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Topic 1:Structure, Bonding and Hybridization in Organic Molecules

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

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Topic 1:Structure, Bonding and Hybridization in Organic Molecules

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  1. 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

  2. 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

  3. 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)

  4. 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

  5. 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

  6. 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 (1,3-diaxial interactions) • Calculation and comparison of G for conformational changes

  7. 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

  8. 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 andformation of regioisomers) • Steric and Electronic Factors Affecting Regioselectivity

  9. 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

  10. 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

  11. Topic 7: Streochemistry • 7.1 Introduction to Stereochemistry • Stereogenic Carbons/Stereocenters • Enantiomers • Non-superimposablemirror 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

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

  13. Topic 8: Alkyl halides: Free radical reactions and Organometallic compounds • 8.1 Free 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. • 8.2 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

  15. 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

  16. Topic 9: Nucleophilic Substitution Reactions and Elimination Reactions, (SN1, SN2, E1, E2) contd. • 9.2The 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

  17. Topic 9: Nucleophilic Substitution Reactions and Elimination Reactions, (SN1, SN2, E1, E2) contd. • 9.3Steric 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

  18. 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

  19. Topic 10: Conjugated  Systems • 10.1 Conjugated  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 Y2 • 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. • 10.2 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

  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 • 12.1 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

  23. 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 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, 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  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 pKb 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. • 18.2 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

  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 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

  38. 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

  39. 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

  40. 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

  41. 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

  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. • 20.2 Nutrition Labeling and Organic Compounds • Nutrition facts on Fat • Fatty acids, triacylglycerides • Nutrition facts on Cholesterol • Nutrition facts on Carbohydrates • Sugars • Starch vs cellulose

  44. 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

  45. 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

  46. 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

  47. 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

  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

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