SECTION 1 – STRUCTURAL, BONDING, AND MOLECULAR PROPERTIES OF
ORGANIC MOLECULES
1-1 -- Organic Chemistry: The Study of Compounds of Carbon
Naturally Occurring Compounds
Synthetic Compounds
1-1 -- A Review of Lewis Structures
Octet Rule
Formal Charges
1-3 -- Three-Dimensional Geometry of a Molecule (VSEPR Theory)
1-4 -- Bond Dipoles
Molecular Dipole Moments
1-5 -- Electronic Structure and Orbitals
Atomic Orbitals as Wave Functions
p-Orbitals
Nodal Planes
1-6 -- Bonding and Antibonding Molecular Orbitals (MO’s)
Why Does H2 Form?
MO Diagrams for CH4 (methane) and C2H4 (ethylene)
π-Bond Construction
MO Diagram for Acetylene, C2H2
1-10 – Resonance Structures
Generating Resonance Structures
Sigma Bonds (σ-bonds) and Pi Bonds (π-bonds)
1-13 -- Rules for Determining the Most Important Resonance Structures
1-15 -- Hybridization Effects on Resonance Structures
1-15 -- Acids and Bases
Bronsted Acids and Bronsted Bases
Two Things that Increase the Acidity of “HA”
Acid-Base Equilibria
Lewis Acids and Lewis Bases
1-19 -- Skeletal Structures of Carbon Compounds
Homogeneous Mixtures
Pure Substances
Compounds and Elements
SECTION 2 – THE NATURE OF ORGANIC COMPOUNDS: ALKANES AND
CYCLOALKANES
2-1 -- Classification of Functional Groups
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Alkanes
Alkenes
Alkynes
Alcohols
Ketones
Esters
2-2 -- Hydrocarbons
Aliphatic Hydrocarbons (alkanes, alkenes, and alkynes)
Aromatic Hydrocarbons (benzene)
2-2 -- Alkanes (Unbranched, Branched, and Cyclic Alkanes)
Homologous Series
Constitutional (“Structural”) Isomers
2-4 -- Types of Carbon Atoms
Primary Carbons (1°)
Secondary Carbons (2°)
Tertiary Carbons (3°)
Quaternary Carbons (4°)
2-5 -- Various Types of Alkyl Groups (Branches, or Substituents)
2-7 -- Systematic Nomenclature of Alkanes (IUPAC)
Four Rules for Naming Alkanes (Rules 1-4)
How to Find the Parent Hydrocarbon (“Parent Chain,” or “Main Chain”)
How to Number the Atoms in the Parent Chain
How to Identify and Number the Branches (“Substituents”)
How to Write the IUPAC Name of the Compound
2-11 -- Naming Complex Branches in Organic Compounds
2-12 -- Common Names (“non-IUPAC”) for Some Simple Alkyl Branches
2-13 -- Examples of Alkane Nomenclature
2-15 -- Nomenclature of Alkyl Halides (R-X)
2-15 -- Disubstituted Cycloalkanes
Stereoisomerism
Cis/Trans Isomers
2-16 -- Properties of Alkanes (5 Key Points)
Nonpolar (“Hydrophobic”) Properties of Alkanes
Boiling Point Trends
The Effects of Branching
Melting Point Trends
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Combustion of Alkanes (Calorimetry and Product Analysis)
SECTION 3 – STEREOCHEMISTRY OF ALKANES AND CYCLOALKANES: 3-D
STRUCTURE OF MOLECULES
3-1 -- Stereochemistry
3-1 -- Conformation of Alkanes
Rotations Around Sigma (σ) Bonds
Conformational Isomers
Conformers of Ethane (Staggered vs. Eclipsed)
3-2 -- Newman Projections
Dihedral Angles (θ)
Staggered vs. Eclipsed
Energy Diagrams for Corresponding Newman Projections
Newman Projections for Butane - Gauche Conformers and Anti Conformers
Steric Interactions Between Substituents
Preferred Combinations of n-Alkanes (all-Anti)
3-4 -- Stability of Alkanes
Enthalpies (ΔH), Heats of Combustion (ΔHcomb) and Heats of Formation (ΔHf)
Branched Alkanes (Relative b.p.’s, m.p.’s, and ΔHf values
3-5 – Cycloalkane Stability
Cyclopropane, Cyclobutane, and Cyclopentane
Angle Strain (Planarity vs. Non-planarity)
3-7 -- Three Different Sources of Strain in Cycloalkanes
Angle Strain, Steric Strain, and Torsional Strain
3-8 -- Detailed Look at the Stereochemistry of Cyclohexane
Chair Conformations
Axial H’s and Equatorial H’s
The Newman Projection of Cyclohexane
Ring-Flip Between Chair Conformations
Monosubstituted Cyclohexanes
1,3-Diaxial Interactions
Disubstituted Cyclohexanes (cis vs. trans)
3-11 -- A Closer Look at the Cyclohexane Ring-Flip
The “Twist-Boat” Intermediate
3-12 -- Bicyclic Compounds
Bicyclo[l.m.n]alkanes
Bridge Carbons and General Structure of Bicyclic Compounds
3-13 -- Steroid Skeletal Structures
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Always Trans
Chair Conformations for Steroid Molecules
SECTION 4 – THE STUDY OF ORGANIC REACTIONS: AN OVERVIEW
4-1 -- Types of Organic Reactions
Addition Reactions (A + B C)
Elimination Reactions (A B + C)
Substitution Reactions (A + B C + D)
Rearrangement Reactions (A B)
4-2 -- Reaction Mechanisms
Use of “Arrow-Pushing”
Heterolytic Bond Breaking and Heterogenic Bond Forming
Homolytic Bond Breaking and Homogenic Bond Forming
4-4 -- Polar Reactions and How They Occur
Electron-Rich (δ-) Sites of a Molecule
Electron-Poor (δ+) Sites of a Molecule
Nucleophiles and Electrophiles
Mechanisms for Polar Reactions
4-6 -- Radical Reactions and How They Occur
Free Radical Reactions
Mechanisms for Radical Reactions (Chain Reactions)
Initiation, Propagation, and Termination Steps
4-8 -- Thermodynamics of Organic Reactions
Equilibrium Expressions
Standard Free-Energy Changes (ΔG°)
Bond Dissociation Energies (BDE)
Table of BDE Values
4-10 -- Kinetics of Organic Reactions
Energy Diagrams and Transition States
Activation Energies (Ea), Reaction Rates, and Rate Laws
Multi-Step Reactions and Their Mechanisms
Reaction Intermediates
The Rate-Limiting Step (“Rate-Determining Step”)
First-Order Reactions vs. Second-Order Reactions (More Rate Laws)
SECTION 5 – STRUCTURE AND REACTIVITY OF ALKENES
5-1 -- Alkenes (“Olefins”)
Strength of a Double Bond (d.b) Relative to a Single Bond (s.b)
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5-1 -- Stereoisomerism of Alkenes (Cis/Trans)
5-1 -- Nomenclature of Alkenes
6 Rules for Naming Alkenes
Numbering the Principal Chain (Main Chain)
Identifying Locator #’s for Double Bonds
Endings / Suffixes (-ene, -diene, -triene, and –tetraene)
5-3 -- Naming Branched Alkenes
Alkenyl Substituents (Alkenes as Branches)
5-4 -- Naming Alkenes that Exhibit Stereoisomerism
E-Configurations and Z-Configurations (E/Z Stereochemistry)
Priority System within Nomenclature (E/Z Stereochemistry)
5-7 -- Relative Stabilities of Alkenes
Trans-Alkenes vs. Cis-Alkenes
Cyclic Alkenes
Alkyl Group Substitution (Branches) Stabilize Alkenes
5-8 -- Electrophilic Addition Reactions
Electrophilic Addition of HX (X = -Cl, -Br, -I)
Regiospecific Reactions
5-9 -- Markovnikov's Rule
Carbocation Stability
Hyperconjugaton and Electron Delocalization
Resonance Picture of Carbocations
5-11 -- The Hammond Postulate
5-12 -- Rearrangement of Carbocations
1,2-Hydride Shifts (:H-)
1,2-Alkyl Shifts (:R-)
5-13 -- Degree of Unsaturation
Calculating the Degree of Unsaturation
General Formula for Degree of Unsaturation
SECTION 6 – REACTIONS AND SYNTHESIS OF ALKENES
6-1 -- Addition of Halogens (X2)
Stereochemistry (Anti-Addition Observed)
Bromonium Ion Intermediate
Nucleophilic Solvent (H2O) vs. Inert Solvent (CCl4)
6-2 -- Halohydrin Formation
Use of Hypobromous Acid (HO-Br)
Anti-Addition of –Br and -OH
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6-3 -- Hydration Reactions
Conversion of Alkenes to Alcohols
Markovnikov Regiochemistry
Acid-Catalyzation of Hydration Reactions
The Principle of Microscopic Reversibility
6-5 -- Oxymercuration Reaction
Markovnikov Addition of –H and -OH
Use of NaBH4 as a Source of Hydride (:H-)
No Carbocation Rearrangements Observed
Hydride Shift
6-6 -- Hydroboration Reaction
Borane, BH3
Replacing Borane’s –H’s with Alkyl Groups (Substitution)
Mechanism for Hydroboration is “Concerted”
Reaction of BH3 with the Solvent Tetrahydrofuran (THF)
Steric Effects Control the Regiochemistry of the Observed Products
Syn-Addition (“Cis”-like)
6-9 -- Non-Markovnikov Addition of HBr
Does Not Work with the Reagents HCl or HI
Free-Radical Chain Mechanism
Initiation and Propagation Steps of the Mechanism
3° Radical vs. 1° Radical Intermediates (Stability)
Radical Stabilities
Polymer Production (Teflon, Polystyrene, Polyvinylchloride [PVC], and Plexiglass)
6-11 -- Catalytic Hydrogenation Reaction
Syn-Addition of H2 Across a Double Bond
6-11 -- Hydroxylation Reaction
Conversion of an Alkene to a Diol
6-12 -- Oxidative Cleavage Reactions
The Ozonolysis Reaction
Permanganate Reactions (MnO4-)
6-12 -- Carbene Additions Across a Double Bond
Their Use in Producing 3-Membered Rings
How Carbenes are Generated
6-13 -- The Simmons-Smith Reaction
Carbenoids
Zn(Cu) = “Zn-Cu” Couple
6-14 -- Periodic Acid Cleavage
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Cleavage of Diols to Produce 2 Carbonyl Compounds
SECTION 7 – ALKYNES
7-1 -- Definition, Bond Length, and BDE of Alkynes
7-1 -- Alkyne Nomenclature
“-yne” Ending
Alkenynes – Compounds Having Both Double Bonds and Triple Bonds
Alkynl Substituents (Branches)
7-2 -- Stabilities of Alkynes
Alkyl Groups (-R) Stabilize Triple Bonds
Terminal Alkynes vs. Internal Alkynes
Cycloalkynes
7-3 -- Hydration of Alkynes
Markovnikov Addition of H2O
Tautomerization
Use of Hg2+ as a Catalyst
7-5 -- Addition of HX Across the Triple Bond
Markovnikov Regiochemistry
The –H and –X Add Trans
Two Consecutive Markovnikov Additions of HX are Observed
7-5 -- Addition of X2 Across the Triple Bond
X2 = Cl2 or Br2
Mixtures of Products (Cis and Trans)
7-6 -- Hydroboration
Non-Markovnikov Addition of H2O
Internal Alkynes vs. Terminal Alkynes
Internal Alkynes and Increased Steric Hindrance
Terminal Alkynes and Use of Disiamyl Borane
Tautomerization is Observed
7-7 -- Addition of H2 Across a Triple Bond – 2 Ways
Catalytic Hydrogenation
Use of the “Lindlar Catalyst”
Syn-Addition Gives Cis Product (Catalytic Hydrogenation)
Reduction of Alkynes with Li (or Na) in NH3(l)
Anti-Addition Gives Trans Product (Reduction Reaction)
7-8 -- Alkylation of Terminal Alkynes
The “Acetylide Ion” as a Nucleophile
pKa of Alkynes
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Use of Sodamide (NaNH2)
7-10 -- Oxidative Cleavage of Alkynes
Formation of 2 Carboxylic Acids
Use of KMnO4 and H3O+
7-10 -- Synthesis of Organic Compounds
“Working Backwards” When Given a Final Product to Synthesize
7-11 -- Retrosynthetic Analysis
SECTION 8 – STEREOCHEMISTRY – A DETAILED LOOK
8-1 -- Definitions
Chiral, Achiral, Enantiomers, and Stereogenic Centers
Interior Mirror Planes
8-2 -- Enantiomers
Interactions of Enantiomers with Other Reactants (ex. Acylose)
Rotation of Plane-Polarized Light
Angle of Rotation
Dextrorotatory (D) or (+) vs. Levorotatory (L) or (-)
Absolute Configurations “R” and “S”
Racemic Mixtures and Racemates
8-4 -- Specifying Absolute Configurations
How to Determine “R” and “S” Enantiomers
Cyclic Permutations
8-5 -- Compounds with Multiple Stereocenters
Diastereomers
Meso Compounds and Planes of Symmetry
8-6 -- Cyclic Compounds
8-7 -- Isomer Types – A Summary
8-8 -- Fischer Projections
8-9 -- Manipulating Fischer Projections
Allowed Operations
180° Rotation (Allowed)
Cyclic Permutations of 3 Substituents (Allowed)
Forbidden Operations
Swapping only 2 Substituents (Forbidden)
90° Rotation in the Plane (Forbidden)
8-10 -- Organic Reactions – Stereochemical Considerations
Achiral Reactants
Diastereomers
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Optically Active (Chiral) Reactants
8-15 -- Conformational Enantiomers
Chair Conformations and Enantiomeric Cyclohexanes
Racemates of Substituted Cyclohexane Products
SECTION 9 – ALKYL HALIDES (R-X)
9-1 -- Preparation of Alkyl Halides from Alkanes
Chlorination Reaction (Cl2) - Unselective
Bromination Reaction (Br2) – Much More Selective
9-1 -- Why is Bromination Easier to Control than Chlorination?
Radical Stabilization
Thermochemistry of Bromination and Chlorination Reactions
Analysis of Transition States
9-4 -- Allylic Hydrogens
Resonance-Stabilization of the Allylic Radical
Allylic Bromination and the Use of NBR
Reactants that Produce 2 Types of Allylic Radicals
9-6 -- Benzylic Hydrogens
Low Bond Dissociation Energy (BDE)
Most Favorable Resonance Structure Preserves the Aromatic Ring
Benzyl Radicals
9-7 -- Preparation of Alkyl Halides from Alcohols
Via the Addition of HX
Via the Use of Thionyl Chloride (SOCl2) in Pyridine Solvent
Via the Use of Phosphorus Tribromide (PBr3)
9-8 -- Organometallic Compounds
Carbon-Metal Bonds (Organometallics)
Carbanions
Grignard Reagents
Organolithium Reagents (the Alkyllithium Reagent)
Organocopper Reagents (the Lithium Dialkyl Copper Reagent)
9-10 -- Various Ways to Form New C-C Bonds
Formation of New C-C Single Bonds (σ-bonds)
SECTION 10 – SUBSTITUTION REACTIONS (SN1, SN2) AND
ELIMINATION REACTIONS (E1, E2)
10-1 -- Overview of Nucleophilic Substitutions and Eliminations
SN2 Reaction
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SN1 Reaction
E2 Reaction
E1 Reaction
10-1 -- The SN2 Reaction
Bimolecular, Nucleophilic, Substitution
Stereochemistry
“Back-side Displacement” and Inversion of Absolute Configuration
Effect of Alkyl Halide Structure (1°, 2°, 3°)
Branching at the Beta-Carbon (β-Carbon)
Nucleophilicity and its Dependence on the Solvent
Steric Bulk Considerations
Leaving Groups (l.g.’s)
The Tosylate Leaving Group (-OTs, or p-toluenesulfonate)
Intramolecular SN2 Reactions
10-9 -- The E2 Reaction
Bimolecular Elimination; Beta-Elimination (β-Elimination)
Stereochemistry
C-H and C-X = Periplanar
Syn-Periplanar vs. Anti-Periplanar
Regiochemistry Concerns
Multiple β-H’s
Zaitsev’s Rule
Small Bases vs. Large Bulky Bases
Cyclic Systems (Rings) and the E2 Reaction
The E2 Reaction and Cyclohexane Chair Conformations
10-14 -- Competition Between SN2 and E2 Reactions
3° Halides, 2° Halides, and 1° Halides
10-15 -- E2 Elimination of Vinyl Halides
Converting Alkenes to Alkynes
10-16 -- SN1 and E1 Reactions
Unimolecular (First-Order)
Ionization of the Alkyl Halide (R-X)
The Rate-Determining Step (“Rate-Limiting Step”)
Solvolysis
Ionization Step in Detail
Best Leaving Groups
Formation of Allylic and Benzylic Carbocations
Alkyl Substitution and Carbocation Stability
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Solvent Effects on the SN1 / E1 Ionization Step
Polar or Non-Polar Solvents?
The Dielectric Constant (Є)
Product Determining Step(s)
Carbocations
SN1 Stereochemistry
E1 Regiochemistry and Zaitsev’s Rule
10-21 -- SN2 vs. E2 vs. SN1/E1
When are SN2 and E2 Favored?
Is There a Good Leaving Group (l.g)?
Is There a Good Nucleophile Present?
When are SN1 and E1 Favored?
SECTION 11 – MASS SPECTROMETRY AND IR SPECTROSCOPY
11-1 -- Mass Spectrometry (MS)
Molecular Weight Determination
Fragmentation into Smaller Radicals and Cations
Purpose of Magnetic Field
A Typical Mass Spectrum: n-Octane
Parent Peak and Base Peak
Mass-to-Charge Ratio (m/z)
Parent Ion (or “Molecular Ion”)
Fragment Peaks (Fragment Ions) and Isotope Peaks (Isotope Ions)
Relative Intensity
11-5 -- Review of Electromagnetic Radiation (“light”)
Energy Equations
Variables and Constants
Wavenumber (cm-1)
11-5 -- Infrared Spectroscopy
Definition of IR Spectroscopy
Graphical Plot of % Transmittance vs. Wavenumber (cm-1)
Stretching vs. Bending
The “Fingerprint Region”
11-7 -- Frequency (Wavenumber) and Intensity of IR Absorption
Types of IR Vibrations
Bond Strengths
CΞC > C=C > C-C
C(sp)-H > C(sp2)-H > C(sp3)-H
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Frequency Dependence on Masses of Bonded Atoms
Intensity of Absorption and its Dependence on Dipole Moments
The Number of Identical Bonds Influences the Intensity of IR Peaks
11-8 -- Table of IR Stretches for Common Functional Groups
11-9 -- Four Sample IR Spectra
SECTION 12 – NMR SPECTROSCOPY
12-1 -- Nuclear Magnetic Resonance (NMR)
1H NMR and 13C NMR
12-1 -- 1H NMR
α Spin-State and β Spin-State
Magnetic Field (Ho)
Spin Flips (α β)
Shielding (Hp Ξ Ho)
12-3 -- A Sample NMR Spectrum
Use of Tetramethyl Silane (TMS)
ppm Scale
“Downfield” vs. “Upfield”
δ-Values and Chemical Shifts
12-4 -- Characteristic Chemical Shifts for Various Functional Groups
12-5 -- 6 Factors That Allow Us to Understand 1H NMR
12-6 -- Relative Areas Under NMR Absorption Peaks
Electronic Integration
Integral Step Heighths
12-6 -- Spin-Spin Splitting (Coupling)
Relative Intensities of NMR Absorption Peaks
Pascal’s Triangle and Multiplets
Singlet, Doublet, Triplet, Quartet, etc.
The Coupling Constant (J)
Equivalent Protons Do Not Couple
Cyclohexane: Axial-H’s vs. Equatorial-H’s
12-11 -- Alcohols and NMR
Alcohol Proton (1H) is a Very Broad Singlet
D2O Exchange Identifies the Alcohol Proton in 1H NMR
12-12 -- Complex Splitting in NMR
Vinylic Coupling
Use of Tree Diagrams
J(geminal)
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J(trans) vs. J(cis)
What’s a “Doublet of Doublets”?
12-13 -- The Effect of Cyclohexane Conformation on Coupling
Coupling Constant (J) Depends on the Dihedral Angle (θ)
Karplus Curve
12-14 -- "Types” of Coupling
Vicinal Coupling (3-Bond Couplings)
Geminal Coupling (2-Bond Couplings)
Long-Range Coupling (Greater Than 3-Bond Couplings)
12-15 -- 1H NMR and Dynamic Effects
Deuterated Cyclohexane (C6D11H)
Ring-Flip at Room Temperature (25°C)
Cooling to Slow Down the Ring-Flip
12-16 -- 13C NMR
Typical Absorption Ranges (0ppm – 250ppm)
13C Chemical Shifts for Various Functional Groups
Proton-Decoupled 13C NMR (“Normal Spectrum”)
Off-Resonance Decoupling (“Spin-Coupled Mode”)
Singlet, Doublet, Triplet, Quartet
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