Title: Topic 1:Structure, Bonding and Hybridization in Organic Molecules
1Topic 1Structure, 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
2Topic 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
3Topic 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)
4Topic 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
5Topic 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
6Topic 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
7Topic 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
8Topic 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
9Topic 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
10Topic 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
11Topic 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
12Topic 7 Streochemistry contd.
- 7.3 Biochemical Roles of Enantiomers
- Stereoselective substrate binding
- Enzyme binding
- Iboprofen
- Thalidomide
- Morphine
- Levorphanol
- Dextrorphan
13Topic 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
14Topic 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
15Topic 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
16Topic 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
17Topic 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
18Topic 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
19Topic 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
20Topic 10 Conjugated ? Systems contd.
- 10.2 The Diels-Alder Reaction
- 42 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
21Topic 11 Benzene and Aromaticity
- Benzene and Aromatic Compounds
- Ball and stick and space-filling models
- Aromaticity
- Planar, cyclic
- Conjugated
- (4n2) pi electrons (Huckels Rule)
- Orbital Diagrams
- Bonding, antibonding orbitals, nodal planes, e
distribution, energy levels - Application of Huckels Rule to
- Monocyclic systems and polycyclic aromatic
systems - Annulenes
- Aromatic Heterocycles
- Furan, pyridine, indole (hybridization)
- Aromatic Ions
- Cyclopropenyl, cyclopentadienyl, tropylium
cations - Application of Huckels Rule to
- Non-aromatic systems, Anti-aromatic systems
- 10-Annulene
22Topic 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
23Topic 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
24Topic 13 Ethers
- Cyclic Polyethers
- Structures and models of cyclic polyethers
- Size exclusion-ion-chelation
- Selective ion binding
- Applications in industry
25Topic 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 - Crams rule
- Worked Examples
26Topic 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
27Topic 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
28Topic 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
29Topic 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
30Topic 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
31Topic 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
32Topic 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
33Topic 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
34Topic 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
35Topic 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
36Topic 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
37Topic 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
38Topic 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
39Topic 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
40Topic 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
41Topic 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
42Topic 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
43Topic 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
44Topic 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
45Topic 21Nucleic 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
46Topic 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
47Topic 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
48Topic 23 Special Topics
- Special Topic Host -Guest chemistry
- Carcerand-carceplex (irreversible)
- hemicarcerand-hemicarceplex (reversible)
49Topic 24 Self Tests
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