1. Topic 1:Structure, Bonding and Hybridization in Organic Molecules 1.1Atomic Structure of CarbonStructure of Carbon –Orbital Shapes Atomic Orbitals s, p –Hybridization Formation of sp 3, sp 2, sp orbitals 1.2Bonding in Organic MoleculesBonding 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

2. Topic 2: Molecular Properties and Molecular Models –Molecular Modeling of Organic MoleculesMolecular Modeling of Organic Molecules Ball and stick model Space-filling model –Molecular Dynamics –Visualization Aids Molecular models –Comparison of 3D and 2D structures

3. Topic 3: Nature of Organic Compounds 3.1Functional Groups3.1Functional 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 3.2Alkyl Groups3.2Alkyl 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 (1 o ), Secondary (2 o ), Tertiary (3 o ), Quartenary (4 o )

4. Topic 4: Structure and Conformations of Alkanes and Cycloalkanes 4.1Conformations of Ethane4.1Conformations of Ethane –3D Visualization –Newman Projections - eclipsed, staggered conformations –Energy profile diagrams of  bond rotations 4.2Conformations of Butane4.2Conformations of Butane –Antiperiplanar conformation, Synperiplanar conformation, Gauche conformation –Rotational Barriers –Newman Projections – Energy profile diagrams of  bond rotations

5. Topic 4: Structure and Conformations of Alkanes and Cycloalkanes. 4.3Cycloalkane Structure and Conformations4.3Cycloalkane 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

6. Topic 4: Structure and Conformations of Alkanes and Cycloalkanes contd. 4.4Conformation of Cyclohexanes4.4Conformation 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 (1,3- diaxial interactions) –Calculation and comparison of  G for conformational changes

7. Topic 5: Reactions of Alkenes 5.1Reduction of Alkenes5.1Reduction 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

8. Topic 5: Reactions of Alkenes contd. 5.2Bromination of Alkenes5.2Bromination of Alkenes –Addition of Bromine in CCl 4 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

9. Topic 5: Reactions of Alkenes contd. 5.3Hydroxylation of Alkenes5.3Hydroxylation 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

10. Topic 6: Alkynes of Reactions Alkyne Hydration Acid catalyzed hydrolysis –H 2 SO 4, Hg 2+ 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

11. Topic 7: Streochemistry 7.1 Introduction to Stereochemistry7.1 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 7.2Multiple Stereocenters7.2Multiple 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

12. Topic 7: Streochemistry contd. 7.3Biochemical Roles of Enantiomers7.3Biochemical Roles of Enantiomers –Stereoselective substrate binding –Enzyme binding –Iboprofen –Thalidomide –Morphine –Levorphanol –Dextrorphan

13. Topic 8: Alkyl halides: Free radical reactions and Organometallic compounds 8.1Free Radical Halogenation8.1Free Radical Halogenation –Halogenation of Methane Initiation mechanism Propagation mechanism Termination mechanism –Arrow Notation –Chain Reactions –Worked examples

14. Topic 8: Alkyl halides: Free radical reactions and Organometallic compounds contd. 8.2Reactions of Organometallic Compounds8.2Reactions 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

15. Topic 9: Nucleophilic Substitution Reactions and Elimination Reactions, (S N 1, S N 2, E1, E2) 9.1The S N 2 Reaction9.1The S N 2 Reaction Kinetics and stereochemistry data Inversion of configuration –S N 2 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

16. Topic 9: Nucleophilic Substitution Reactions and Elimination Reactions, (S N 1, S N 2, E1, E2) contd. 9.2The S N 1 Reaction9.2The S N 1 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

17. Topic 9: Nucleophilic Substitution Reactions and Elimination Reactions, (S N 1, S N 2, E1, E2) contd. 9.3Steric Factors in Nucleophilic Substitutions9.3Steric Factors in Nucleophilic Substitutions –Influence of steric factors involving  -C on S N 1 vs S N 2 –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

18. Topic 9: Nucleophilic Substitution Reactions and Elimination Reactions, (S N 1, S N 2, E1, E2) contd. 9.4E2: Bimolecular Eliminations9.4E2: 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 9.5E1: Unimolecular Eliminations9.5E1: Unimolecular Eliminations –Elimination Reaction Mechanism –Protic solvents and solvent assistance to Ionization Stabilization of carbocations via solvation –Worked examples

19. Topic 10: Conjugated  Systems 10.1Conjugated  Systems10.1Conjugated  Systems –Localized and Delocalized  Systems –Orbital Diagrams 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

20. Topic 10: Conjugated  Systems contd. 10.2The Diels-Alder Reaction10.2The 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

21. 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

22. Topic 12: Electrophilic Aromatic Substitution Reactions 12.1Electrophilic Aromatic Substitution12.1Electrophilic 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

23. Topic 12: Electrophilic Aromatic Substitution Reactions contd. 12.2Substituent Effects in EAS12.2Substituent 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 poly- Substitutions 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

24. Topic 13: Ethers Cyclic Polyethers –Structures and models of cyclic polyethers –Size exclusion-ion-chelation –Selective ion binding –Applications in industry

25. 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, OH 2, ROH, RO - –Comparison of nitrogen nucleophiles, NH 3, NH 2 R, NH 2 - –Comparison of carbon nucleophiles RMgX, RLi, CN - –Hydrides LiAlH 4, NaBH 4 Asymmetric induction –Addition of cyanide - Cram’s rule Worked Examples

26. Topic 14: Reactions of Aldehydes and Ketones contd. 14.2Tautomerization14.2Tautomerization –Acid catalyzed tautomerization mechanism Enol formation Keto-enol tautomers –Enol tautomers in Phenols B-Diketones Thymines Imidazole

27. Topic 14: Reactions of Aldehydes and Ketones contd. 14. 3 Hemiacetal-Acetal Formation14. 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

28. Topic 14: Reactions of Aldehydes and Ketones contd. 14.4Aldol Reaction14.4Aldol 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

29. Topic 15: Carboxylic Acids and Derivatives 15.1Carboxylic Acids and Derivatives15.1Carboxylic 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

30. Topic 15: Carboxylic Acids and Derivatives contd. 15.2 Methanolysis of Acetyl Chloride15.2 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

31. Topic 16: Polymers 16.1Introduction to Polymers16.1Introduction 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

32. Topic 16: Polymers contd. 16.2 Survey of polymers16.2 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

33. 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 pK b of Alkylamines, ammonia, arylamines

34. 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

35. Topic 18: Carbohydrates contd. 18.2Disaccharides and Polysaccharides18.2Disaccharides 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

36. 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

37. Topic 18: Carbohydrates contd. 18.4 Anti-inflammatory Agents –Sialyl Lewis x 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 Lewis x

38. Topic 19: Proteins 19.1Amino Acids and the Peptide bond19.1Amino 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

39. Topic 19: Proteins contd. 19.2Beta pleated Sheet19.2Beta 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 19.3Alpha helix19.3Alpha helix 3D modeling of coiled backbone illustrating –Right handed helix –Side chain positions –H-bonding –Net dipole –Comparison of  -helix and 3 10 helix

40. Topic 19: Proteins contd. 19.4Protein Organization19.4Protein Organization –I o -IV o 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

41. Topic 20: Lipids 20.1Classification of Lipids20.1Classification 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 PGE 2 –Arachidonic acid to prostaglandin

42. 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

43. Topic 20: Lipids contd. 20.2Nutrition Labeling and Organic Compounds20.2Nutrition Labeling and Organic Compounds –Nutrition facts on Fat Fatty acids, triacylglycerides –Nutrition facts on Cholesterol –Nutrition facts on Carbohydrates Sugars Starch vs cellulose

44. Topic 21: Nucleic Acids 21.1 Structure of Heterocycles21.1 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

45. Topic 21:Nucleic Acids contd. 21.2 Components of DNA21.2 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

46. Topic 21: Nucleic Acids contd. 21.3 DNA Macrostructure21.3 DNA Macrostructure –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 Molecules21.4 Self-Replicating Synthetic Molecules –Mechanism of formation of complementary strand on template –Synthetic mutants

47. Topic 22: Electrocyclic Reactions Pericyclic ReactionsPericyclic 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

48. Topic 23: Special Topics -Special Topic: Host -Guest chemistry Carcerand-carceplex (irreversible) hemicarcerand-hemicarceplex (reversible)

49. Topic 24: Self Tests Self Test 1 Self Test 2