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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, secbutyl, 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 stereochemistryenantiomers, 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 • 10.1 – 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 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 Topic 16: Polymers • 16.1 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 Topic 19: Proteins • 19.1 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 Topic 19: Proteins contd. • 19.4 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 Topic 21: Nucleic Acids • 21.1 – – – – 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 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. • 21.3 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 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