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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
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–
–
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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
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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
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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
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–
–
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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
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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
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•
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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
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Phenols
B-Diketones
Thymines
Imidazole
Topic 14: Reactions of Aldehydes and Ketones contd.
• 14.3 Hemiacetal-Acetal Formation
• Hemiacetal formation mechanism
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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
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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
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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
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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
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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
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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
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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
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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