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Full Table of Contents

Chapter 1: Introduction to organic structure and bonding I

Section 2: Chemical Bonds

  1. Ionic bonds
  2. Covalent bonds and Lewis structures
  3. Formal charges

Section 3: Drawing organic structures

  1. Common bonding patterns in organic structures
  2. Using the 'line structure' convention
  3. Constitutional isomers
  4. The Index of Hydrogen Deficiency

Section 4: Functional groups and organic nomenclature

  1. Common functional groups in organic compounds
  2. Naming organic compounds
  3. Abbreviated organic structures

Section 5: Valence bond theory

  1. Formation of sigma bonds: the H2 molecule
  2. Hybrid orbitals: sp3 hybridization and tetrahedral bonding
  3. Formation of pi bonds: sp2 and sp hybridization
  4. The valence bonding picture in carbocations, carbanions, and carbon free radicals

Chapter 2: Introduction to organic structure and bonding II

Section 1: Molecular orbital theory

  1. Another look at the H2 molecule: bonding and antibonding sigma molecular orbitals
  2. MO theory and pi bonds: conjugation
  3. Aromaticity

Section 2: Resonance

  1. The meaning of resonance contributors: benzene and its derivatives
  2. Resonance contributors of the carboxylate group
  3. Rules for drawing resonance structures
  4. Major vs minor resonance contributors - four more rules to follow
  5. More examples of resonance: peptide bonds, enolates, and carbocations

Section 3: Non-covalent interactions

  1. Dipoles
  2. Ion-ion, dipole-dipole and ion-dipole interactions
  3. van der Waals forces
  4. Hydrogen bonds

Section 4: The relationship between noncovalent interactions physical properties

  1. Solubility
  2. Illustrations of solubility concepts - metabolic intermediates, lipid bilayer membranes, soaps and detergent
  3. Boiling points and melting points
  4. The melting behavior of lipid structures

Chapter 3: Conformations and Stereochemistry

Section 1: Conformations of straight-chain organic molecules

  1. Conformations of ethane
  2. Conformations of butane

Section 2: Conformations of cyclic organic molecules

  1. Introduction to sugars and other cyclic molecules
  2. Ring size
  3. Conformations of glucose and other six-membered ring structures
  4. Conformations of pentose and other five-membered ring structures
  5. The importance of conformation in organic reactivity

Section 7: Diastereomers

  1. Compounds with multiple stereocenters
  2. Meso compounds
  3. Stereoisomerism of alkenes

Section 10: Prochirality

  1. Prochiral substituents on tetrahedral carbons
  2. Carbonyl and imine carbons as prochiral centers

Chapter 4: Structure determination part I: Infrared spectroscopy, UV-visible spectroscopy, and mass spectrometry

Section 1: Introduction to molecular spectroscopy

  1. The electromagnetic spectrum
  2. Molecular spectroscopy – the basic idea

Section 3: Ultraviolet and visible spectroscopy

  1. Electronic transitions
  2. Looking at UV-vis spectra
  3. Applications of UV spectroscopy in organic and biological chemistry

Section 4: Mass Spectrometry

  1. The basics of mass spectrometry
  2. Looking at mass spectra
  3. Gas Chromatography - Mass Spectrometry
  4. Mass spectrometry of proteins - applications in proteomics

Chapter 5: Structure determination part II- Nuclear magnetic resonance spectroscopy

Section 1: The origin of the NMR signal

  1. NMR-active nuclei
  2. Nuclear precession, spin states, and the resonance condition

Section 3: The NMR experiment

  1. The basics of an NMR experiment
  2. The chemical shift
  3. Signal integration

Section 4: The basis for differences in chemical shift

  1. Diamagnetic shielding and deshielding
  2. Diamagnetic anisotropy
  3. Hydrogen-bonded protons

Section 5: Spin-spin coupling

  1. The source of spin-spin coupling
  2. Coupling constants
  3. Complex coupling

Section 6: 13C-NMR spectroscopy

  1. The basics of 13C-NMR spectroscopy
  2. 13C-NMR in isotopic labeling studies

Chapter 6: Introduction to organic reactivity and catalysis

Section 1: A first look at reaction mechanisms

  1. acid-base (proton transfer) reaction
  2. one-step nucleophilic substitution reaction (SN2)
  3. Two-step nucleophilic substitution reaction (SN1)

Section 4: Protein structure

  1. Amino acids and peptide bonds
  2. Visualizing protein structure: X-ray crystallography
  3. The four levels of protein structure
  4. The molecular forces that hold proteins together

Section 5: How enzymes work

  1. The active site
  2. Transition state stabilization
  3. Site-directed mutagenesis
  4. Enzyme inhibition
  5. Catalysts in the laboratory

Chapter 7: Organic compounds as acids and bases

Section 1: The ‘basic’ idea of an acid-base reaction

  1. The Brønsted-Lowry definition of acidity
  2. The Lewis definition of acidity

Section 2: Comparing the acidity and basicity of organic functional groups– the acidity constant

  1. Defining Ka and pKa
  2. Using pKa values to predict reaction equilibria
  3. pKa and pH: the Henderson-Hasselbalch equation

Section 3: Structural effects on acidity and basicity

  1. Periodic trends
  2. The resonance effect
  3. The inductive effect

Section 4: More on resonance effects on acidity and basicity

  1. The acidity of phenols
  2. The basicity of nitrogen-containing groups: aniline, imines, pyridine, and pyrrole

Chapter 8: Nucleophilic substitution reactions, part I

Section 2: Two mechanistic models for a nucleophilic substitution reaction

  1. Associative nucleophilic substitution: the SN2 reaction
  2. Dissociative nucleophilic substitution: the SN1 reaction
  3. Nucleophilic substitutions occur at sp3-hybridized carbons

Section 3: More about nucleophiles

  1. What makes a nucleophile?
  2. Protonation states and nucleophilicity
  3. Periodic trends in nucleophilicity
  4. Resonance effects on nucleophilicity
  5. Steric effects on nucleophilicity

Section 4: Electrophiles and carbocation stability

  1. Steric effects on electrophilicity
  2. Stability of carbocation intermediates

Section 5: Leaving groups

  1. What makes a good leaving group?
  2. Leaving groups in biochemical reactions
  3. Synthetic parallel - conversion of alcohols to alkyl halides, tosylates and mesylates
  4. SN1 or SN2? Predicting the mechanism.

Section 6: Epoxides as electrophiles in nucleophilic substitution reactions

  1. Epoxide structure
  2. Epoxide ring-opening reactions - SN1 vs SN2, regioselectivity, and stereoselectivity

Chapter 9: Nucleophilic substitution reactions, part II

Section 1: Methyl group transfers: examples of SN2 reactions

  1. SAM methyltransferase
  2. Synthetic parallel – the Williamson ether synthesis

Section 3: Protein prenyltransferase - a hybrid SN1/SN2 substitution

  1. The biological relevance of the protein prenyltransferase reaction
  2. Determining the mechanism of protein prenyltransferase with fluorinated substrate analogs
  3. The zinc-thiolate interaction in protein prenyltransferase - 'tuning' the nucleophile

Section 4: Biochemical nucleophilic substitutions with epoxide electrophiles

  1. Hydrolysis of stearic acid epoxide: investigating the mechanism with kinetic isotope effect experiments
  2. Fosfomycin - an epoxide antibiotic

Chapter 10: Phosphoryl transfer reactions

Section 1: Overview of phosphates and phosphoryl transfer reactions 

  1. Nomenclature and abbreviations
  2. Acid constants and protonation states
  3. Bonding in phosphines and phosphates
  4. Phosphoryl transfer reactions - the general picture 
  5. Phosphoryl transfer reactions - associative, addition-elimination, or dissociative?

Section 2: Phosphorylation reactions - kinase enzymes

  1. ATP  - the principle phosphoryl group donor
  2. Monophosphorylation of alcohols
  3. Diphosphorylation of alcohols
  4. Phosphorylation of carboxylates
  5. Generation of nucleotide phosphates
  6. Regeneration of ATP from ADP

Section 4: Phosphate diesters

  1. Phosphate diesters as the backbone for DNA and RNA
  2. The chemistry of genetic engineering

Chapter 11: Nucleophilic carbonyl addition reactions

Section 3: Hemiacetals, hemiketals, and hydrates

A. The general picture
B. Simple sugars are hemiacetals and hemiketals

Section 4: Acetals and ketals

A. Glycosidic bonds revisited
B. Synthetic parallel: cyclic acetals/ketals as 'protecting groups' for ketones and aldehydes

Section 6: Imine (Schiff base) formation

A. Imines-the general picture 
B. Pyridoxal phosphate coenzyme links to enzymes by a Schiff base
C. Schiff base formation in aldolase reactions 

Chapter 12: Acyl substitution reactions

Section 1: Introduction to carboxylic acid derivatives and the nucleophilic acyl substitution reaction

A: Carboxylic acid derivatives and acyl groups
B: The nucleophilic acyl substitution reaction
C: The relative reactivity of carboxylic acid derivatives

Section 2: Acyl phosphates as activated carboxylic acids

A: Glutamine synthetase 
B: Asparagine synthetase 
C: Glycinamide ribonucleotide synthetase
D: Synthetic parallel - activated carboxylic acids in the lab

Section 3: Thioesters

A: Introduction to thioesters and Coenzyme A
B: Activation of fatty acids by coenzyme A - a thioesterification reaction
C: Transfer of fatty acyl groups to glycerol: a thioester to ester substitution
D: More transthioesterification reactions
E: Hydrolysis of thioesters

Section 4: Esters

A: Nonenzymatic esterification: synthesis of ‘banana oil’
B: Nonenzymatic ester hydrolysis and the soap-making process
C: Enzymatic ester hydrolysis: acetylcholinesterase and sarin nerve gas
D: More enzymatic ester hydrolysis: lipase, the resolution of enantiomers, and dehalogenation 
E: Transesterification: the chemistry of aspirin and biodeisel 

Section 5: Nucleophilic acyl substitution reactions involving peptide bonds 

A: Formation of peptide bonds on the ribosome 
B: Hydrolysis of peptide bonds: HIV protease
C: The chemical mechanism of penicillin

Chapter 13: Reactions with stabilized carbanion intermediates, part I - isomerization, aldol and Claisen condensation, and decarboxylation

Section 1: Tautomers

  1. Keto-enol tautomerization
  2. Imine/enamine tautomerization 

Section 2: Isomerization reactions

  1. Carbonyl isomerization
  2. Stereoisomerization at chiral carbons

Section 3: Aldol reactions

  1. The general mechanism for an aldol reaction
  2. Typical aldolase reactions: three variations on a theme
  3. Going backwards: the retroaldol reaction
  4. Going both ways: transaldolase

Section 4: Claisen reactions

  1. Claisen condensations 
  2. Retro-Claisen cleavages  
  3. Enolates as nucleophiles in SN2 displacements

Section 5: Carboxylation and decarboxylation reactions

  1. The metabolic context of carboxylation and decarboxylation
  2. The carboxylation mechanism of Rubisco 
  3. Decarboxylation 

Section 6: Synthetic parallel - carbon nucleophiles in the lab

  1. Lab reactions with enolate /enamine intermediates
  2. The Wittig reaction
  3. Terminal alkynes as carbon nucleophiles
  4. Grignard, Gilman, and organolithium reagents

Chapter 14: Reactions with stabilized carbanion intermediates, part II: Michael additions, eliminations, and electron sink cofactors

Section 14.1: Michael additions and beta-eliminations

  1. Overview of Michael addition and beta-elimination mechanisms
  2. Stereochemistry of Michael additions and beta-eliminations
  3. NMR experiments to determine the stereochemistry of a Michael addition 
  4. More examples of elimination and addition reactions

Section 14.2: Variations on the Michael reaction

  1. Cis/trans alkene isomerization
  2. Nucleophilic aromatic substitution 
  3. Synthetic parallel - Michael addition reactions in the laboratory

Section 14.3: Elimination by the E1 and E2 mechanisms

  1. E1 and E2 reactions in the laboratory
  2. Enzymatic E1 and E2 reactions

Section 14.4: Pyridoxal phosphate - an electron sink cofactor

  1. PLP and the Schiff-base linkage to lysine
  2. PLP-dependent amino acid racemases 
  3. PLP-dependent decarboxylation
  4. PLP-dependent retroaldol reactions
  5. PLP-dependent transaminase reactions (aspartate aminotransferase) 
  6. PLP-dependent β-elimination and β-substitution reactions
  7. PLP-dependent γ-elimination and γ-substitution reactions
  8. Altering the course of a PLP reaction through site-directed mutagenesis  

Section 14.5: Thiamine diphosphate-dependent reactions

  1. The benzoin condensation reaction
  2. The transketolase reaction
  3. Pyruvate decarboxylase 
  4. Synthetic parallel - carbonyl nucleophiles via dithiane anions

Section 14.6: The transition state geometry of reactions involving pi bonds

  1. Transition state geometry of E2 reactions
  2. Transition state geometry of PLP-dependent reactions

Chapter 15: Electrophilic reactions

Section 2: Electrophilic addition

  1. The general picture
  2. The regiochemistry of electrophilic addition 
  3. Enzymatic electrophilic additions
  4. Synthetic parallel - electrophilic additions in the laboratory

Section 3: Electrophilic isomerization and substitution (addition/elimination)

  1. Alkene isomerization
  2. Substitution by electrophilic addition/elimination

Section 5: Electrophilic aromatic substitution

  1. The general picture
  2. Some representative enzymatic electrophilic aromatic substitution reactions

Section 6: Synthetic parallel - electrophilic aromatic substitution in the lab

  1. Friedel-Crafts reactions
  2. Ring directing effects in SEAr reactions

Section 7: Carbocation rearrangements

  1. Hydride and alkyl shifts
  2. Enzymatic reactions with carbocation rearrangement steps
  3. The acyloin, pinacol, and Hoffman rearrangements (isoleucine biosynthesis).

Chapter 16: Oxidation and reduction reactions

Section 4: Hydrogenation/dehydrogenation reactions of carbonyls, imines, and alcohols

  1. Nicotinamide adenine dinucleotide - a hydride transfer coenzyme
  2. Carbonyl hydrogenation and alcohol dehydrogenation - the general picture
  3. Stereochemistry of carbonyl hydrogenation and alcohol dehydrogenation
  4. Examples of redox reactions involving alcohols, carbonyl groups, and imines

Section 5: Hydrogenation of alkenes and dehydrogenation of alkanes

  1. Alkene hydrogenation in fatty acid biosynthesis 
  2. The flavin coenzymes
  3. Alkane dehydrogenation in fatty acid degradation 
  4. More examples of enzymatic alkene hydrogenation

Section 7: NAD(P)H, FADH2 and metabolism - a second look

  1. NADH and FADH2 as carriers of hydrides from fuel molecules to water
  2. The source of NADPH for reductive biosynthesis

Section 11: Halogenation of organic compounds

  1. Enzymatic halogenation 
  2. Synthetic parallel - halogenation of alkenes in the lab

Section 12: Redox reactions involving thiols and disulfides

  1. Disulfide bridges in proteins
  2. The role of disulfides in the pyruvate dehydrogenase reaction

Section 13: Redox reactions in the organic synthesis laboratory

  1. Metal hydride reducing agents
  2. Catalytic hydrogenation and the trans fat issue
  3. Reduction of carbonyl carbons to methylene 
  4. Laboratory oxidation reactions

Chapter 17: Radical reactions

Section 1: Structure and reactivity of radical species

  1. The geometry and relative stability of carbon radicals.
  2. The diradical character of triplet oxygen

Section 2: Radical chain reactions

  1. The three phases of radical chain reactions
  2. Radical halogenation in the lab
  3. Useful polymers formed by radical chain reactions
  4. Destruction of the ozone layer by CFC radicals
  5. Harmful radical species in cells and natural antioxidants

Section 3: Enzymatic reactions with free radical intermediates

  1. Hydroxylation of alkanes
  2. Reductive dehydroxylation of alcohols
  3. Radical mechanisms for flavin-dependent reactions 


Table 1: Some characteristic absorption frequencies in IR spectroscopy
Table 2: Typical values for 1H-NMR chemical shifts
Table 3: Typical values for 13C-NMR chemical shifts
Table 4: Typical coupling constants in NMR
Table 5: The 20 common amino acids
Table 6: Structures of common coenzymes
Table 7: Representative acid constants
Table 8: Some common laboratory solvents, acids, and bases
Table 9: Examples of common functional groups in organic chemistry