Text Contents

Jonathan W. Steed and Jerry L. Atwood

Contents (2nd Edition)

Chapter 1: Concepts1.1 Definition and Development of Supramolecular Chemistry

• 1.1.1 What is Supramolecular Chemistry?
• 1.1.2 Host – Guest Chemistry
• 1.1.3 Development

1.2 Classification of Supramolecular Host-Guest Compounds

1.3 Receptors, Coordination and the Lock and Key Analogy

1.4 Binding Constants

• 1.4.1 Definition and Use
• 1.4.2 Measurement of Binding Constants

1.5 Co-operativity and the Chelate and Effect

1.6 Preorganisation and Complementarity

1.7 Kinetic and Thermodynamic Selectivity

1.8 Nature of Supramolecular Interactions

• 1.8.1 Ion-Ion Interactions
• 1.8.2 Ion-Dipole Interactions
• 1.8.3 Dipole-Dipole Interactions
• 1.8.4 Hydrogen Bonding
• 1.8.5 Cation-π Interactions
• 1.8.6 Anion-π Interactions
• 1.8.7 π-π Interactions
• 1.8.8 Van der Waals Forces and Crystal Close Packing
• 1.8.9 Closed Shell Interactions

1.9 Solvation and Hydrophobic Effects

• 1.9.1 Hydrophobic Effects
• 1.9.2 Solvation

1.10 Supramolecular Concepts and Design

• 1.10.1 Host Design
• 1.10.2 Informed and Emergent Complex Matter
• 1.10.3 Nanochemistry

Chapter 2: The Supramolecular Chemistry of Life2.1 Biological Inspiration for Supramolecular Chemistry

2.2 Alkali Metal Cations in Biochemistry

• 2.2.1 Membrane Potentials
• 2.2.2 Membrane Transport
• 2.2.3 Rhodopsin: A Supramolecular Photonic Device

2.3 Porphyrins and Tetrapyrrole Macrocycles

2.4 Supramolecular Features of Plant Photosynthesis

• 2.4.1 The Role of Magnesium Tetrapyrrole Complexes
• 2.4.2 Manganese Catalysed Oxidation of Water to O2

2.5 Uptake and Transport of O2 by Haemoglobin

2.6 Enzymes and Coezymes

• 2.6.1 Characteristics of Enzymes
• 2.6.2 Mechanism of Enzymatic Catalysis
• 2.6.3 Coenzymes
• 2.6.4 The Example of Coenzyme B12

2.7 Neurotransmitters and Hormones

2.8 Semiochemistry in the Natural World

2.9 DNA

• 2.9.1 DNA Structure and Function
• 2.9.2 Site Directed Mutagenesis
• 2.9.3 The Polymerase Chain Reaction
• 2.9.4 Binding to DNA
• 2.9.5 DNA Polymerase: A Processive Molecular Machine

2.10 Biochemical Self-Assembly

Chapter 3: Cation Binding Hosts
3.1 Introduction to Coordination Chemistry

• 3.1.1 Supramolecular Cation Coordination Chemistry
• 3.1.2 Useful Concepts in Coordination Chemistry
• 3.1.3 EDTA – a Classical Supramolecular Host

3.2 The Crown Ethers

• 3.2.1 Discovery and Scope
• 3.2.2 Synthesis

3.3 Lariat Ethers and Podands

• 3.3.1 Podands
• 3.3.2 Lariat Ethers
• 3.3.3 Bibracchial Lariat Ethers

3.4 The Cryptands

3.5 The Spherands

3.6 Nomenclature of Cation Binding Macrocycles

3.7 Selectivity of Cation Complexation

• 3.7.1 General Considerations
• 3.7.2 Conformational Characteristics of Crown Ethers
• 3.7.3 Chelate Ring Size and Donor Group Orientation Effects
• 3.7.4 Cation Binding by Crown Ethers
• 3.7.5 Cation Binding by Lariat Ethers
• 3.7.6 Cation Binding by Cryptands
• 3.7.7 Preorganisation: Thermodynamic Effects
• 3.7.8 Preorganisation: Kinetic and Dynamic Effects

3.8 Solution Behaviour

• 3.8.1 Solubility Properties
• 3.8.2 Solution Applications

3.9 Synthesis: The Template Effect and High Dilution

• 3.9.1 The Template Effect
• 3.9.2 High Dilution Synthesis

3.10 Soft Ligands for Soft Metal Ions

• 3.10.1 Nitrogen and Sulfur Analogues of Crown Ethers
• 3.10.2 Nitrogen and Sulfur Analogues of Cryptands
• 3.10.3 Azamacrocycles: Basicity Effcts and the Example of Cyclam
• 3.10.4 Phosphorus-Containing Macrocycles
• 3.10.5 Mixed Cryptates
• 3.10.6 Schiff Bases
• 3.10.7 Phthalocyanines
• 3.10.8 Torands

3.11 Proton Binding: The Simplest Cation

• 3.11.1 Oxonium Ion Binding by Macrocycles in the Solid State
• 3.11.2 Solution Chemistry of Proton Complexes

3.12 Complexation of Organic Cations

• 3.12.1 Binding of Ammonium Cations by Corands
• 3.12.2 Binding of Ammonium Cations by Three Dimensional Hosts
• 3.12.3 Ditopic Receptors
• 3.12.4 Chiral Recognition
• 3.12.5 Amphiphilic Receptors
• 3.12.6 Case Study: Herbicide Receptors

3.13 Alkalides and Electrides

3.14 The Calixarenes

• 3.14.1 Cation Complexation by Calixarenes
• 3.14.2 Phase Transport Equilibria
• 3.14.3 Cation Complexation by Hybrid Calixarenes

3.15 Cation-π Complexes

• 3.15.1 Mixed C-Heteroatom Hosts
• 3.15.2 Hydrocarbon Hosts

3.16 The Siderophores

• 3.16.1 Naturally Occurring Siderophores
• 3.16.2 Synthetic Systems

Chapter 4: Anion Binding
4.1 Introduction

• 4.1.1 Scope
• 4.1.2 Challenges in Anion Receptor Chemistry

4.2 Biological Anion Receptors

• 4.2.1 Anion Binding Proteins
• 4.2.2 Argenine as an Anion Binding Site
• 4.2.3Main Chain Anion Binding Sites in Proteins: Nests
• 4.2.4 Pyrrole-Based Biomolecules

4.3 Concepts in Anion Host Design

• 4.3.1 Preorganisation
• 4.3.2 Entropic Considerations
• 4.3.3 Considerations Particular to Anions

4.4 From Cation Hosts to Anion Hosts – a Simple Change in pH

• 4.4.1 Tetrahedral Receptors
• 4.4.2 Shape Selectivity
• 4.4.3 Ammonium-Based Podands
• 4.4.4 Two Dimensional Hosts
• 4.4.5 Cyclophane Hosts

4.5 Guanidinium-Based Receptors

4.6 Neutral Receptors

• 4.6.1 Zwitterions
• 4.6.2 Amide-Based Hosts
• 4.6.3 Urea and Thiourea Derivatives
• 4.6.4 Pyrrole Derivatives
• 4.6.5 Peptide-Based Receptors

4.7 Inert Metal-Containing Receptors

• 4.7.1 General Considerations
• 4.7.2 Organometallic Receptors
• 4.7.3 Hydride Sponge and Other Lewis Acid Chelates
• 4.7.4 Anticrowns

4.8 Common Core Scaffolds

• 4.8.1 The Trialkylbenzene Motif
• 4.8.3 Cholapods

Chapter 5: Ion Pair Receptors5.1 Simultaneous Anion and Cation Binding

• 5.1.1 Concepts
• 5.1.2 Contact ion pairs
• 5.1.3 Cascade receptors
• 5.1.4 Remote Anion and Cation Binding Sites
• 5.1.5 Symport and Metal Extraction
• 5.1.6 Dual Host Salt Extraction

5.2 Labile Coordination Complexes as Anion Hosts

5.3 Receptors for Zwitterions

Chapter 6: Molecular Guests in Solution6.1 Molecular Hosts and Molecular Guests

• 6.1.1 Introduction
• 6.1.2 Some General Considerations

6.2 Intrinsic Curvature: Guest Binding by Cavitands

• 6.2.1 Building Blocks
• 6.2.2 Calixarenes and Resorcarenes
• 6.2.3 Dynamics of Guest Exchange in Cavitates
• 6.2.4 Glycouril-Based Hosts

6.3 Cyclodextrins

• 6.3.1 Introduction and Properties
• 6.3.2 Preparation
• 6.3.3 Inclusion Chemistry
• 6.3.4 Industrial Applications

6.4 Molecular Clefts and Tweezers

6.5 Cyclophane Hosts

• 6.5.1 General Aspects
• 6.5.2 Cyclophane Nomenclature
• 6.5.3 Cyclophane Synthesis
• 6.5.4 Molecular ‘Iron Maidens’
• 6.5.5 From Tweezers to Cyclophanes
• 6.5.6 The Diphenylmethane Moiety
• 6.5.7 Guest Inclusion by Hydrogen Bonding
• 6.5.8 Charge-Transfer Cyclophanes

6.6 The Cryptophanes

• 6.6.1 Construction of Containers from a Curved Molecular Building Block
• 6.6.2 Complexation of Halocarbons
• 6.6.3 Competition with Solvent
• 6.6.4 Complexes with Alkyl Ammonium Ions
• 6.6.5 Methane and Xenon Complexation

6.7 Covalent Cavities: Carcerands and Hemicarcerands

• 6.7.1 Definitions and Synthesis
• 6.7.2 Template Effects in Carcerand Synthesis
• 6.7.3 Complexation and Constrictive Binding
• 6.7.4 Carcerism
• 6.7.5 Inclusion reactions
• 6.7.6 Giant Covalent Cavities

Chapter 7: Solid-State Inclusion Compounds7.1 Solid-State Host-Guest Compounds

7.2 Clathrate Hydrates

• 7.2.1 Formation
• 7.2.2 Structures and Properties
• 7.2.3 Problems and Applications

7.3 Urea and Thiourea Clathrates

• 7.3.1 Structure
• 7.3.2 Guest Order and Disorder
• 7.3.3 Applications of Urea Inclusion Compounds

7.4 Other Channel Clathrates

• 7.4.1 Trimesic Acid
• 7.4.2 Helical Tubulands and Other Di-ols
• 7.4.3 Perhydrotriphenylene: Polarity Formation

7.5 Hydroquinone, Phenol, Dianin’s Compound and The Hexahost Strategy

7.6 Tri-o-thymotide

• 7.6.1 Inclusion Chemistry
• 7.6.2 Synthesis and Derivatives
• 7.6.3 Applications

7.7 Cyclotriveratrylene

• 7.7.1 Properties
• 7.7.2 Synthesis
• 7.7.3 Inclusion Chemistry

7.8 Inclusion Compounds of the Calixarenes

• 7.8.1 Organic-Soluble Calixarenes
• 7.8.2 Fullerene Complexation
• 7.8.3 Water-Soluble Calixarenes

7.9 Solid-Gas and Solid-Liquid Reactions

• 7.9.1 The Importance of Gas Sorption
• 7.9.2 Gas and Liquid Sorption by Calixarenes
• 7.9.3 Gas Sorption by Channel Hosts
• 7.9.4 Gas Sorption by Coordination Complex Hosts

Chapter 8: Crystal Engineering8.1 Concepts

• 8.1.1 Introduction
• 8.1.2 Tectons and Synthons
• 8.1.3 The Special Role of Hydrogen Bonding

8.2 Crystal Nucleation and Growth

• 8.2.1 Theory of Crystal Nucleation and Growth
• 8.2.2 NMR Spectroscopy as a Tool to Probe Nucleation
• 8.2.3 Crystal Growth at Air-Liquid Interfaces
• 8.2.4 Chirality Induction: The Adam Effect
• 8.2.5 Dyeing Crystal Interfaces
• 8.2.6 Hourglass Inclusions
• 8.2.7 Epitaxy: Engineering Crystals
• 8.2.8 Crystals as Genes?
• 8.2.9 Mechanochemistry and Topochemistry

8.3 Understanding Crystal Structures

• 8.3.1 Graph Set Analysis
• 8.3.2 Etter’s Rules
• 8.3.3 Crystal Deconstruction
• 8.3.4 Crystal Engineering Design Strategies

8.4 The Cambridge Structural Database

8.5 Polymorphism

• 8.5.1 The Importance of Polymorphism
• 8.5.2 Types of Polymorphism
• 8.5.3 Controlling Polymorphism

8.6 Co-crystals

• 8.6.1 Scope and Nomenclature
• 8.6.2 Designer Co-crystals
• 8.6.3 Hydrates

8.7 Z’ > 1

8.8 Crystal Structure Prediction

• 8.8.1 Soft Predictions
• 8.8.2 Computational Methods
• 8.8.3 The CCDC Blind Tests

8.9 Hydrogen Bond Synthons – Common and Exotic

• 8.9.1 Hydrogen bonded rings
• 8.9.2 Hydrogen bonds to halogens
• 8.9.3 Hydrogen bonds to cyanometallates
• 8.9.4 Hydrogen bonds to carbon monoxide ligands
• 8.9.5 Hydrogen bonds to metals and metal hydrides
• 8.9.6 CH donor hydrogen Bonds

8.10 Aromatic Rings

• 8.10.1 Edge-to-Face and Face-to-face Interactions
• 8.10.2 Aryl Embraces
• 8.10.3 Metal-π interactions

8.11 Halogen Bonding and Other Interactions

8.12 Crystal Engineering of Diamondoid Arrays

Chapter 9: Network Solids9.1 Definitions

• 9.1.1 Concepts and Classification
• 9.1.2 Network Topology
• 9.1.3 Porosity

9.2 Zeolites

• 9.2.1 Composition and Structure
• 9.2.2 Synthesis
• 9.2.3 MFI Zeolites in the Petroleum Industry

9.3 Layered Solids and Intercalates

• 9.3.1 General Characteristics
• 9.3.2 Graphite Intercalates
• 9.3.3 Controlling the Layers: Guanidinium Sulfonates

9.4 In the Beginning: Hoffman Inclusion Compounds and Werner Clathrates

9.5 Coordination Polymers

• 9.5.1 Coordination Polymers, MOFs and Other Terminology
• 9.5.2 0D Coordination Clusters
• 9.5.3 1D, 2D and 3D Structures
• 9.5.4 Magnetism
• 9.5.5 Negative Thermal Expansion
• 9.5.6 Interpenentrated Structures
• 9.5.7 Porous and Cavity-Containing Structures
• 9.5.8 Metal-Organic Frameworks
• 9.5.9 Catalysis by MOFs
• 9.5.10 Hydrogen Storage by MOFs

Chapter 10: Self-Assembly10.1 Introduction

• 10.1.1 Scope and Goals
• 10.1.2 Concepts and Classification

10.2 Proteins and Foldamers: Single Molecule Self-Assembly

• 10.2.1 Protein Self-Assembly
• 10.2.2 Foldamers

10.3 Biochemical Self-Assembly

• 10.3.1 Strict Self-Assembly: The Tobacco Mosaic Virus and DNA
• 10.3.2 Self-Assembly with Covalent Modification

10.4 Self-Assembly in Synthetic Systems: Kinetic and Thermodynamic Considerations

• 10.4.1 Template Effects in Synthesis
• 10.4.2 A Thermodynamic Model: Self-Assembly of Zinc Porphyrin Complexes
• 10.4.3 Cooperativity and the Extended Site Binding Model
• 10.4.4 Double Mutant Cycles – Quantifying Weak Interactions
• 10.4.5 Probability of Self-Assembly

10.5 Self-Assembling Coordination Compounds

• 10.5.1 Design and Notation
• 10.5.2 A Supramolecular Cube
• 10.5.3 Molecular Squares and Boxes
• 10.5.4 Self Assembly of Metal Arrays

10.6 Self-Assembly of Closed Complexes by Hydrogen Bonding

• 10.6.1 Tennis Balls and Softballs: Self-Complementary Assemblies
• 10.6.2 Heterodimeric Capsules
• 10.6.3 Giant Self-Assembling Capsules
• 10.6.4 Rosettes

10.7 Catenanes and Rotaxanes

• 10.7.1 Overview
• 10.7.2 Statistical Approaches to Catenanes and Rotaxanes
• 10.7.3 Rotaxanes and Catenanes Involving Stacking Interactions
• 10.7.4 Hydrogen Bonded Rotaxanes and Catenanes
• 10.7.5 Metal and Auxiliary Linkage Approaches to Catenanes and Rotaxanes
• 10.7.6 Molecular Necklaces

10.8 Helicates and Helical Assemblies

• 10.8.1 Introduction
• 10.8.2 Synthetic Considerations
• 10.8.3 [4 + 4] Helicates
• 10.8.4 [6 + 6] Helicates
• 10.8.5 Self Recognition and Positive Cooperativity
• 10.8.6 Cyclic Helicates
• 10.8.7 Anion-Based Helices
• 10.8.8 Hydrogen Bonded Helices

10.9 Molecular Knots

• 10.9.1 The Topology of Knots
• 10.9.2 Trefoil Knots
• 10.9.3 Other Knots
• 10.9.4 Borromean Rings

Chapter 11: Molecular Devices11.1 Introduction

• 11.1.1 Philosophy of Molecular Devices
• 11.1.2 When is a Device Supramolecular?

11.2 Supramolecular Photochemistry

• 11.2.1 Photochemical Fundamentals
• 11.2.2 Mechanisms of Energy and Electron Transfer
• 11.2.3 Bimetallic Systems and Mixed Valence
• 11.2.4 Bipyridine and Friends as Device Components
• 11.2.5 Bipyridyl-Type Light Harvesting Devices
• 11.2.6 Light Conversion Devices
• 11.2.7 Non-Covalently Bonded Systems

11.3 Information and Signals: Semiochemistry and Sensing

• 11.3.1 Supramolecular Semiochemistry
• 11.3.2 Semiochemistry in the Natural World
• 11.3.3 Photophysical Sensing and Imaging
• 11.3.4 Colourimetric Sensors and the Indicator Displacement Assay
• 11.3.5 Electrochemical Sensors

11.4 Molecule-Based Electronics

• 11.4.1 Molecular Electronic Devices
• 11.4.2 Molecular Wires
• 11.4.3 Molecular Rectifiers
• 11.4.4 Molecular Switches
• 11.4.5 Molecular Logic
• 11.4.6 Towards Addressable Molecular Electronics

11.5 Molecular Analogues of Mechanical Machines

11.6 Non-Linear Optical Materials

• 11.6.1 Origins of Non-linear Optical Effects
• 11.6.2 Second Order NLO Materials
• 11.6.3 Third Harmonic Generation NLO Materials

Chapter 12: Biological Mimics and Supramolecular Catalysis12.1 Introduction

• 12.1.1 Understanding and Learning from Biochemistry
  
• 12.1.2 Characteristics of Biological Models
  

12.2 Cyclodextrins as Enzyme Mimics

• 12.2.1 Enzyme Modelling Using an Artificial Host Framework
• 12.2.2 Cyclodextrins as Esterase Mimics
• 12.2.3 Functionalised Cyclodextrins

12.3 Corands as ATPase Mimics

12.4 Cation Binding Hosts as Transacylase Mimics

• 12.4.1 Chiral Corands
• 12.4.2 A Structure and Function Mimic

12.5 Metallobiosites

• 12.5.1 Haemocyanin Models
• 12.5.2 Zinc-Containing Enzymes

12.6 Heme Analogues

• 12.6.1 Models of O2 Uptake and Transport
• 12.6.2 Cytochrome P-450 Models
• 12.6.3 Cytochrome c Oxidase Models

12.7 Vitamin B12 Models

12.8 Ion Channel Mimics

12.9 Supramolecular Catalysis

• 12.9.1 Abiotic Supramolecular Catalysis
• 12.9.2 Dynamic Combinatorial Libraries
• 12.9.3 Self-Replicating Systems
• 12.9.4 Emergence of Life

Chapter 13: Interfaces and Liquid Assemblies13.1 Order in Liquids

13.2 Surfactants and Interfacial Ordering

• 13.2.1 Surfactants, Micelles and Vesicles
• 13.2.2 Surface Self-Assembled Monolayers

13.3 Liquid Crystals

• 13.3.1 Nature and Structure
• 13.3.2 Design of Liquid Crystalline Materials
• 13.3.3 Supramolecular Liquid Crystals
• 13.3.4 Liquid Crystalline Polymers
• 13.3.5 Applications: Liquid Crystal Displays

13.4 Ionic Liquids

13.5 Liquid Clathrates

Chapter 14: Supramolecular Polymers, Gels and Fibres14.1 Introduction

14.2 Dendrimers

• 14.2.1 Structure and Nomenclature
• 14.2.2 Preparation and Properties of Molecular Dendrimers
• 14.2.3 Dendrimer Host-Guest Chemistry
• 14.2.4 Supramolecular Dendrimer Assemblies
• 14.2.5 Dendritic Nanodevices

14.3 Covalent Polymers with Supramolecular Properties

• 14.3.1 Amphiphilic Block Copolymers
• 14.3.2 Molecular Imprinted Polymers

14.4 Self-Assembled Supramolecular Polymers

14.5 Polycatenanes and Polyrotaxanes

14.6 Biological Self-Assembled Polymers and Fibres

• 14.6.1 Amyloids, Actins and Fibrin
• 14.6.2 Bacterial S-Layers

14.7 Supramolecular Gels

14.8 Polymeric Liquid Crystals

Chapter 15: Nanochemistry15.1 When is Nano really Nano?

15.2 Nanotechnology: the ‘top down’ and ‘bottom up’ approaches

15.3 Templated and Biomimetic Solids, and Emergence

15.4 Nanocale Photonics

15.5 Micro- and Nanofabrication

15.6 Assembly and Manipulation on the Nanoscale

• 15.6.1 Chemistry with a Microscope Tip
• 15.6.2 Self-Assembly on Surfaces
• 15.6.3 Addressing Single Molecules
• 15.6.4 Atomic-Level Assembly of Materials

15.7 Nanoparticles

• 15.7.1 Nanoparticles and Colloids: Definition and Description
• 15.7.2 Gold Nanoparticles
• 15.7.3 Quantum Dots
• 15.7.4 Non-Spherical Nanoparticles

15.8 Endohedral Fullerenes, Nanotubes and Graphene

• 15.8.1 Fullerenes as Hosts
• 15.8.2 Carbon Nanotubes
• 15.8.3 Graphene
• 15.8.4 Afterword – Damascus Steel