Chemistry 3720 Spring 2012 Class Notes



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Lecture Slides from Chapter 12 with Audio Commentary

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Jan 18, 20: Lecture 1 + Intro: Aromatic Substitution; Chapter 12

An introduction to the Chemistry 3720 class, overview of grading scale, exam dates, resources, etc. Beginning of Carey-Giuliano Chapter 12; review of benzene structure and introduction to Electrophilic Aromatic Substitution (EAS). Details of mechanisms of nitration and sulfonation.

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Jan 23: Lecture 2: Aromatic Substitution; Chapter 12

Bromination and chlorination mechanisms; Lewis acid catalysis and complex formation. Discussion of Friedel-Crafts reactions, limited use of alkylation chemistry and skeletal rearrangements. F-C acylation route to aryl ketones, a useful alternative to alkylation.

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Jan 25: Lecture 3: Aromatic Substitution; Chapter 12

Further detail on Friedel-Crafts alkylation and acylation reactions. Inter- and intramolecular examples and manipulation of products by oxidation or reduction. Activating and deactivating groups and their role in rates of subsequent EAS reactions compared to benzene.

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Jan 27: Lecture 4: Aromatic Substitution; Chapter 12

Directing effects in EAS; discussion of ortho/meta/para outcomes based on relative intermediate carbocation stability. Conversion of products by oxidation/reduction and use in multistep synthesis; design of polysubstituted derivatives.

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Jan 30: Lecture 5: Aromaticity; Chapter 12

Synthesis of polysubstituted benzene derivatives; relative directing effects of substituents in terms of sterics and electronics. Design of synthesis and timing of steps to maximize chances of desired outcome. Participation of electron-poor systems in SNAr reactions.

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Lecture Slides from Chapter 13 with Audio Commentary (2 parts)

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Feb 1: Lecture 6: Spectroscopy; Chapter 13

Introduction to spectroscopic techniques used to analyze the structures of organic molecules: Infra-Red, Nuclear Magnetic Resonance, Ultra-Violet/Visible, and Mass Spectrometry. Use of IR to probe the functional groups within a compound; description of spectra.

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Feb 3: Lecture 7: Spectroscopy; Chapter 13

Definition of magnetically active nuclei of interest and how the modern NMR spectrometer works. Standardization of data using ppm, geography of the spectrum and definitions of terms. Introduction to chemical shift and spectra of simple compounds; deshielding effects.

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Feb 6: Lecture 8: Spectroscopy; Chapter 13

Introduction to spin-spin splitting and signal shape; n+1 rule for first order spectra. Common splitting patterns and alkyl groups; coupling constants (J values) and their use in defining relationships. Integration of signals and effect of splitting on signal intensity.

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Feb 8: Lecture 9: Spectroscopy; Chapter 13

Constrained alkene systmes and proton-proton coupling constants; different couplings leading to signals such as doublet of doublets. Problems with exchangeable protons such as OH groups in alcohols; broad signals often observed. Introduction to 13C NMR scale and spectra.

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Feb 10: Lecture 10: Spectroscopy; Chapter 13

Continuation of 13C NMR spectroscopy, chemical shift and signal intensity. Use in determining local and/or global symmetry in molecules. C-H coupling in spectra and presentation of data. Overview of UV and MS spectra and use of unsaturation number in structure determination.


Lecture Slides from Chapter 14 with Audio Commentary

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Feb 13: Lecture 11: Organometallics; Chapter 14

Introduction to the use of metals in Organic Chemistry for the formation of organometallic reagents. The switching of polarization compared to the precursor alkyl halides, and the reaction of basic organometallics with protic solvents. Application of organometallics as nucleophiles in nucleophilic addition reactions.

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Feb 15: Lecture 12: Organometallics; Chapter 14

Application of organometallic reagents in the synthesis of alcohols through nucleophilic addition to aldehydes and ketones. Design of alcohol products using the concepts of retrosynthetic analysis. Use of deuterium oxide as a way to label compounds by quenching organolithium and organomagnesium reagents.

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Feb 20: Lecture 13: Organometallics; Chapter 14

Reactions of organometallics with esters; two equivalents needed to make the process a useful tertiary alcohol synthesis. Use of this chemistry in retrosynthetic design. Dicussion of sequential mechanisms; nucleophilic acyl substitution and then nuclophilic addition. Introduction to metal hydrides (Ch. 15).


Lecture Slides from Chapter 15 with Audio Commentary

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Feb 22: Lecture 14: Synthesis and Reactions of Alcohols; Chapter 15

Mechanism of reduction of aldehydes and ketones with NaBH4 and LiAlH4; differences in reactivities and choice of solvent. Reduction of carboxylic acids and esters with LiAlH4 and possibility of selectively reducing aldehydes and ketones using NaBH4. Opening of epoxides with Grignard reagents.

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Feb 24: Lecture 15: Synthesis and Reactions of Alcohols; Chapter 15

Review of alcohol conversions to alkenes, halides, tosylates, etc. Discussion of the Williamson ether synthesis and its use in making non-symmetrical ethers. Acid-catalyzed ether synthesis and mechanisms of inter- and intramolecular variants. Introduction to Fischer esterification and mechanism.

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Feb 27: Lecture 16: Reactions of Alcohols; Chapter 15

Esterification of alcohols with acid chlorides and acid anhydrides; use of pyridine as solvent and requirement for only equimolar amounts of alcohol and acylating reagent. Introduction to oxidation at carbon; relationships between alcohols and aldhydes/ketones/carboxylic acids. Use of chromic acid in alcohol oxidation.


Lecture Slides from Chapter 16 with Audio Commentary

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Feb 29: Lecture 17: Reactions of Alcohols; Chapter 15-16

Mechanism of chromic acid oxidation of primary and secondary alcohols. Importance of hydrate in oxidation process and the use of anhydrous PDC and PCC to prevent this and result in aldehyde isolation. Miscellaneous oxidations such as the OsO4/NaIO4 sequence for alkene oxidation, which is analogous to ozonolysis. Basic thiol chemistry and introduction to ethers (Ch. 16).

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March 2: Lecture 18: Synthesis and Reactions of Ethers; Chapter 16

Properties of ethers and uses in synthesis (solvents, crown ethers). Synthesis through addition to alkenes, acid-catalyzed substitution, base-induced Williamson method. Formation of epoxides with peracids and from bromohydrins. Reactions of ethers with HX, opening of epoxides under basic or acidic conditions. Description and synthesis of sulfides. Introduction to acetal chemistry (Ch. 17).


Lecture Slides from Chapter 17 with Audio Commentary

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March 5: Lecture 19: Aldehydes and Ketones; Chapter 17

Structure and nomenclature of aldehydes and ketones and examples in medicine and biology. Discussion of hydrate formation and the factors involved in rates of reaction and equilibrium populations. Comparison of E.D.G. and E.W.G. effects on equilibrium position, as well as steric environment in different systems. Introduction to base- and acid-catalyzed hydration processes.

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March 7: Lecture 20: Aldehydes and Ketones; Chapter 17

Base- and acid-catalyzed formation of acetals; mechanisms and conditions applied. Uses of acetals as carbonyl protecting groups - base/nucleophile-stable but acid-labile. Examples of syntheses that fail unless protection of aldehyde or ketone is applied. Conditions for hydrolysis of acetals; mechanism for regenaration of carbonyl group.

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March 19: Lecture 21: Aldehydes and Ketones; Chapter 17

Reaction of aldehydes with cyanide in acid to produce cyanohydrins; mechanism and catalysis by cyanide. Classification of amines as primary, secondary, or tertiary. Reactions of aldehydes and ketones with primary amines to give imines; mechanism and loss of water overall. Reactions with secondary amines to form enamines through similar pathway. Introduction to the Wittig reaction.

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March 21: Lecture 22: Aldehydes and Ketones; Chapter 17

Mechanism of the Wittig olefination reaction. Use of the process in synthesis and limitations; application in retrosynthetic analysis of alkenes. Review of oxidation-reduction chemistry studied thus far; interconversion of alchols and carbonyl functional groups. Baeyer-Villager oxidation of ketones to esters; mechanism, examples, and regiochemical/stereochemical issues.


Lecture Slides from Chapter 18 with Audio Commentary

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March 23: Lecture 23: Carboxylic Acids; Chapter 18

Structure and reactivity of carboxylic acids; stabilization through delocalization. Acid strength based on local environment; EWG lowering pKa and stabilizing the conjugate base. Synthesis of carboxylic acids through oxidation of alcohols and aldehydes; use of organometallics and CO2; introduction and hydrolysis of nitriles. Reactions of carboxylic acids with bases, reducing agents, and alcohols.


Lecture Slides from Chapter 19 with Audio Commentary

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March 26: Lecture 24: Carboxylic Acid Derivatives; Chapter 19

Decarboxylation from malonic acid and beta-ketoester derivatives; enolization to carbonyl form (Ch. 18). Classification of carboxylic acid derivatives; acyl halides, anhydrides, esters, amides, etc., and survey of the nomenclature used for each family. Discussion of relative stability/reactivity of each kind of derivative based on delocalization and leaving group ability. Overview of nucleophilic acyl substitution reactions.

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March 28: Lecture 25: Carboxylic Acid Derivatives; Chapter 19

Reactions of acyl chlorides to form esters, anhydrides, and carboxylic acids. Examples of anhydrides and methods for producing symmetrical and unsymmetrical products. Physical properties of esters and examples of structures in nature such as odour components. Hydrolysis of esters under acidic and basic conditions; difference in mechanisms at different pH and discussiuon of irreversible step in saponification process.

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March 30: Lecture 26: Carboxylic Acid Derivatives; Chapter 19

Structures and properties of amides; hydrogen-bonding capability and examples in polypeptides and materials such as kevlar. Synthesis of amides through NAS reactions, also hydrolysis under strongly acidic or basic conditions. Dehydration of amides to form nitriles, complementary to displacememnt on alkyl halides with cycanide anion. Addition of organometallics to nitriles to produce imines, then hydrolysis to give ketones.


Lecture Slides from Chapter 20 with Audio Commentary

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April 4: Lecture 28: Enols and Enolates; Chapter 20

Definitions of the alpha proton and of enols and enolates. Relative acid strengths of aldehydes, ketones, and esters; factors involved in stability of each conjugate base. Use of different bases in deprotonation of aldehydes and ketones; reversible versus irreversible and conseqeunces in terms of the species present in solution. Kinetic versus thermodynamic deprotonations in unsymmetrical ketones using large base and irreversible deprotonation or small base and reversible conditions, respectively. Introduction to the aldol reaction.

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April 6: Lecture 29: Enols and Enolates; Chapter 20

The aldol condensation to produce alpha-beta unsaturated systems; elimination of water under basic conditions; examples of inter- and intramolecular processes. Crossed (mixed) aldol reactions using a non-enolizable substrate. Deprotonation of esters to produce ester enolates; choice of base being important; hydroxide leads to saponification whereas the correct alkoxide leads to the Claisen condensation to form beta-ketoesters.

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April 9: Lecture 30: Enols and Enolates; Chapter 20

The Dieckmann cyclization (intramolecular variant of the Claisen condensation); mechanism and examples of. Crossed (mixed) Claisen reactions using one non-enolizable substrate. Acylation of ketones with diethylcarbonate to give beta-keto esters. Alkylation of enolates at the alpha C; kinetic versus thermodynamic control.

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April 11: Lecture 31: Enols and Enolates; Chapter 20

Multistep synthesis using ethyl acetoacetate; the Acetoacteic Ester synthesis. Deprotonation between two EWG to produce a stabilized anion that is then alylated; repeat sequence to yield alpha,alpha-disubstituted beta-keto ester. Saponification and quenching to produce the beta-ketocarboxylic acid; subsequent thermolysis to induce decarboxylation. Discussion of enol-ketone tautomerism that reveals the final product.

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April 13: Lecture 32: Enols and Enolates; Chapter 20

The Malonic Ester synthesis; sequential deprotonations and alkylations followed by saponification and decarboxylation; synthesis of alpha,alpha-disubstituted carboxylic acids. Enols and their equilibrium concentrations; examples of where the enol is favoured over the keto form. Base- and acid-catalyzed enolizations; application of enol nucleophile in the alpha-bromination of ketones.

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April 16: Lecture 33: Enols and Enolates; Chapter 20

Alpha-halogenation of ketones in detail; mechanism and enol presence. Iodoform reaction of methyl ketones; iterative deprotonation/halogenation steps and subsequent saponification-like nucleophilic substitution. Hell-Volhard-Zelinsky process to make alpha-bromo carboxylic acids; need for PBr3 reagent. Introduction to alpha,beta-unsaturated systems.

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April 18: Lecture 34: Enols and Enolates; Chapter 20

Alpha,beta-unsaturated systems; 1,2- versus 1,4-addition outcomes. Reaction of Grignard nucleophiles to attack the carbonyl carbon in an irreversible process in which the ketone is lost. Addition of cyanide nucleophile with formation of the thermodynamically favoured 1,4-product in which the ketone is retained. Michael and Robinson systems to create cycles. Addition of cuprates to enones.


Lecture Slides from Chapter 21 with Audio Commentary

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April 2: Lecture 27: Amines; Chapter 21

Structures and properties of amines; hydrogen-bonding capability, boiling points, and basicity. Formation of amines by alkylation of ammonia (and limitations). Review of efficient syntheses of amines; azide reduction, amide reduction, reductive amination, etc. Use of the Gabriel amine synthesis for the efficient production of primary amines; detailed mechanism and limitations.

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April 23: Lecture 35: Special Topics; Chapters 22-29

Introduction to macromolecular chemistry in Biology and Polymer Science. Definitions of monomer, dimer, trimer, oligomer, polymer and examples of simple building blocks in Chemistry and Biology. Discussion of chemical linkers and their "robustness" and ability to be permanent or temporaray. Examples of addition mechanisms to form polymers; examples of condensation polymerization.

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April 25: Lecture 36: Special Topics; Chapters 22-29

Continuation of polyester synthesis and properties; uses as fabrics and plastics. Discussion of polyamides as condensation polymers; Nylon 6 and Nylon 6,6 as examples. Introduction to carbohydrates and biological monomers and polymers; D-glucose structure and reactivity. Formation of glycosidic linkages to simple alcohols; definitions of alpha nad beta isomers; examples of simple disaccharides.

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April 27: Lecture 37: Special Topics; Chapters 22-29

Monosaccharide monomers and occurrence in polysaccharides; GlcNAc in chitin, glucose in starch and cellulose. Comparison of laboratory glycoside synthesis/hydrolysis versus enzymatic processes; many isomers possible, only one is usually produced through enzymatic pathways. Amino acids as biological monomers and incorporation into biological heteropolymers such proteins. Challenges in laboratory synthesis of peptides.

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April 30: Lecture 38: Special Topics; Chapters 22-29

Nucleic acid monomers; structures of base and sugar component and linkages through furanose hydroxyls. Discussion of hydron bonding and base pairing, as well drugs that prevent chain elongation. Introduction to important classes of biomolecules based on their relative polarities. Analysis of Claisen-like biological synthesis of fatty acids using Acetyl Coenzyme A. Introduction to terpene chemistry and biosynthesis.

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May 2: Lecture 39: Special Topics; Chapters 22-29

Cholesterol biosynthesis; transition from organic mechanisms to biochemical and biologcal pathways. Detail on each step and molecules and enzymes involved. Phosphate and pyrophosphate as leaving groups, decarboxylation processes, aldol and elimination reactions. Enzymes as biological catalysts and targets for intervention with pharmaceuticals such as statins. Cylization cascade involving epoxide in squalene oxide.

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May 4: Lecture 40: Special Topics; Chapters 22-29

Polar carbohydrates as biomolecular recognition units. Proteins associated with carbohydrate binding, especially enzymes such as glycosyl hydrolases which hydrolyze acetal linkages. The targetting of such enzymes with inhibitors such as iminosugars and C-glycosides. Introduction to glycolysis and the interconversion of aldoses and ketoses through enolization processes.