanes, with links to information on specific catalysts. ELECTRONIC FLASH CARDS Online flash card format for memorizing reactions of many classes of organic reactions. A few rings to look at Some representitive cyclic alkanes, with links to molecular coordinate files. Cycloalkane Conformations Interactive Chime visualizations of basic and substituted cycloalkane conformations. Top of page Chapter 5Recent Literature Examples of Stereospecific Syntheses A few examples of reactions where the stereochemistry of the production is maintained in the absence of racemization (requires Chime). Stereochemistry Online Exercises on the determination of chirality in organic molecules (requires Chime). Chirality ShockWave program on stereochemistry. Chirality Tutorial A Chime-based tutorial on stereochemistry. Basic Stereochemistry A series of brief descriptions on stereochemistry: isomers, diastereomers and prochirality. Stereochemistry Resources Links to publications, research groups and images related to stereochemistry. Top of page Chapter 6Organic Reaction Animations: E2 QuickTime animations of E2 reactions using ball-and-stick and spacefilling representations. Organic Reaction Animations: Friedel-Crafts QuickTime animations of Friedel-Crafts reactions using ball-and-stick and spacefilling representations. Nucleophilic Substitution and Elimination Reaction Chart A chart of reaction type based on nucleophile and type of alkyl halide. Nucleophilic Substitution Dry Laboratory A self-assessment exercise on the steric and inductive effects in nucleophilic substition reactions using Chime. Carbocation Stability Brief discussion of carbocations using images generated by a quantum mechanics visualization program. Review of Reaction Mechanisms Synopsis of SN1, SN2, E1 and E2 reaction mechanisms. Sizzling Organic Chemistry Dramas! Short, humorous scripts for enacting four major reaction mechanisms. SN1 and SN2 ShockWave program on SN1 and SN2 reactions. Top of page Chapter 7Practice Questions for Chapter 5 Self-assessment questions on compound stability, reaction mechanisms and polymers. Practice Questions for Chapter 6 Self-assessment questions on alkyne reactions and mechanisms. Reactions of Alkynes Reactions of alkynes, with links to information on specific catalysts. Synthesis of Alkynes Synthetic reactions of alkynes, with links to information on specific catalysts. Alkyne Reactions and Syntheses Quiz Self-assessment quiz on the material covered in the previous two links. Alkenes and Alkynes II- Addition Reactions Detailed outline of a large number of reactions. The Alkyne Family Illustrated overview of alkyne nomenclature, structure, reactions and synthesis. Alkenes and Alkynes Synopsis of nomenclature, stereoisomerism and reactions of alkenes and alkynes. Top of page Chapter 8Simulated Reactions Animations of several different types of simulated reactions. Krebs Cycle II The anti-Markovnikov addition of water across the double bond in one of the reactions in the Krebs cycle. Alkenes and Alkynes II- Addition Reactions Additions, hydrogenations, and oxidations of alkenes. Unsymmetrical adding reagents to Asymmetrical Alkenes:Markovnikov Rule Overview of the selective hydrogenation of asymmetric alkenes. Reactions of alkenes Slide show on the reactions of alkenes. Additions to Alkenes: Regiochemistry A discussion of Markovnikov's rule, with self-test questions. Fischer Carbenes Structure, synthesis and reactions of Fischer carbene ligands. Top of page Chapter 9Proton NMR Tutorial ShockWave-based tutorial on proton NMR spectra. Nuclear Magnetic Resonance (NMR) Slide show describing NMR technology. Carbon-13 NMR Tutorial ShockWave-based tutorial on 13C NMR spectra. The World-Wide Web NMR SPECTROMETER A web-controlled NMR spectrometer. The Basics of NMR An online textbook on NMR techniques. Enhanced NMR Periodic Table Click on an element in this periodic table and see its atomic and isotopic propterties as well as its ionic states. Public database of NMR spectra Downloadable file of NMR spectra with embedded structures. Online Information on Spectroscopic Databases Links to databases containing machine-readable spectroscopic data. NMR Data of Known Compounds Images of NMR spectra of 14 compounds. High Performance Liquid Chromatography (HPLC): A Users Guide The history, theory and applications of HPLC. Gas Chromatography Resource Links, resources and research groups interested in gas chromatography. Introductory Theory Quiz Self-test on the theory behind chromatography. Analytical Chemistry Basics Gravimetric analysis, titration, electrochemistry, spectroscopy and separations. Organic Structure Elucidation Workbook 54 practice problems on structural determination from spectral data. Top of page Chapter 10Study Guide-Alkyl halides Outline on substitution reactions of alkyl halides, including radical addition reactions. Free Radical Addition Reaction mechanism of addition by a free radical. Rate Constants for Reactions of Peroxyl Radicals in Fluid Solution Searchable database of rate constants for reactions of alkylperoxyl and substituted alkylperoxyl radicals with inorganic and organic compounds in aqueous and non-aqueous fluid solutions. Direct Free-Radical Substitutions on Allyl and Vinyl Halides Using Alkyl Halides/Hexabutylditin Brief research report on experiments with tin-mediated substitutions by alkyl radicals. Synthesis of Alkyl Halides Synthesis of alkyl halides, with links to information on specific catalysts. Ozone Depletion Nontechnical information on the depletion of Earth's ozone layer by chlorofluorocarbons. Basic chemistry of ozone depletion Illustrated synopsis of the reactions responsible for depletion of the ozone layer. Top of page Chapter 11How to Tackle Organic Syntheses Grignard, enolate and Wittig reactions, plus an overview of organic reactions in general. Synthesis of Ethers and Epoxides Synthetic reactions that generate ethers and epoxides. Reactions of Ethers and Epoxides SN1 and SN2 reactions involving ethers and epoxides. Quiz for Ethers and Epoxides Self-test on syntheses and reactions of ethers and epoxides. Reactions of Alcohols Substitution and elimination reactions involving alcohols. Synthesis of Alcohols and 1,2-Diols Synthetic reactions that generate primary, secondary and tertiary alcohols. Alcohol Reactions and Syntheses Quiz Self-test on syntheses and reactions of alcohols. Top of page Chapter 12Organic Redox Reactions How to balance redox reactions involving organic compounds. Aldehydes & Ketones. Part III Reactions of aldehydes and ketones that yield primary and secondary alcohols. Reactions Involving Alcohols Acid catalyzed nucleophilic substitutions, conversion of alcohols to mesylates and tosylates in sN reactions, conversion of alcohols to alkyl halides and oxidations. Aldehydes & Ketones, Oxidation & Reduction Oxidation and reduction reactions involving the carbonyl group of aldehydes and ketones. Organometallic Chemistry Slide show on organometallic compounds and their reactions. Organometallic Mechanisms Online lecture on oxidative-addition reactions, including orthometallation. Davies-Green-Mingos Rules Rules for predicting the direction of nucleophilic attack at cationic metal complexes. Davies-Green-Mingos Rules An online quiz on the Davies-Green-Mingos Rules. Electron Counting A tutorial and quiz on organometallic bonding prediction. Top of page Chapter 13Garlic in the Medicine Cabinet Why garlic has such a characteristic smell. Allylic Substitutions with Acyclic Substrates Review of recent progress on Palladium-catalyzed asymmetric syntheses. Allylic systems - introduction to resonance Slide show on resonance stabilization of allyl radicals. Allyl Ligands Structure, synthesis and reactions of allyl ligands. Direct Free-Radical Substitutions on Allyl and Vinyl Halides Using Alkyl Halides/Hexabutylditin Short research report on tin-mediated substitution reactions. Synthesis of Alkyl Halides Synthetic reactions producing alkyl halides. Reactions of Alkyl Halides Substitution, elimination and reduction reactions of alkyl halides. Quiz on Aromatic Compounds Self-test on reactions of aromatic compounds. Gallery of Quantum Chemistry and Electronic Structure Studies Images and MPEG movies of Diels-Alder reactions. Buckminsterfullerenes: Diels-Alder and Fullerenation Reactions The synthesis of fullerenes via fullerenation of aromatic hydrocarbons and Diels-Alder reactions. Top of page Chapter 14Kekulé Brief profile of the chemist that first proposed the correct structure of benzene. Benzene Overview of benzene's structure. Bromination of Benzene QuickTime animation of a benzene halogenation reaction. Polycyclic Aromatic Hydrocarbons and Cancer The carcinogenicity of aromatic compounds. Benzene and Aromatic Compounds Resonance in aromatic compounds. Aromatic Hydrocarbons Slide show on aromaticity. Fullerene Links Links to researchers, patents, structures and images of fullerenes. Simple Fullerene (Buckyball) Synthesis Writeup of a fullerene synthesis performed by two college students. Phenylalanine Micrograph of the aromatic amino acid phenylalanine. Tryptophan Micrograph of the aromatic amino acid tryptophan. Top of page Chapter 15Electrophilic Aromatic Substitution ShockWave-based slide show on electrophilic aromatic substitution. Electrophilic Aromatic Substitution Slide show on acylation, alkylation, sulfonation, nitration and halogenation reactions. Electrophilic Aromatic Substitution Reactions Acylation, alkylation, sulfonation, nitration and halogenation reactions. Reactions of Aromatic Compounds Acylation, alkylation, sulfonation, nitration and halogenation reactions. Friedel-Crafts Alkylation of Benzene and Its Derivatives Electrophilic substitution via a carbocation intermediate. Friedel-Crafts Acylation of Benzene and Its Derivatives Electrophilic substitution via an acylium intermediate. Electrophilic Aromatic Sulfonation of Benzene Sulfonation of benzene in the presence of SO3 and H2SO4. Electrophilic Aromatic Nitration Of Benzene Nitration of benzene and its derivatives using HNO3 and H2SO4. Electrophilic Aromatic Halogenation Replacement of a proton by a halogen atom on benzene or one of its derivatives. Questions dealing with electrophilic aromatic substitution Study questions with answers on electrophilic aromatic substitution. Practice Questions on Electrophilic Aromatic Substition Self-test on electrophilic aromatic substitution reactions. Top of page Chapter 16Reactions of Ketones and Aldehydes Oxidations, reductions, substitutions and addition reactions involving aldehydes and ketones. Synthesis of Aldehydes and Ketones Synthetic reactions producing aldehydes and ketones. Ketones and Aldehydes Quiz Self-assessment quiz on the syntheses and reactions of aldehydes and ketones. Aldehydes and Ketones Nomenclature, structure and properties of aldehydes and ketones. Aldehyde and Ketone Reactions Several reaction mechanisms and intermediates in aldehyde and ketone reactions. Aldehydes and Ketones Slide show overview of aldehydes and ketones. Aldehydes and Ketones ShockWave-based slide show on aldehydes and ketones. Question 1 Self-test on aldehyde and ketone precursors. Question 2 Self-test on aldehyde and ketone syntheses. Addition Reactions of Aldehydes and Ketones Reversible and irreversible addition reactions of aldehydes and ketones. Lignin The formation of a molecule responsible for the strength of plants and trees. Wittig Reaction Illustrated overview of the Wittig Reaction. Top of page Chapter 17Aldol Condensation Self-test on enolate donors and carbonyl acceptors. Acidity of a-hydrogens Description of a crucial factor in aldol condensations. Type of Reaction How to determine if a conjugated ketone can be synthesized via an aldol condensation. Aldol Cleavage An important reaction in glycolysis. The Problem Introduction to an attempt to the enolisation of pyrrolidin-3-one at C2 rather than the more common C4 site. Aldol Type Reactions of the Pyrrolidinone Fluoride ion- and Lewis acid mediated aldol reactions of pyrrolidin-3-one. Acetone Enolate Resonance Structures The mechanism of an aldol condensation of acetone. Carbonyl Alpha-Substitution Reactions Slide show on enolate reactions of carbonyl groups. Synthesis of Enolates and Enamines Synthetic reactions forming enolates and enamines. Top of page Chapter 18Carboxylic Acid Chloride Reactions Addition/reduction and addition/elimination reactions involving carboxylic acid chlorides. Synthesis of Acid Chlorides One synthetic reaction for producing an acid chloride. Quiz for Carboxylic Acid Chlorides Self-test on the synthesis and reactions of acid chlorides. Organic Acids (Carboxylic Acids) Overview of nomenclature, properties and acidity of carboxylic acids. Carboxylic Acids Reductions, esterifications and decarboxylation reactions of carboxylic acids. Carboxylic Acid Derivatives Acid halides, anhydrides, esters and amides. Carboxylic Acid Derivatives Polymerization and other reactions of anhydrides, esters and amides. Derivatives of Carboxylic Acids Slide show on nomenclature, properties and reactions of organic acid derivatives. Top of page Chapter 19Using Condensation Reactions for Synthesis Condenstation reactions that add carbon-carbon bonds without affecting other reactive sites. The Claisen Condensation The Claisen and Diekmann condensation reactions, and a biological example of a condensation. Knoevenagel Condensation Diagram of a Knoevenagel condensation, with references. Addition and Substitution by Carbon Nucleophiles Slide show describing reactions that form new carbon-carbon bonds. Reactions of Enolates Several different reactions involving enolate ions. Claisen Condensation QuickTime animation of a carbon-carbon bond formation reaction. Enolate Anions* A description of enolate ions and aldol condensations. Synthesis of Enolates and Enamines Synthetic reactions that create enolates and enamines. Quiz on Enolates and their Reactions Self-assessment quiz on syntheses and reactions of enolates and enamines. Top of page Chapter 20Amines ShockWave-based slide show on the basicity and inversion of amines. Reactions of Amines Reactions where amines act as Bronsted bases, nucleophiles or reducing agents. Syntheses of Amines Synthetic reactions producing primary, secondary and tertiary amines. Quiz for Amine Reactions and Syntheses Self-assessment quiz on syntheses and reactions of amines. Amines Slide show describing nomenclature, properties, preparation and reactions of amines. Heterocyclic Amines in Cooked Meats The relationship between cooked meat, heterocyclic amines and cancer. Sulfanilamide (Vagitrol) A micrograph of sulfanilamide crystals. Purine and Pyrimidine Metabolism A review and quiz on purine and pyrimidine biosynthesis and catabolism. Molecular Models from OUC Chime-viewable molecular models of biologically important amines. Serotonin A brief desription of serotonin, an important amine neurotransmitter. Top of page Chapter 21Aromatic Substitution Reactions Nucleophilic addition and substitution reactions. Reactions of Aromatic Compounds Outline of substitution and addition reactions, as well as substituent effects. Quiz on Aromatic Compounds Self-quiz on aromatic compound reactions. Phenols Reactions of aromatic alcohols. Nomenclature of Monosubstituted Benzene Derivatives The naming of benzene derivatives with a single substitution. Claisen rearrangement Chime-based animation of a Claisen rearrangement. Claisen rearrangement (traditional) Diagram of a tandem Claisen rearrangement. Solar Powered Molecular Machines A research project that uses quinones and other biological macromolecules to generate a proton gradient powered by light. Alcohols, Phenols, and Thiols Nomenclature, acidity and basicity, and reactions of phenols. Phenols, Acidity, Ethers Reactivity of phenols, alcohols ethers Top of page Chapter 22Cellulose Brief overview of the most abundant organic molecule in nature. Lignin The formation of a molecule responsible for the strength of plants and trees. Carbohydrates Structural overview of the major classes of carbohydrates. Carbohydrates Slide show on classification, nomenclature, polymers and reactions of carbohydrates. Reactions of Carbohydrates Isomerization, oxidation, reduction and polymerization reactions of carbohydrates. Complex Carbohydrates Chime-based descriptions and images of maltose, cellobiose, sucrose and lactose. Carbohydrates Concise overview of projections, conformations, and reactions of sugars. Structural Determination of Polysaccharides Several laboratory protocols for determining the structure of unknown polysaccharides. Carbohydrates Brief but richly illustrated synopis of carbohydrate structures and reactions. HERMANN EMIL FISCHER A short biography of Hermann Fischer, who was awarded the 1902 Nobel Prize in chemistry for his work on sugar and purine syntheses. Top of page Chapter 23Fatty Acid Tutorial Comprehensive tutorial on fatty acid nomenclature, structure, metabolism, and transport. Lipid Practice Problems A short list of questions, with answers, on lipids. Notes for Biosynthesis of Terpenoids from Mevalonic Acids in Germinating Pea Seeds Background information on a laboratory exercise for studying terpene biosynthesis. Regulation of Gene Expression in Eukaryotes: Steroid Hormones Hyperlinked outline of steroid hormone control of eukaryotic gene expression. Model of Gene Regulation by Steroid Hormone Simple animation of steroid hormone action after entering a target cell. Steroid Production and Drugs Outline of some steroid compounds that are used as drugs. Regulation of Steroid Synthesis in Ovarian Follicles Overview of the mammalian estrous cycle. Structure of Steroid Receptor Complexes A current model of steroid receptor structure. The Prostaglandin Collection Micrographs of prostaglandin crystals. Phospholipids Brief desription of phospholipid structure. Lipid-Quiz Review Self-quiz on lipids. Top of page Chapter 24Amino Acid Anatomy A series of pages using animations to illustrate the structure of amino acids and polypeptides. The Chemistry of Amino Acids Links to software, publications, research groups and databases of amino acids. Amino Acid Viewer Chime-based viewer of all 20 amino acids, including textual descriptions. Amino Acid Identification Quiz Self-assessment of amino acid names, three-letter abbreviations and one-letter codes. Amino Acids, Peptides, and Proteins Acid-base properties, peptide and disulfide bonds, and protein structure. Introduction To Amino Acids Short introduction to amino acid structure, stereochemistry and polymers. The Amino Acid Collection Micrographs of all the amino acids as crystals. Amino Acid Information General information, suggested substitutions, and chemical, structural and genetic properties. Enzymes Images, including interactive 3D models, of several enzymes. Note: to view the 3D models you will need the appropriate helper applications. ExPASy - ENZYZME top page A database of enzyme nomenclature. WMU Biology Dept.:Bios 150 Enzymes Lab Introduction to enzymes in general, with specific information on catechol oxidase. Interactive Biochemistry Enzyme tutorial covering kinetics, amino acid titration curves, and reversible inhibition (requires Java and Chime plugin). Yale's metabolic database A list-based metabolic database. Enzyme Biochemistry Chemical energetics, enzymatic mechanisms, kinetics, and regulation. Top of page Chapter 25Translation Translating mRNA into proteins, with an emphasis on prokaryotes. Web Warrior's Protein Sequencing Page Links to information about protein structure, sequencing, translation and gene regulation. Codon Usage Database The frequency of codon use in each organism from the GenBank sequence database is searchable through this World Wide Web site. Online Macromolecular Museum Interactive images of biologically important macromolecules, organized by function and arranged like rooms in a museum (requires Chime plugin). Swiss-PDB Viewer A program for comparing the three-dimensional structure of several proteins at once, view electron density maps, and generating ray-traced model images. Microbiology -- Nucleic Acids in Microbial Cells Replication and transcription in prokaryotes. IMB Jena Image Library of Biological Molecules Links to information on amino acids and nucleic acids. Determination of secondary structure, Watson and Crick's paper on DNA structure, and three-dimensional models of macromolecules. Biology Animation Library Standalone or ShockWave animations of Polymerase Chain Reaction and other biotechnology techniques. |