Structure & Reactivity in Organic, Biological and Inorganic Chemistry

Table of Contents

Part I.  Structure

AT. Atoms

AT1.  From Democritus to the 19th Century

AT2.  Old Quantum Mechanics

AT3.  New Quantum Mechanics

AT4.  Quantum Numbers

AT5.  The Aufbau Process

AT6.  Periodic Trends

AT7.  Solutions to Selected Problems

 

ME.  Metals

ME1.  Structure and Properties of Metals

ME2.  Metal Packing: Layers

ME3.  Metal Packing: Three Dimensions

ME4.  Application Problems

ME5.  Solutions to Selected Problems


IC. Ionic Compounds

IC1. Ions

IC2. Counterions

IC3. Physical Properties

IC4.  Solubility

IC5. Solid State Structures

IC6. Application Problems

IC7.  Naming Ionic Compounds

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

CA3. Conformation of Butane

CA4. A Conformational Basis Set

CA5. Molecular Modeling

CA6. Cyclic Systems

CA7. Cyclohexanes

CA8. Diamond Lattice Drawings

CA9. Substituted 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

SP1. The properties of water

SP2.  Changes of state

SP3.  Kinetic molecular theory

SP4.  London attractions

SP5. Dipole-dipole attractions

SP6.  Hydrogen bonding

SP7.  Ionic attractions

SP8.  Isomerism and properties

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

IB6.  Biomolecule Applications

MP0.  Cross-Reference: Tutorial on the Cell

 

NW. Network Solids and Related Materials

NW1.  A Network Solid: Diamond

NW2.  Other Forms of Carbon

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

MM1.  What are macromolecules?

MM2.  Viscosity and entanglement

MM3.  Glass transition and reptation

MM4.  Polymer architectures

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

MO3. Lessons from Dihydrogen

MO4. Sigma Bonding with P Orbitals

MO5. Pi Bonding with P Orbitals

MO6a. Assembling the Complete Diagram

MO6b. Electron Population

MO7. Experimental Evidence

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

AB6. Coordination Complexes

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

 

IR. Infrared Spectroscopy

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

IR7. Carbon Nitrogen 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

MS4. MS and Molecular Ions

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

Glossary

 

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

TD7.  Equilibrium and Acidity

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

CC4.   Chelation and Denticity

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

CO5.  MO Picture of Carbonyls

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

CX8.  Condensation Polymers

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

EZ1. Introduction to Enzymes

EZ2.  Binding in Enzymes

EZ3.  Catalytic Strategies in Enzymes

EZ4.  Enzyme Inhibition

EZ5.  Types of Reversible Inhibitors

EZ6.  Covalent Modification

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

GL2. Overview of Glycolysis

GL3.  Phase One: Phosphorylation and Isomerisation

GL4.  Phase One: Scission

GL5.  Catalysis in Phase One

GL6.  Phase Two

GL7.  Catalysis in 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

LS5.  Activation Parameters

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

OA3.  Polar Oxidative Addition

OA4. Concerted Oxidative Addition

OA5.  Catalytic Hydrogenation

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

RO6.  Reduction of Metal Ores

RO7.  Reduction in Batteries

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

MB2. Effect of Complex Charge

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

NF2.  The Haber-Bosch Process

NF3.  Nitrogenase

NF4.  Model Studies for Nitrogen Binding

NF5.  Model Studies for Nitrogen Reduction

NF6.  Solutions for Selected Problems

 

Radical Reactions

RR1.  Introduction to Radicals

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

RR9.  Radical Polymerization

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

OC3.  The Diels Alder Reaction

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

ER2. Pinacol Rearrangement

ER3. Baeyer-Villiger Rearrangement

ER4.  Beckmann 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

MP5. Coordination Polymers

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

SM2. Cationic Polymerization

SM3. Living Cationic Polymerization

SM4. Anionic Polymerization

SM5. Living Anionic Polymerization

SM6. Ring-Opening Polymerization

SM7. Radical 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

PP6.  Microphase Separation

PP7.  Stress-Strain Relationships

PP8.  Storage & Loss Modulus

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

DI3. Trapping Intermediates

DI4.  Radical Clocks

DI5. Site-Directed Mutagenesis

DI6.  Solutions to Selected Problems

 

Part VII.  Appendices

AX. Appendix: Useful Tables

The Elements

The Periodic Table

Periodicity and Electronegativity

Pauling Electronegativity Values

Periodicity and Covalent Radius

Periodicity and Ionic Radius

 Structure Determination & Spectroscopy

IR Spectroscopy

NMR Spectroscopy

Spectrochemical Series

Reactions

pKa Values

Standard Reduction Potentials

Biochemistry

Amino Acids Table

Organic Chemistry

Abbreviations for Solvents

Abbreviations for Reagents

Inorganic Chemistry

Examples of Ligands

 

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

Roadmap Problems

 

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.

Creative Commons License
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.

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