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Topic 1:Structure, Bonding and Hybridization in Organic Molecules • 1.1 Atomic Structure of Carbon – Orbital Shapes • Atomic Orbitals s, p – Hybridization • Formation of sp3, sp2, sp orbitals • 1.2 – – – – Bonding in Organic Molecules Bonding and antibonding orbitals Overlap of hybridized orbitals to form sigma() and pi() bonds Comparison of bonding in alkanes, alkenes and alkynes Bonding in ethane, ethylene, acetylene Topic 2: Molecular Properties and Molecular Models – Molecular Modeling of Organic Molecules • Ball and stick model • Space-filling model – Molecular Dynamics – Visualization Aids • Molecular models – Comparison of 3D and 2D structures Topic 3:Nature of Organic Compounds • 3.1 Functional Groups – C skeleton (C-C, C-H Framework) – Heteroatoms and Bonds• Alkenes, alkynes, haloalkanes, acyl halides, alcohols, ethers, aldehydes, ketones, carboxylic acids and carboxylic acid derivatives, amines and amides • 3.2 Alkyl Groups – Nomenclature: Common names and systematic IUPAC names – Alkyl Groups (R groups) • Methyl, ethyl, propyl, n-butyl, isopropyl, isobutyl, sec-butyl, tert-butyl, neopentyl – Classification of Alkyl Carbons • Primary (1o), Secondary (2o), Tertiary (3o), Quartenary (4o) Topic 4: Structure and Conformations of Alkanes and Cycloalkanes • 4.1 Conformations of Ethane – 3D Visualization – Newman Projections - eclipsed, staggered conformations – Energy profile diagrams of bond rotations • 4.2 Conformations of Butane – Antiperiplanar conformation, Synperiplanar conformation, Gauche conformation – Rotational Barriers – Newman Projections – Energy profile diagrams of bond rotations Topic 4: Structure and Conformations of Alkanes and Cycloalkanes. • 4.3 Cycloalkane Structure and Conformations – Cyclopropane • Angle strain • Ring strain – Cyclobutane • Puckered conformation, dynamics of rotations – Cyclopentane • Envelope conformation, dynamics of rotations – Cyclohexane • Chair conformation – Cycloheptane • Bicyclic alkanes, cis- and trans- decalin – Norbornane – Steroid Nuclues Topic 4: Structure and Conformations of Alkanes and Cycloalkanes contd. • 4.4 Conformation of Cyclohexanes – Chair Conformations • Axial substituents and Equatorial substituents • Newman projection • Gauche interactions – Boat Conformations • Flagpole, transannular interactions – Twist-boat Conformation • Dynamic conformer changes • Relief of torsional and flagpole strain – Comparison of energy of cyclohexane conformations – Monosubstituted cyclohexanes • Chair, half chair, boat • Ring flips • Comparison of steric effects of different substituents (1,3diaxial interactions) – Calculation and comparison of G for conformational changes Topic 5: Reactions of Alkenes • 5.1 Reduction of Alkenes – Heterogeneous Catalysis – Hydrogenation Mechanism – Stereochemistry of Addition • Stereospecific syn addition of hydrogen • Addition to prochiral faces to form enantiomers • Worked examples of syn additions Topic 5: Reactions of Alkenes contd. • 5.2 Bromination of Alkenes – Addition of Bromine in CCl4 to Bonds – Stereochemistry of Bromine Addition – Anti-Addition Mechanism – Bromonium ion formation – Arrow notation – Antiperiplanar conformation resulting from stereospecific anti addition – Determining resultant product stereochemistry – Regioselectivity (addition of competing nucleophiles and formation of regioisomers) – Steric and Electronic Factors Affecting Regioselectivity Topic 5: Reactions of Alkenes contd. • 5.3 Hydroxylation of Alkenes – Stereospecific Hydroxyl Additions – Syn-Hydroxylation Forming cis-Diols in Cyclic Systems – Syn-Addition Mechanism – Syn addition of hydroxyls via permanganate ion esters – Arrow notation – Synperiplanar conformation of product – Resultant product stereochemistry-enantiomers, meso etc. – Anti-Hydroxylation to form trans-Diols in Cyclic Systems • Epoxide ring opening Mechanism – Epoxidation by peroxides – Addition of nucleophiles to epoxides – Antiperiplanar conformation of product – Worked Examples Topic 6: Alkynes of Reactions • Alkyne Hydration • Acid catalyzed hydrolysis – H2SO4, Hg2+ • Hydroboration-oxidation – Disiamyl borohydride – Pi Orbital Structure of Alkynes – Regioselectivity of Electrophile Attack • H+ addition vs boron electrophile addition – Hydration and Enol formation mechanism • Hydroboration, peroxide oxidation, hydrolysis, tautomerization – Arrow Notations – Comparison of Regioselectivity of the Electrophiles – Worked Examples Topic 7: Streochemistry • 7.1 Introduction to Stereochemistry – Stereogenic Carbons/Stereocenters – Enantiomers • Non-superimposable mirror images • Chirality • Cahn-Ingold-Prelog R,S nomenclature for determination of absolute configuration – Fischer projections • 7.2 – – – – – Multiple Stereocenters Classification of isomers Diastereomers Enantiomers Calculation of maximum number of possible stereoisomers Stereochemistry in Cyclic Compounds • Cis and trans diastereomers, meso diastereomer • Alkene diastereomers • Stereogenic centers in taxol – Worked examples Topic 7: Streochemistry contd. • 7.3 – – – – – – – Biochemical Roles of Enantiomers Stereoselective substrate binding Enzyme binding Iboprofen Thalidomide Morphine Levorphanol Dextrorphan Topic 8: Alkyl halides: Free radical reactions and Organometallic compounds • 8.1 Free Radical Halogenation – Halogenation of Methane • Initiation mechanism • Propagation mechanism • Termination mechanism – Arrow Notation – Chain Reactions – Worked examples Topic 8: Alkyl halides: Free radical reactions and Organometallic compounds contd. • 8.2 Reactions of Organometallic Compounds – Reverse polarity on carbon in organometallic compounds – Organolithium reagents • Tight-ion pairs • Basicity and nucleophilicity of alkyl anions • Basic character • Nucleophilic ability of carbanions – Grignard Reagents • Nucleophilic addition mechanism • Formation of alcohols via Grignards • Arrow notations – Dialkyl Cuprates • Substitutions with alkyl halides – Worked Examples Topic 9: Nucleophilic Substitution Reactions and Elimination Reactions, (SN1, SN2, E1, E2) • 9.1 The SN2 Reaction • Kinetics and stereochemistry data • Inversion of configuration – SN2 Reaction Mechanism • Backside attack • Change in hybridization • Leaving groups • Change in relative configuration (R or S) • Arrow notation of concerted reactions – Reaction Profile Energy Diagram – Worked examples Topic 9: Nucleophilic Substitution Reactions and Elimination Reactions, (SN1, SN2, E1, E2) contd. • 9.2 – – – – – The SN1 Reaction Unimolecular nucleophilic substitution Solvolysis of alkyl halides Formation of carbocations Racemization Solvolysis Mechanism • Arrow notation • Hybridization changes • Formation of achiral carbocation intermediate • Pro-R face, pro-S face – Reaction profile energy diagram – Worked Examples Topic 9: Nucleophilic Substitution Reactions and Elimination Reactions, (SN1, SN2, E1, E2) contd. • 9.3 – – – – – Steric Factors in Nucleophilic Substitutions Influence of steric factors involving -C on SN1 vs SN2 Primary, secondary, and tertiary alkyl halides Factors promoting backside attack vs carbocation formation carbon branching and rotation of branched substituents Steric hindrance due to nucleophile – Worked examples Topic 9: Nucleophilic Substitution Reactions and Elimination Reactions, (SN1, SN2, E1, E2) contd. • 9.4 E2: Bimolecular Eliminations – – – – Formation of alkenes Rate expression Bases used for eliminations Stereoselective Elimination Mechanism • Trans vs cis alkene formation • Concerted reactions • Hybridization changes – Arrow notation – Newman projections illustrating stereoselectivity • 9.5 E1: Unimolecular Eliminations – Elimination Reaction Mechanism – Protic solvents and solvent assistance to • Ionization • Stabilization of carbocations via solvation – Worked examples Topic 10: Conjugated Systems Conjugated Systems – Localized and Delocalized Systems – Orbital Diagrams • 10.1 • Bonding, HOMO orbitals • Antibonding LUMO orbitals • Transitions * – Allyl Systems • • • • • • Cation, anion, radical allyl systems Molecular orbital diagrams Bonding orbitals Non-bonding orbitals 2 Antibonding orbitals Nodal planes and electron density distribution – Butadiene • Bonding and antibonding orbitals • Nodal planes and electron distribution • Coplanar s-cis, s-trans dienes – Octatetraene – Summary Energy Diagram of Conjugated systems – Absorption of electromagnetic radiation UV-Vis range Topic 10: Conjugated Systems contd. • 10.2 The Diels-Alder Reaction – [4+2] Cycloaddition • Rotation of s-cis to s-trans of diene – Diene-dieneophile interaction mechanism – HOMO-LUMO interactions – Hybridization changes • Overlapping of Frontier Orbitals • Effect of electron withdrawing groups and electron donating groups on Diels-Alder reaction • Stereochemistry of product • Endo vs exo orientation and secondary orbital interactions • Kinetic vs thermodynamic product control • Stereochemistry of products – Formation of enantiomers, diastereomers Topic 11: Benzene and Aromaticity • Benzene and Aromatic Compounds • Ball and stick and space-filling models – Aromaticity • Planar, cyclic • Conjugated • (4n+2) pi electrons (Huckel’s Rule) – Orbital Diagrams • Bonding, antibonding orbitals, nodal planes, e distribution, energy levels – Application of Huckel’s Rule to • Monocyclic systems and polycyclic aromatic systems – Annulenes – Aromatic Heterocycles • Furan, pyridine, indole (hybridization) – Aromatic Ions • Cyclopropenyl, cyclopentadienyl, tropylium cations – Application of Huckel’s Rule to • Non-aromatic systems, Anti-aromatic systems • [10]-Annulene Topic 12: Electrophilic Aromatic Substitution Reactions • 12.1 Electrophilic Aromatic Substitution • Electrophilic Aromatic Substitution Mechanism • • • • Electrophile attack Arenium ion - complex Resonance stabilization Removal of proton and regaining aromaticity – Reaction profile energy diagram – Examples of electrophiles Topic 12: Electrophilic Aromatic Substitution Reactions contd. • 12.2 Substituent Effects in EAS – Reactivity and regioselectivity • Reaction profile energy diagram cf. Rates of activators vs deactivators • Resonance in phenol • Resonance in benzaldehyde – Directing Effects of Substituents on di- and polySubstitutions • Hammond's postulate • Distribution of charges on substituted benzenes • Steric effects • bromination of toluene mechanism • Bromination of nitrobenzene • Relationship between relative reactivity and regioselectivity – Worked examples Topic 13: Ethers • Cyclic Polyethers – – – – Structures and models of cyclic polyethers Size exclusion-ion-chelation Selective ion binding Applications in industry Topic 14: Reactions of Aldehydes and Ketones • 14.1 Aldehydes and Ketones – Structure of carbonyl group – Orbital diagrams • Polarity • Nucleophile-electrophile sites of interactions – Nomenclature examples – Dynamics of axial and equatorial addition to cyclohexanone – Nucleophile addition Mechanism – Tetrahedral intermediates – Comparison of oxygen nucleophiles, OH2, ROH, RO– Comparison of nitrogen nucleophiles, NH3, NH2R, NH2– Comparison of carbon nucleophiles RMgX, RLi, CN– Hydrides LiAlH4, NaBH4 • Asymmetric induction – Addition of cyanide - Cram’s rule • Worked Examples Topic 14: Reactions of Aldehydes and Ketones contd. • 14.2 Tautomerization – Acid catalyzed tautomerization mechanism • Enol formation • Keto-enol tautomers – Enol tautomers in • • • • Phenols B-Diketones Thymines Imidazole Topic 14: Reactions of Aldehydes and Ketones contd. • 14.3 Hemiacetal-Acetal Formation • Hemiacetal formation mechanism • • • • Protonation of carbonyl, resonance forms Nucleophile attack Tetrahedral intermediate Deprotonation - protonation – Acetal formation mechanism • Dehydration • Formation of methoxy cations – Acetals and Hemiacetals Hydrolysis – Reversibility of acetal reaction mechanisms – Acetal to aldehyde Topic 14: Reactions of Aldehydes and Ketones contd. • 14.4 Aldol Reaction – Enolate formation mechanism – Resonance stabilized enolate ion formation • Removal of -C-H proton • Condensation Reactions – Arrow notation – Stereochemistry of aldol reactions • Pro-R Face • Pro-S Face Topic 15: Carboxylic Acids and Derivatives • 15.1 Carboxylic Acids and Derivatives – Acidity of carboxylic acids – Modeling of acyl groups • • • • Acyl chloride, Cyclic and acyclic acid anhydride Esters and Lactones Amides -primary/secondary/tertiary acyclic and cyclic (lactams) • Nitriles – Relative reactivity of derivatives • Conversion of more reactive to less reactive derivative – Nucleophilic acyl substitution mechanism – Examples of Nucleophilic Acyl Substitutions • Base hydrolysis • Addition of Grignards • Amide hydrolysis Topic 15: Carboxylic Acids and Derivatives contd. • 15.2 Methanolysis of Acetyl Chloride – Nucleophilic acyl substitution mechanism – Influence of leaving group – Addition of nucleophile to Carbonyl – Tetrahedral intermediate formation – Deprotonation – Internal nucleophilic displacement of leaving group • Arrow notation of reactions • 16.1 Topic 16: Polymers Introduction to Polymers – Monomers – Polymers • Backbone • Side chains – Tacticity • Stereochemistry of substituents • Relative and absolute configuration – Syndiotactic (R,S alternating) – Isotactic (all R or all S) – Atactic (R and S random) • Illustration of tacticity with – Polyethylene polymers (no tacticity) – Polypropylene polymers – Recycling Topic 16: Polymers contd. • 16.2 Survey of polymers – Addition Polymers • Addition to pi bonds – PVC, Teflon, polystyrene, polymethacrylate • Macroscopic properties – Crystalline (HDPE) – Amorphous – Random conformation • 3-D space-filling modeling of PVC, Teflon, styrene, polymethacrylate • Uses of polymers – Condensation Polymers • • • • • Co-polymers Formation of condensation polymers PET (polyethyleneterephthalate) Nylon (6,6) Worked examples Topic 17: Amines • Amines: Structure and Properties – Primary, secondary, tertiary, and quaternary amines – Models illustrating • Hybridization of N in – Alkylamines – Enamines – Arylamines – Model of diazonium salt – Models of N-heterocyclic systems • Pyrrolidine, pyridine, indole, imidazole • Alkaloid example - cocaine – Inversion at N and hybridization changes – Basicity of amines • Protonation mechanism • Comparison of pKb of • Alkylamines, ammonia, arylamines Topic 18: Carbohydrates • 18.1 Monosaccharides – Aldoses – Stereochemistry of 3C, 4C, 5C and 6C aldoses – Relative configurations • • • • D, L-Stereoisomers Fischer projections Enantiomers Diastereomers – Epimers – Internal cyclizations • Arrow notations • Haworth projections • Anomeric centers – Relative stereochemistry of anomers • Furanose and pyranose hemiacetals • Interconversion/mutarotation • 3D Models of carbohydrates Topic 18: Carbohydrates contd. • 18.2 Disaccharides and Polysaccharides – Disaccharides • Glycosidic linkages • Reducing and non-reducing disaccharides • Glycosidic linkages and 3 D structures of – Cellobiose – Sucrose – Maltose – Polysaccharides • 3 D Models illustrating assembly and H-bonding in – Linear polymers » cellulose – Helical/curved polymers » Amylose, details of 12-mer-helix – Branched polymers » Amylopectin – Shape - function relationship Topic 18: Carbohydrates contd. • 18.3 Applications of Carbohydrate Polymers – Cyclodextrin Roxatanes – Formation of polymeric nanotubes • 3D Modeling of – -cyclodextrin – -cyclodextrin • 3D Modeling of Roxatanes – Polyethylenoxy bisamine – Barbell shaped molecules with stoppers • Cyclodextrin roxatanes – Formation of molecular necklace – Covalent linking to form nanotubes/pores Topic 18: Carbohydrates contd. • 18.4 Anti-inflammatory Agents – Sialyl Lewisx • 3D modeling of the structure • Cell adhesion and anti-inflammatory response – Cytokines – Leukocytes-selectin adhesions • Repair of injury by leukocytes • Inflammation blocking-potential use of Sialyl Lewisx • 19.1 Topic 19: Proteins Amino Acids and the Peptide bond • Classification of amino acids with regard to the side chains – Models of polar, non-polar, acidic, basic and neutral amino acids • Stereochemistry, L-amino acids – Zwitterions – Peptide Bond • Details of peptide bond geometry – Restricted rotation, plane of peptide bonds • C-terminus and N-terminus of polypeptide • Modeling of conformation – Peptide bond conformations, Side chain conformations – Protein organization • Secondary structures (alpha helix and beta pleated) • Tertiary structures Topic 19: Proteins contd. • 19.2 Beta pleated Sheet • -strand ex. Polyvaline • 2D and 3D modeling – Details of linear and stacked chain » Top view, side view and end view • H-bonding fit • Parallel and anti-parallel orientation • 3D Modeling of silk polymer • 19.3 Alpha helix • 3D modeling of coiled backbone illustrating – – – – – Right handed helix Side chain positions H-bonding Net dipole Comparison of -helix and 310 helix • 19.4 – – – – Topic 19: Proteins contd. Protein Organization Io-IVo structures Peptide linkages Covalent crosslinking Supersecondary structures • Folding motifs • Topological diagrams and 2D and 3D models of – -turn- hairpin turns and plane of peptide bonds – -turn-, -turn-, other turns, -meander etc. – Tertiary structures • Globular proteins – Bacteriorodopsin – Quaternary structures • Non-covalent aggregates of dimers, tetramers, hexamer Topic 20: Lipids • 20.1 Classification of Lipids – Steroids: Models illustrating • Rings A-D, 5, 5 • Cortisone • Lanosterol formation from squalene – Epoxide formation, cascading – Terpenes – Isoprene units – Head-tail linkages • Limonene, vitamin A – Prostaglandins – Models of PGE2 – Arachidonic acid to prostaglandin Topic 20: Lipids contd. • Fats and Oils • Triacylglycerols • Hydrolysis – Saturated fatty acids – Unsaturated fatty acids • Phospholipids • Chemistry of polar heads, nonpolar chains – Cephalins – Lecithins – Phosphatidyl serine – Phosphatidyl choline » Neurotransmitters, emulsifier, LDL – Stacking of phospholipids in membrane bilayer – Worked examples Topic 20: Lipids contd. • 20.2 Nutrition Labeling and Organic Compounds – Nutrition facts on Fat • Fatty acids, triacylglycerides – Nutrition facts on Cholesterol – Nutrition facts on Carbohydrates • Sugars • Starch vs cellulose • 21.1 – – – – Topic 21: Nucleic Acids Structure of Heterocycles Oxygen heterocycles Sulfur heterocycles Nitrogen heterocycles Aromatic nitrogen heterocycles • Purines, pyrimidines – Macrocyclic nitrogen heterocycles • Phophines • Drugs for aids – AZT, ddI • Stimulants • Neurotransmitters • Antibiotics – Penicillins, keflex pulvule, cefotetan, toradol • Antinausea agents – Scopalamine • Antiviral agents – Ribavirin, acylclovir Topic 21:Nucleic Acids contd. • 21.2 Components of DNA – Bases • Purines, pyrimidines • H-bonding-donor, acceptor sites • Linkage to sugar – Sugars • 2-deoxy ribose – Endo conformation in B-DNA – Nucleosides • Anti-syn conformation for purines and pyrimidines – Nucleotides: 3D modeling of • Mononucleotides • Dinucleotides 5’-3’ phosphodiester linkage – Base pairing • Details of conformations of base pairs – A-T, G-C pairing – Major groove, minor groove – H-donor-acceptor sites in grooves – Stacking of nucleotides Topic 21: Nucleic Acids contd. DNA Macrostructure • 21.3 – 3D solid and wire modeling illustrating • • • • • • • Pitch (turn) Diameter Backbone Bases Inclination Propeller twist Major and minor Grooves – DNA binding agents: 3D Modeling of • Antibiotic Lexitropsin binding in minor groove • 21.4 Self-Replicating Synthetic Molecules – Mechanism of formation of complementary strand on template – Synthetic mutants Topic 22: Electrocyclic Reactions • Pericyclic Reactions – Concerted mechanism – Cyclic transition state – Interconversion of bonds – Electrocyclic Reactions – MO diagrams – Thermal reactions (HOMO) – Photochemical reactions (LUMO) – Thermal and photochemical 4n and [4n+ 2] electron systems ring closure – – – – MO diagram of butadiene hexatriene Thermal photochemical ring closures Stereochemistry of ring closure Conrototory vs disrototory – Woodward-Hoffman Rules – Cycloadditions- Go to Int. Mod. 10 for Diels Alder Reaction Topic 23: Special Topics - Special Topic: Host -Guest chemistry • Carcerand-carceplex (irreversible) • hemicarcerand-hemicarceplex (reversible) Topic 24: Self Tests • Self Test 1 • Self Test 2