Structure & Reactivity in Organic, Biological and Inorganic Chemistry by Chris Schaller is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License.
Structure & Reactivity in Organic, Biological and Inorganic Chemistry
Table of Contents
Part I. Structure
AT. Atoms
AT1. From Democritus to the 19th Century
AT4. Quantum Numbers
AT5. The Aufbau Process
AT6. Periodic Trends
AT7. Solutions to Selected Problems
ME. Metals
ME1. Structure and Properties of Metals
ME3. Metal Packing: Three Dimensions
ME4. Application Problems
ME5. Solutions to Selected Problems
IC1. Ions
IC2. Counterions
IC3. Physical Properties
IC4. Solubility
IC6. Application Problems
IC8. Solutions for Selected Problems
IM. Introduction to Molecules
IM.1. Why molecules matter
IM.2. Lewis structures
IM.3. Lewis & multiple bonds
IM.4. Lewis & valence
IM.5. Lewis & formal charge
IM.6. Lewis & resonance
IM.7. Ionic bonds
IM.8. Line drawings
IM.9. Three dimensional drawings
IM10. Other geometries
IM11. Controversies in drawing structures
IM12. Organic functional groups
IM13. Common biological molecules
IM.14. Drawing biological macromolecules
IM15. Application Problems
IM16. Solutions to problems
SC. Stereochemistry
SC1. Introduction to Stereochemistry
SC2. Stereoisomers: cis & trans
SC3. Enantiomers
SC4. Simple Organic Enantiomers
SC5. Biological Small Molecules
SC6. Optical Rotation
SC7. The Polarimetry Experiment
SC8. Biological Building Blocks: Carbohydrates
SC9. Carbohydrates and Diastereomers
SC10. Diastereomers and Physical Properties
SC11. Carbohydrates in Cyclic Form
SC12. Biological Building Blocks: Amino Acids
SC13. Macromolecular Structures: Alpha-Helices
SC14. Diastereomers and Optical Resolution
SC15. Another Kind of Stereochemistry: Alkene Isomers
SC16. E and Z Alkene Isomers
SC17. Stereochemistry in Octahedra: Cis vs Trans and Fac vs. Mer
SC18. Enantiomers in Octahedra
SC19. Chiral Catalysts for Production of Enantiomers
SC20. More Practice with Stereochemistry
SC21. Solutions to Selected Problems
CA. Conformational Analysis
CA1. Introduction to Conformation
CA2. Simple Molecules
CA4. A Conformational Basis Set
CA5. Molecular Modeling
CA6. Cyclic Systems
CA7. Cyclohexanes
CA10. Disubstituted Cyclohexanes
CA11. Other Rings
CA12. Rings with Heteroatoms
CA13. More Practice with Conformation
CA14. Application Problems
CA15. Solutions to Selected Problems
SP. Intermolecular Attractions & Structure-Property Relationships
SP2. Changes of state
SP4. London attractions
SP5. Dipole-dipole attractions
SP6. Hydrogen bonding
SP7. Ionic attractions
SP9. Miscibility
SP10. Solubility
SP11. Hydrogen bond donors & acceptors
SP12. Heterogeneous mixtures
SP13. Intermolecular attractions in biomolecules
SP14. Application problems
SP.15. Solutions to selected problems
IB. Introduction to Biomolecules
Contribution from Henry Jakubowski.
IB1. Lipids
IB2. Proteins
IB3. Nucleic Acids
IB5. Carbohydrates
MP0. Cross-Reference: Tutorial on the Cell
NW. Network Solids and Related Materials
NW3. Silicates
NW4. Aluminosilicates
NW5. Solutions to Selected Problems
TM. Transition Metal Complexes
TM1. Introduction
TM2. Building Blocks: Metal Ions and Ligands
TM3. Electron Counting
TM4. Chelation
TM5. Isomers
TM6. Naming Coordination Complexes
TM7. Geometry
TM8. Solutions to Selected Problems
MM. Macromolecules and Supramolecular Assemblies
MM2. Viscosity and entanglement
MM3. Glass transition and reptation
MM5. Morphology and microphase separation
MM6. Polymer synthesis
MM7. Molecular weight
MM8. Supramolecular assemblies
MM9. Solutions for selected problems
MO. Molecular Orbital Theory
MO1. Introduction
MO2a. Wave Behaviour
MO2b. Dihydrogen
MO4. Sigma Bonding with P Orbitals
MO5. Pi Bonding with P Orbitals
MO6a. Assembling the Complete Diagram
MO6b. Electron Population
MO8. Symmetry & Mixing
MO9. Bonding Between Different Atoms
MO10. S and P Mixing in HF
MO11. Polyatomic Geometry and Symmetry
MO12. Approximations in Complicated Structures
MO13. Building MO from Smaller Pieces
MO14. Delocalization
MO15. Polyenes
MO16. Aromatics
MO17. Heteroaromatics
MO18. Frontier Orbitals
MO19. Solutions to Selected Problems
AB. Concepts of Acidity
AB1. General Acidity and Basicity
AB2. Lewis Bases
AB3. Lewis Acids
AB4. Lewis Acid-Base Complexes
AB4b. Molecular Orbital Interactions in Lewis Acid-Base Reactions
AB5. Reversibility of the Coordinate Bond
AB7. Proton as a Common Lewis Acid
AB8. Proton Transfer from One Basic Site to Another
AB8b. Molecular Orbital Interactions in Proton Transfers
AB9. Proton Donor Strength: pKa
AB10. Proton Donation and Structure
AB11. Factors affecting Bronsted-Lowry Acidity: Local Factors
AB12. Factors affecting Bronsted-Lowry Acidity: Distal Factors
AB13. Factors affecting basicity (proton binding)
AB14. Direction of Proton Transfer
AB15. pKa and Amino Acids
AB16. Solvent Effects
AB17. The Meaning of pKa: Product-to-Reactant Ratio and Equilibrium Constant
AB18. pH and Buffers
AB19. Application Problems
AB20. Solutions to Selected Problems
Part II. Structure, Spectroscopy and Purification
SD. Structure Determination
SD. Introduction to Spectroscopy
UV. Ultraviolet-Visible Spectroscopy
UV1. Introduction to UV-Visible Spectroscopy
UV2. UV-Visible Spectroscopy and Metal Ions
UV3. UV-Visible Spectroscopy and Organic Compounds
UV4. Solutions for Selected Problems
IR1. What Does an IR Spectrum Look Like?
IR2. Hydrocarbon Spectra
IR3. Subtle Points of IR Spectroscopy
IR4. Carbon Carbon Multiple Bonds
IR5. Carbon Oxygen Single Bonds
IR6. Carbon Oxygen Double Bonds
IR8. More Complicated IR Spectra
IR9. Misleading Peaks
IR10. More Practice with IR Spectra
IR11. Solutions for Selected Problems
IR12. Appendix: IR Table
NMR. Nuclear Magnetic Resonance Spectroscopy
NMR1. Introduction to NMR
NMR2. Carbon-13 NMR
NMR3. Symmetry in NMR
NMR4. 13C NMR and Geometry
NMR5. 13C NMR and Electronics
NMR6. More About Electronics
NMR7. Intro to 1H NMR
NMR8. Chemical Shift in 1H NMR
NMR9. Integration
NMR10. Multiplicity
NMR11. More About Multiplicity
NMR12. Structure Determination with Combined Spectra
NMR13. NMR Spectroscopy in Lab: Solvent Impurities
NMR14. NMR Spectroscopy in Lab: Following Reactions
NMR15. NMR Spectroscopy in Lab: Measuring Compositions
NMR16. More Practice with NMR Spectroscopy
NMR17. 2D NMR
NMR2D.1. COSY Spectra
NMR2D.2. TOCSY Spectra
NMR2D.3. HMQC and HMBC Spectra
NMR2D.4. NOESY Spectra
NMR2D.5. Proteins
NMR2D.6. More Practice with 2D
NMR2D.7. Solutions
NMR18. Solutions for Selected Problems
NMR Appendix. Useful Charts for NMR identification
MS. Introductory Mass Spectrometry
MS1. Introduction to Mass Spectrometry
MS2. The Mass Spectrometry Experiment
MS3. GC-MS and LC-MS
MS5. Molecular Formula and Degrees of Unsaturation
MS6. Isotopes: 13C
MS7. Isotopes: Br and Cl
MS8. Molecular Ion and Nitrogen
MS9. High Resolution vs Low Resolution
MS10. Fragmentation: Stable Cations
MS11. Fragmentation Pathways
MS12. Solutions for Selected Problems
PM. Purification of Molecular Compounds
PM1. Evaporation
PM2. Filtration
PM3. Distillation
PM4. Sublimation
PM5. Recrystallization
PM6. Solvent Partitioning (Liquid - Liquid Extraction)
PM7. Acid-Base Extraction
PM8. Chromatography I: TLC (Normal Phase)
PM9. Chromatography II: Column (Normal Phase)
PM10. Chromatography III: Reverse Phase
PM11. Chromatography IV: Size Exclusion
PM12. Chromatography V: Ion Exchange
PM13. Chromatography VI: Affinity
PM14. Chromatography VII: Electrophoresis
PM15. Instrumental Methods: GC and HPLC
PM16. Solutions for Selected Problems
Part III: Reactions of Nucleophiles, Part I
TD. Thermodynamics
TD1. Introduction to Thermodynamics
TD2. Enthalpy Changes in Reactions
TD3. Entropy Changes in Reactions
TD4. Free Energy Changes in Reactions
TD5. Reversibility and le Chatelier
TD6. Free Energy and Equilibrium
TD8. Hess' Law
TD9. Solutions to Selected Problems
CC. Coordination Compounds
CC1. Introduction to Metal-Ligand Binding
CC2. How Tightly Do Ligands Bind?
CC3. Electron Counting in Transition Metal Complexes
CC5. Pi Coordination: Donation from Alkenes
CC6. Hapticity
CC7. Hard-Soft Acid & Base Concepts
CC8. Ligand Field Theory
CC9. Ligand Field Stabilisation Energy
CC10. Spectrochemical Series
CC11. Ligand Field and Lability
CC12. Jahn-Teller Distortion
CC13. Multiple Bonds in Coordination Compounds
CC14. Solutions to Selected Problems, CC1-CC6.
CC15. Solution to Selected Problems, CC7-CC13.
CO. Addition to Carbonyls
CO1. Carbonyls in Biology
CO2. Carbonyls are Electrophiles
CO3. General Reactivity Patterns
CO3b. General Reactivity Patterns, Part B
CO4. Reaction Mechanism
CO6. Relative Reactivity of Carbonyls
CO7. Elementary Steps: Nucleophilic Addition
CO8. Elementary Steps: Protonation of Oxygen
CO9. What is a Good Nucleophile?
CO10. What is a Solvent?
CO11. Semi-Anionic Nucleophiles: Grignards and Complex Hydrides
CO12. Enolate Addition: Aldol Reactions
CO13. Activation of Carbonyls
CO14. Addition of Neutral, Protic Nucleophiles
CO15. Elementary Steps: Proton Transfer Steps
CO16. Elementary Steps: Pi Donation Steps
CO17. Sugars: Pyranose and Furanose Forms
CO18. The Anomeric Center
CO19. Biological Reduction
CO20. Oxidation
CO21. Ylide Addition
CO22. Conjugate Addition
CO23. Conjugate Addition-Elimination in Aromatics
CO24. Carbonyl in Synthesis: Getting Started
CO25. Carbonyl Addition Summary: Mechanistic Steps
CO26. Additional Problems
CO27. Solutions to Selected Problems, CO1-12
CO28. Solutions to Selected Problems, CO13-26
MI. Insertion
MI1. Insertion
MI2. CO Binding
MI3. Hydride & Alkyl Migratory Insertion
MI4. b-Hydride Insertion and Elimination
MI5. Solutions for Selected Problems
CX. Substitution at Carboxyloids
CX1. Introduction to Carboxyloids (Carboxylic Acid Derivatives)
CX2. General Reactivity Patterns
CX3. Comparative Energies: The Ski Hill
CX4. Interconversion: Going Downhill
CX5. Getting Towed Uphill
CX6. Semi-Anionic Nucleophiles
CX7. Enolates: Claisen Condensation
CX7b. Enolates: Decarboxylation
CX8b. Ring-Opening Trans-Esterification Polymerisation
CX9. Peptides and Proteins: Laboratory Synthesis
CX10. Biosynthesis of Proteins and Peptides
CX11. Protein Modifications
CX12. Additional Problems
CX13. Solutions For Selected Problems
EZ. Enzyme Catalysis
EZ2. Binding in Enzymes
EZ3. Catalytic Strategies in Enzymes
EZ4. Enzyme Inhibition
EZ5. Types of Reversible Inhibitors
EZ7. Solutions to Selected Problems
MP. Metabolic Pathways
Contributions from Henry Jakubowski, CSB/SJU
MP1. Overview of Metabolic Pathways: Catabolism
MP2. Overview of Metabolic Pathways: Anabolism
MP3. Metabolic Maps
MP4. Regulation of Metabolic Pathways: How Is Enzyme Activity Regulated?
MP5. Regulation of Metabolic Pathways: What Enzymes Are Optimal for Regulation?
GL. Mechanisms of Glycolysis.
GL1. Introduction: Respiration and Energy
GL3. Phase One: Phosphorylation and Isomerisation
GL4. Phase One: Scission
GL6. Phase Two
GL8. Thermodynamics of Glycolysis
GL9. Thermodynamics: The Role of Concentrations
GL10. Gluconeogenesis
GL11. Regulation
GL12. Solutions for Selected Problems
TC. Mechanisms of the Tricarboxylic Acid Cycle
TC1. Overview of the TCA Cycle
TC2. Transformations in the TCA Cycle
TC3. Catalysis in the TCA Cycle
TC4. Solutions for Selected Problems
FA. Fatty Acid Synthesis
FA1. Overview of Fatty Acid Synthesis
FA2. Transformations in Fatty Acid Synthesis
FA3. Catalysis in Fatty Acid Synthesis
FA4. Solutions to Selected Problems
Part IV: Reactions of Nucleophiles, Part 2
RK. Reaction Kinetics
RK1. Introduction to Reaction Kinetics
RK2. Reaction Rates
RK3. Activation Barriers
RK4. Collisions and Phase
RK5. Collisions and Concentration
RK6. Rate Laws
RK7. Elementary Steps
RK8. Catalysis
RK9. Solutions to Selected Problems
LS. Ligand Substitution in Coordination Complexes
LS1. Introduction to Ligand Substitution
LS2. Mechanism of Ligand Substitution
LS3. Kinetics of Associative Mechanism
LS4. Kinetics of Dissociative Mechanism
LS6. Some Reasons for Differing Mechanisms
LS7. The Trans Effect
LS8. Solutions to Selected Problems
NS. Aliphatic Nucleophilic Substitution
with problems contributed by Kate Graham
NS1. Introduction to Aliphatic Nucleophilic Substitution
NS2. Possible Mechanisms of Nucleophilic Substitution
NS3. Rate Laws in Nucleophilic Substitution
NS4. Stereochemistry in Nucleophilic Substitution
NS5. Regiochemistry in Nucleophilic Substitution
NS6. Structural Effects in Nucleophilic Subsitution
NS7. Solvent Effects in Nucleophilic Substitution
NS8. Nucleophilicity in Nucleophilic Substitution
NS9. Enolate Nucleophiles
NS10. Leaving Group Formation
NS11. Nucleophilic Addition to Strained Rings
NS12. Complications: Elimination Reactions
NS13. Regiochemistry in Elimination
NS14. Stereochemistry in Elimination
NS15. Factors Affecting Elimination Mechanism
NS16. Nucleophilic Substitution in Synthesis: Alcohols and Ethers
NS17. Nucleophilic Substitutions in Synthesis: Amines
NS18. Nucelophilic Substitution at Silicon
NS19. Extra Problems
NS20. Solutions for Selected Problems
OA. Oxidative Addition and Reductive Elimination
OA1. Introduction to Oxidative Addition
OA2. Overview of Oxidative Addition
OA4. Concerted Oxidative Addition
OA6. Coupling Reactions
OA7. Solutions to Selected Problems
EA. Electrophilic Addition to Alkenes
EA1. Introduction to Electrophilic Addition
EA2. Cations in Electrophilic Addition
EA3. Solvent Effects in Electrophilic Addition
EA4. Stabilized Cations
EA5. Addition to Alkene Complexes
EA6. Insertion into Coordinated Alkenes
EA7. Concerted Additions
EA8. Epoxidation
EA9. Cyclopropanation
EA10. Alkene Oxidations
EA11. Alkene Polymerisation
EA12. Living Cationic Polymerisation
EA13. Ziegler-Natta Polymerisation
EA14. Solutions for Selected Problems
AR. Electrophilic Aromatic Substitution
with problems contributed by Ed McIntee
AR1. Introduction to Electrophilic Aromatic Substitution
AR2. Mechanism of Electrophilic Aromatic Substitution
AR3. Formation of Electrophiles
AR4. Activation and Deactivation
AR5. Directing Effects
AR6. Solutions to Selected Problems
Part V: Advanced Reactivity: Single Electrons, Photochemistry, and Reactions Under Orbital Control
Reduction & Oxidation Reactions
RO1. Oxidation State
RO2. Redox Reactions
RO3. Reduction Potentials
RO4. Reduction Potentials and Energy Levels
RO5. Factors that Influence Reduction Potential
RO8. Balancing Redox Reactions
RO9. Electron Transfer Mechanisms: Outer Sphere
RO10. Electron Transfer: Inner Sphere
RO11. Cyclic Voltammetry
RO12. Redox in Organic Carbonyls
RO13. Potential and Concentrations
RO14. Solutions for Selected Problems
Reduction Potentials of Metal Ions in Biology
MB1. Introduction
MB3. Effect of Medium
MB4. pH Effects
MB5. Hard & Soft Acid & Base Considerations
MB6. Effect of Geometry
MB7. Evidence for Oxidation State: Magnetism
MB8. Solutions for Selected Problems
Understanding Mechanism
UM1. Intermediates
UM2. Energetics
UM3. Arrow Conventions
UM4. Solutions
Oxygen Binding & Reduction
OR1. Introduction
OR2. Oxygen Binding
OR3. Oxygen Reduction
OR4. Metal Oxos
OR5. Solutions to Selected Problems
Nitrogen Reduction
NF1. Introduction to Nitrogen Reduction
NF3. Nitrogenase
NF4. Model Studies for Nitrogen Binding
NF5. Model Studies for Nitrogen Reduction
NF6. Solutions for Selected Problems
Radical Reactions
RR2. Initiation: Bond Homolysis
RR3. Initiation: Radical Stability
RR4. Initiation: Single Electron Transfer
RR5. Radical Chain Reactions: Propagation
RR6. Radical Chain Reactions: Termination
RR7. Radical Substitution
RR8. Radical Addition to Alkenes
RR10. Living Radical Polymerization
RR11. Detection of Unpaired Electrons: EPR
RR12. Solutions to Selected Problems
Oxidative Phosphorylation
OP1. Introduction to Oxidative Phosphorylation
OP2. Complex I
OP3. Complex II
OP4. Complex III
OP5. Complex IV
OP6. Complex V
OP7. Solutions for Selected Problems
Photochemical Reactions
PC1. Absorbance
PC2. Rules of Electronic Excitation
PC3. Fluorescence & Phosphorescence
PC4. Photolysis
PC5. Atmospheric Chemistry: Ozone
PC6. Photoredox Chemistry
PC7. Photoredox Catalysis in Organic Chemistry
PC8. Solutions for Selected Problems
Photosynthesis
PS1. Introduction to Photosynthesis
PS2. Photosystem II: Gathering Photons
PS3. Photosystem II: Electron Transfer
PS4. Photosystem II: The Oxygen-Evolving Complex
PS5. Adding a Proton Pump: The Cytochrome b6/f Complex
PS6. Photosystem I
PS7. ATP Synthesis
PS8. Carbohydrate Synthesis: RuBisCO
PS9. Problems
PS10. Solutions for Selected Problems
Reactions Under Orbital Control
OC1. Introduction to Pericyclic Reactions
OC2. Cope and Claisen Rearrangements
OC4. Regiochemistry in the Diels Alder Reaction
OC5. Endo and Exo Reactivity in the Diels Alder Reaction
OC6. Photochemically-Allowed Pericyclic Reactions
OC7. Facial Selectivity in Pericyclic Reactions
OC8. Alkene Oxidations
OC9. Decarboxylations
OC10. Olefin Metathesis
OC11. Sigma Bond Metathesis
OC12. Solutions to Selected Problems
Electrophilic Rearrangement
ER1. Introduction
ER3. Baeyer-Villiger Rearrangement
ER5. Wolff Rearrangement
ERX. Solutions
Part VI. Special Topics
Polymers
Monomers and Polymers
MP1. Difunctional Carboxyloids
MP2. Cyclic Carboxyloids
MP3. Olefins
MP4. Cyclic Olefins
MP6. Supramolecular Assemblies
MP7. Other Monomers
MP8. Polymer Topology
MP9. Solutions for Selected Problems
Synthetic Methods in Polymer Chemistry
SM1. Step-Growth and Chain-Growth
SM3. Living Cationic Polymerization
SM5. Living Anionic Polymerization
SM6. Ring-Opening Polymerization
SM8. Living Radical Polymerization: RAFT
SM9. Living Radical Polymerization: ATRP
SM10. Ziegler-Natta Polymerization
SM11. Solutions to Selected Problems
Kinetics and Thermodynamics in Polymer Chemistry
KP1. Thermodynamics of Polymerization
KP2. Kinetics of Step-Growth Polymerization
KP3. Kinetics of Chain Polymerization
KP4. Kinetics of Catalytic Polymerization
KP5. Solutions
Polymer Properties
PP1. Molecular Weight
PP2. Viscosity
PP3. Rheology
PP4. Glass Transition
PP5. Crystallinity
PP7. Stress-Strain Relationships
PP9. Modulus, Temperature, Time
PP10. Solutions to Problems
Mechanistic Determination
MK. Mathematical Tools in Reaction Kinetics
MK1. Determining the Activation Parameters
MK2. The Rate Law Has Different Forms
MK3. Determining the Rate Law Experimentally
MK4. The Relationship Between Elementary Steps and Rate Law
MK5. Enzyme Kinetics and Inhibition
MK6. Characterizing Enzyme Kinetics
MK7. Potential Energy Surfaces
MK8. Using Kinetics to Map Potential Energy Surfaces
MK9. Using Computational Chemistry to Map Potential Energy Surfaces
MK10. Determination of Bond Strengths
MK11. Kinetic Isotope Effects
MK12. Linear Free Energy Relationships
MK13. Reaction Progress Kinetics
MK14. Solutions to Selected Problems in MK1-6
MK15. Solutions to Selected Problems in MK7-13
Detection of Intermediates
DI1. Isotopic Labeling
DI2. Direct Observation
DI4. Radical Clocks
DI5. Site-Directed Mutagenesis
DI6. Solutions to Selected Problems
Part VII. Appendices
AX. Appendix: Useful Tables
The Elements
Periodicity and Electronegativity
Pauling Electronegativity Values
Periodicity and Covalent Radius
Structure Determination & Spectroscopy
Reactions
Biochemistry
Organic Chemistry
Abbreviations for Reagents
Inorganic Chemistry
FG. Common Organic Structural Features (Functional Groups)
FG1. Hydrocarbons
FG2. Simple Heteroatomics
FG3. Simple Carbonyls
FG4. Carboxyloids
FG5. Halides
FG6. Aromatics
FG7. Imines & Nitriles
FG8. Sulfur & Phosphorus
FG9. Solutions
FG10. Quick Reference: Functional Groups and Names
OS. Organic Synthesis
This site is written and maintained by Chris P. Schaller, Ph.D., College of Saint Benedict / Saint John's University (with contributions from other authors as noted). It is freely available for educational use.
Structure & Reactivity in Organic, Biological and Inorganic Chemistry by Chris Schaller is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License.
Send corrections to cschaller@csbsju.edu
This material is based upon work supported by the National Science Foundation under Grant No. 1043566.
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
Navigation: