Halogen Bonding in Solution

Stefan Huber is Associate Professor of organic chemistry at Ruhr-University Bochum, Germany. His research interest is the development of applications for halogen bonding and chalcogen bonding in solution, with a strong focus on organocatalysis and molecular recognition. He has, inter alia, received an ERC Starting Grant, the Hoechst Dozentenpreis by the Aventis Foundation and the Robert-Sauer-Prize of the Bavarian Academy of Sciences.

• Preface xi1 Halogen Bonding: An Introduction 1Daniel A. Decato, Eric A. John and Orion B. Berryman1.1 Introduction 11.1.1 The Halogen Bond: Definition, Characteristics, Representations, and Parallels to the Hydrogen Bond 21.1.2 Parallels to the Hydrogen Bond 31.1.3 Notation and Terminology 41.1.4 Solid-state Halogen Bond Contacts 41.1.5 Halogen Bond Features 51.1.6 Additional Nomenclature 61.2 Historical Perspective 61.2.1 Rediscovery 101.3 Crystallographic Studies 111.3.1 CSD Evaluations 121.3.2 Fundamental Studies and Halogen Bond–Hydrogen Bond Interplay 131.3.3 Metal Complexes and Charge-assisted Halogen Bonding Systems 171.3.4 Alternative Motifs and Solid-state Reactivity 191.3.5 Crystallographic Studies Conclusion 201.4 Computational Studies 211.4.1 Introduction 211.4.2 Electrostatics of the Halogen Bond and the σ-Hole 211.4.3 Limitations on Electrostatic Potential 241.4.4 Atomic Orbital Theory and the σ-Hole 241.4.5 Charge Transfer 241.4.6 Dispersion and Polarization Component 251.4.7 Decomposition 261.4.8 Biological Computation of Halogen Bonding 261.4.9 Computational Conclusion 271.5 Materials 281.5.1 Introduction 281.5.2 Liquid Crystals 281.5.3 Supramolecular Polymers 291.5.3.1 LC Polymers 291.5.3.2 Light-sensitive Polymers 301.5.3.3 Block Polymers 301.5.3.4 Self-healing Polymers 311.5.4 Supramolecular Gels 311.5.5 Materials Conclusion 331.6 Conclusion 33Acknowledgments 34References 342 Thermodynamics of Halogen Bonding in Solution 43Mark S. Taylor2.1 Introduction 432.2 Molecular Halogens and Interhalogens 442.2.1 Uncharged Lewis Bases 442.3 N-Halo and N-Halonium Compounds 462.4 Haloalkynes 472.4.1 Uncharged Lewis Bases 472.5 Haloarenes 512.5.1 Uncharged Lewis Bases 512.5.2 Anionic Lewis Bases 582.6 Halogenated Heterocycles 612.6.1 Uncharged Lewis Bases 622.6.2 Anionic Lewis Bases 642.7 Haloalkanes and Haloalkenes 672.7.1 Uncharged Lewis Bases 672.7.2 Anionic Lewis Bases 712.8 Summary and Outlook 72References 733 Recognition with Macrocycles and Interlocked Systems 83Andrew Docker and Paul D. Beer3.1 Introduction 833.2 Recognition by XB Macrocyclic Hosts 863.3 XB Interlocked Hosts for Recognition and Sensing 873.3.1 XB-Anion Templation of Interlocked Molecules 903.3.2 [2]Rotaxane Hosts for Anion Recognition 923.3.3 [2]Catenanes for Anion Recognition 973.3.4 XB Interlocked Hosts Constructed via Active Metal Template Methodology 1003.3.5 Interlocked Host Molecules for Sensing Applications 1073.4 Foldamer Architectures for Recognition 1133.5 Summary and Conclusions 117References 1184 The Three-Center Halogen Bond 121Lotta Turunen and Máté Erdélyi4.1 Introduction 1214.2 Three-Center Halogen Bond 1224.2.1 Features of the Three-Center Halogen Bond 1234.2.1.1 Symmetry and Dynamics of the Three-Center Halogen Bonds 1234.2.1.2 The Influence of the Identity of Halonium Ions 1264.2.1.3 The Influence of Lewis Basicity 1284.2.1.4 The Influence of Solvent and Counterions 1314.2.2 The Three-Center Halogen Bond of N-Halosuccinimides and N-Halosaccharins 1324.2.3 Trihalide Ions 1344.2.4 Stability of the Three-Center Halogen Bond 1354.3 Synthetic Applications 1374.3.1 Halonium Transfer Reactions 1374.3.2 Oxidation Reactions 1404.3.3 Enantioselective Halogenations 1414.4 Three-Center Halogen Bonds in Supramolecular Chemistry 1434.5 Summary and Conclusions 147References 1485 Spectroscopy of Halogen Bonding in Solution 153Scott Wilcox, Wouter Herrebout and Mate Erdelyi5.1 Introduction 1535.2 Vibrational Spectroscopy 1545.3 UV–vis Spectroscopy 1585.4 NMR Spectroscopy 1605.4.1 Solvent Effects 1615.4.2 Entropic Effects on Halogen Bonding 1655.4.3 NMR Titration Studies 1685.4.3.1 Direct Detection Techniques 1695.4.3.2 Indirect Detection Techniques 1765.4.4 Nuclear Overhauser Effect (NOE) NMR Spectroscopy 1785.4.4.1 Homonuclear NOE Spectroscopy 1785.4.4.2 Heteronuclear NOE Spectroscopy 1815.4.5 Diffusion NMR 1825.4.6 The Isotopic Perturbation of Equilibrium Method 1845.5 ESR Spectroscopy 1855.6 Summary and Conclusions 187Acknowledgments 189References 1896 Anion Transport in Lipid Bilayer Membranes Using Halogen Bonds 195Andreas Vargas Jentzsch and Stefan Matile6.1 Introduction 1956.1.1 Halogen Bonding in the Context of Ion Transport 1966.1.2 Organization of This Chapter 1986.2 Macrocyclic Systems 1986.2.1 Calix[4]arenes 1986.2.1.1 Synthesis 1996.2.1.2 Ion Transport 1996.2.2 Oxacalix[2]arene[2]triazine 2036.2.2.1 Synthesis 2036.2.2.2 Anion Binding Studies 2036.2.2.3 Crystallographic Studies 2036.2.2.4 Ion Transport 2046.2.2.5 Anticancer Activity 2056.3 Small Molecules 2096.3.1 Iodoperfluoroarenes 2096.3.2 Iodoperfluoroalkanes 2106.3.3 Conductance Experiments in Planar Lipid Bilayers with Small Molecules 2156.3.4 Elucidating the Mechanism of Transport with Small Molecules 2166.3.4.1 Membrane Composition in the HPTS Assay 2166.3.4.2 Hill Coefficients 2176.3.4.3 Molecular Modeling: DFT Calculations 2176.3.4.4 Crystal Structures 2186.4 Halogen Bonding Ion Channels 2186.4.1 Halogen Bonding Cascades 2196.4.1.1 Synthesis 2196.4.1.2 Ion Transport 2196.4.2 Halogen Bonding Self-Assembled Pores and Channels 2226.4.2.1 Synthesis 2226.4.2.2 Ion Transport 2236.4.2.3 Conductance Experiments in Planar Lipid Bilayers 2256.4.2.4 Molecular Dynamics Simulations 2256.4.2.5 Anticancer Activity 2256.5 Discussion and Perspectives 2256.6 Summary 227Acknowledgments 229References 2297 Catalysis by Molecular Iodine 233Jonas J. Koenig and Martin Breugst7.1 Introduction 2337.2 Proposed Activation Mechanisms 2347.2.1 Halogen-Bond Catalysis 2357.2.2 Iodonium-Ion Catalysis 2367.2.3 Brønsted-Acid Catalysis 2387.3 Applications in Catalysis 2397.3.1 Scope and Aim 2397.3.2 Michael Additions 2397.3.3 Knoevenagel Condensations 2427.3.4 Cycloadditions and Related Reactions 2437.3.5 Nazarov-type Reactions 2477.3.6 Esterifications and Transesterifications 2497.3.7 Acetalizations and Related Reactions 2527.3.8 Etherification 2547.3.9 Friedel–Crafts Alkylations and Arylations 2557.3.10 Isomerization of Double Bonds 2577.3.11 Polymerization 2597.3.12 Cascade Reactions 2597.4 Summary and Conclusions 263References 2638 Halogen Bonding in Organocatalysis 269Revannath L. Sutar8.1 Introduction 2698.2 Organic Reactions Involving XB as Primary Interaction 2708.2.1 Activation of Halocarbons 2728.2.2 Activation of Organic Functional Groups 2798.2.3 XB Organocatalysis Through π-Activation 2898.2.4 Asymmetric Catalysis Through Halogen Bonding 2928.3 Reactions Involving XB as Secondary Interaction 2978.4 Conclusion 301References 3019 Halogen Bonding in Electrochemistry 307Claire Fave and Bernd Schöllhorn9.1 Introduction 3079.2 Methods 3099.3 Electrochemistry for Crystal Engineering: Mixed Valence Crystal Structures 3119.4 Redox Switching in Homogeneous Solution 3129.4.1 Concept 3129.4.2 Redox-Active XB Acceptors 3139.4.2.1 Quinones 3139.4.3 Redox-Active XB Donors 3159.4.3.1 Ferrocenes 3159.4.3.2 Tetrathiafulvalenes 3189.4.3.3 Viologens 3239.5 Interfacial Halogen Bonding 3249.5.1 Anion Detection on Self-Assembled Monolayers 3249.5.2 Photovoltaic Systems 3279.6 Activation of Covalent Bonds 3289.6.1 XB-Mediated Redox Reactions: A Perspective 3289.7 Conclusions 329References 33010 Halogen Bonds in Biomolecular Engineering 335Pui S. Ho and Derek M. Anderson10.1 Introduction to Biomolecular Engineering and Halogen Bonds 33510.2 Halogen Bonds in Nucleic Acids 34010.2.1 Controlling DNA Assembly and Structure 34210.2.2 Controlling Conformation 34410.2.3 Structure–Energy Relationships 34410.3 Halogen Bonds in Peptides and Proteins 34610.3.1 Halogen Bonds in Amino Acids and Peptides 34710.3.2 Halogen Bonds Engineered into Proteins 35010.4 Conclusions and Perspectives 35310.4.1 Expanding the Genetic Alphabet 35310.4.2 Multimeric Assemblies 35310.4.3 New Catalysts 35510.4.4 Need for Computational Tools 35510.4.5 Conclusion 356Acknowledgments 356References 35611 The Chalcogen Bond in Solution: Synthesis, Catalysis and Molecular Recognition 363Kamran T. Mahmudov, Vusala A. Aliyeva, M. Fátima C. Guedes da Silva and Armando J. L. Pombeiro11.1 Introduction 36311.2 Chalcogen Bonding in Synthesis 36711.3 Chalcogen Bonding in Catalysis 37111.4 Chalcogen Bonding in Molecular Recognition 37511.5 Conclusions 378Acknowledgments 379References 380Index 383