Metallofoldamers Supramolecular Architectures from Helicates to Biomimetics

Professor Dr. Markus Albrecht: Institut für Organische Chemie, RWTH Aachen, Germany
Professor Albrecht was born in 1964 and studied Chemistry in Würzburg and Münster, spending time as a postdoctoral fellow in the laboratories of Professor Kenneth N. Raymond in Berkeley, and a habilitation at the Institute of Organic Chemistry of the University of Karlsruhe. Since 2002 he has been Professor of Organic Chemistry at the RWTH Aachen, where his main topics of investigation are the self-assembly, structure and property of helicates, and influencing peptide conformations by metal coordination.

Dr. Galia Maayan: The Department of Chemistry, University of Florida, USA
Dr Maayan was born in 1974 and studied Chemistry at Tel Aviv University and at The Weizmann Institute of Science, Israel. She is currently a postdoctoral research associate with Professor Michael D. Ward and Kent Kirshenbaum, in the Molecular Design Institute at New York University, investigating the interaction between biomimetic foldamers and metal ions.

List of Contributors XI

Foreword XIII

Preface XV

1 Metalloproteins and Metallopeptides – Natural Metallofoldamers 1

Vasiliki Lykourinou, Li-June Ming

1.1 Introduction 1

1.2 Metalloproteins 2

1.2.1 Metalloproteins are Nature’s “Metallofoldamers!” 2

1.2.2 Metal-Triggered Conformational Change of Proteins 3

1.2.3 Conformational Change of Metalloproteins Caused by Ligand Binding 7

1.2.4 Protein Misfolding: Causes and Implications – Cu, Zn-Superoxide Dismutase 10

1.3 Metallopeptides 12

1.3.1 Antibiotic Metallopeptides 13

1.3.2 Metallopeptides in Neurodegenerative Diseases 20

1.3.3 Other Metallopeptides 24

1.4 Conclusion and Perspectives 28

References 30

2 Introduction to Unnatural Foldamers 51

Claudia Tomasini, Nicola Castellucci

2.1 General Definition of Foldamers 51

2.2 Biotic Foldamers 53

2.2.1 Homogeneous Foldamers 53

2.2.2 b-Peptides 53

2.2.3 g-Peptides 59

2.2.4 Hybrid Foldamers 60

2.2.5 Aliphatic Urea Foldamers 63

2.2.6 Foldamers of a-Aminoxy Acids 64

2.2.7 Foldamers Containing Amido Groups 65

2.3 Abiotic Foldamers 70

2.4 Organization Induced by External Agents 72

2.4.1 Organization Induced by Solvents 72

2.4.2 Organization Induced by Anions 73

2.5 Applications 78

2.6 Conclusions and Outlook 81

References 81

3 Self-Assembly Principles of Helicates 91

Josef Hamacek

3.1 Introduction 91

3.2 Thermodynamic Considerations in Self-Assembly 93

3.2.1 Mononuclear Coordination Complexes 93

3.2.2 Extension to Polynuclear Edifices 96

3.3 Cooperativity in Self-Assembly 100

3.3.1 Allosteric Cooperativity 101

3.3.2 Chelate Cooperativity 102

3.3.3 Interannular Cooperativity 104

3.4 Kinetic Aspects of Multicomponent Organization 104

3.5 Understanding Self-Assembly Processes 108

3.5.1 Assessment of Cooperativity 108

3.5.2 Thermodynamic Modelling 110

3.5.3 Solvation Energies and Electrostatic Interactions 115

3.6 Secondary Structure and Stabilizing Interactions 118

3.7 Conclusions 118

References 120

4 Structural Aspects of Helicates 125

Martin Berg, Arne L€utzen

4.1 Introduction 125

4.2 Structural Dynamics 127

4.3 Template Effects 129

4.4 Sequence Selectivity 130

4.5 Self-Sorting Effects in Helicate Formation 135

4.6 Diastereoselectivity I – “Meso”-Helicate versus Helicate Formation 138

4.7 Diastereoselectivity II – Enantiomerically Pure Helicates from Chiral Ligands 139

4.7.1 2,20-Bipyridine Ligands 140

4.7.2 2,20:60,200-Terpyridine and 2,20:60,200:600,2-Quaterpyridine Ligands 143

4.7.3 2-Pyridylimine Ligands 144

4.7.4 Further Hexadentate N-Donor Ligands 144

4.7.5 Oxazoline Ligands 144

4.7.6 P-Donor Ligands 145

4.7.7 Hydroxamic Acid Ligands 147

4.7.8 b-Diketonate Ligands 147

4.7.9 Catecholate Ligands and Other Dianionic Ligand Units 148

4.7.10 Non-Covalently Assembled Ligand Strands 150

4.8 Summary and Outlook 150

References 151

5 Helical Structures Featuring Thiolato Donors 159

F. Ekkehardt Hahn, Dennis Lewing

5.1 Introduction 159

5.2 Coordination Chemistry of Bis- and Tris(Benzene-o-Dithiolato) Ligands 162

5.2.1 Mononuclear Chelate Complexes 162

5.2.2 Dinuclear Double-Stranded Complexes 165

5.2.3 Dinuclear Triple-Stranded Complexes 167

5.2.4 Coordination Chemistry of Tripodal Tris(Benzene-o-Dithiolato) Ligands 172

5.3 Coordination Chemistry of Mixed Bis(Benzene-o-Dithiol/Catechol Ligands 176

5.3.1 Dinuclear Double-Stranded Complexes 176

5.3.2 Dinuclear Triple-Stranded Complexes 178

5.4 Subcomponent Self-Assembly Reactions 181

5.5 Summary and Outlook 186

References 186

6 Photophysical Properties and Applications of Lanthanoid Helicates 193

Jean-Claude G. B€unzli

6.1 Introduction 194

6.2 Homometallic Lanthanoid Helicates 197

6.2.1 Influence of the Triplet-State Energy on Quantum Yields 198

6.2.2 Radiative Lifetime and Nephelauxetic Effect 203

6.2.3 Site-Symmetry Analysis 206

6.2.4 Energy Transfer between Lanthanoid Ions 208

6.2.5 Lanthanoid Luminescent Bioprobes 210

6.2.6 Other Investigated Helicates 219

6.3 Heterometallic d-f Helicates 223

6.3.1 Basic Photophysical Properties 223

6.3.2 EuIII-to-CrIII Energy Transfer 227

6.3.3 Control of f-Metal Ion Properties by d-Transition Metal Ions 228

6.3.4 Sensitizing NIR-Emitting Lanthanoid Ions 235

6.4 Chiral Helicates 236

6.5 Extended Helical Structures 239

6.6 Perspectives 240

References 241

7 Design of Supramolecular Materials: Liquid-Crystalline Helicates 249

Raymond Ziessel

7.1 Introduction 249

7.2 Imino-Bipyridine and Imino-Phenanthroline Helicates 252

7.2.1 Liquid Crystals from Imino-Polypyridine Based Helicates 257

7.3 Conclusions 266

7.4 Outlook and Perspectives 267

References 268

8 Helicates, Peptide-Helicates and Metal-Assisted Stabilization

of Peptide Microstructures 275

Markus Albrecht

8.1 Introduction 275

8.2 Selected Examples of Metal Peptide Conjugates 276

8.3 Helicates and Peptide-Helicates 279

8.3.1 Helicates 279

8.3.2 Peptide-Helicates 281

8.4 Metal-Assisted Stabilization of Peptide Microstructures 288

8.4.1 Loops and Turns 288

8.4.2 a-Helices 292

8.4.3 b-Sheets 297

8.5 Conclusion 298

References 300

9 Artificial DNA Directed Toward Synthetic Metallofoldamers 303

Guido H. Clever, Mitsuhiko Shionoya

9.1 Introduction 303

9.1.1 Oligonucleotides are Natural Foldamers 303

9.1.2 Biological Functions and Beyond 305

9.1.3 DNA Nanotechnology 306

9.1.4 Interactions of DNAwith Metal Ions 308

9.2 The Quest for Alternative Base Pairing Systems 309

9.2.1 Modifications of the Hydrogen Bonding Pattern 310

9.2.2 Shape Complementarity 310

9.2.3 Metal Coordination 310

9.3 Design and Synthesis of Metal Base Pairs 311

9.3.1 Rational Design of Metal Base Pairs 311

9.3.2 Model Studies 312

9.3.3 Synthesis of Modified Nucleosides 312

9.3.4 Automated Oligonucleotide Synthesis 314

9.3.5 Enzymatic Oligonucleotides Synthesis 315

9.4 Assembly and Analysis of Metal Base Pairs Inside the DNA Double Helix 315

9.4.1 Strategies for Metal Incorporation 315

9.4.2 Analytical Characterization in Solution 316

9.4.3 X-Ray Structure Determination 317

9.5 Artificial DNA for Synthetic Metallofoldamers 318

9.5.1 Overview 318

9.5.2 The Hydroxypyridone Base Pair 320

9.5.3 The Salen Base Pair 320

9.5.4 The Imidazole, Triazole and 1-Deazaadenine-Thymine Base Pairs 323

9.6 Functions, Applications and Future Directions 324

9.6.1 Duplex Stabilization and Conformational Switching 324

9.6.2 Sensor Applications 325

9.6.3 Magnetism and Electrical Conductance 325

9.6.4 Future Directions 326

References 327

10 Metal Complexes as Alternative Base Pairs or Triplets in Natural and Synthetic Nucleic Acid Structures 333

Arnie De Leon, Jing Kong and Catalina Achim

10.1 Introduction 333

10.2 Brief Overview of Synthetic Analogues of DNA: PNA, LNA, UNA, and GNA 338

10.3 Metal-Containing, Ligand-Modified Nucleic Acid Duplexes 341

10.3.1 Design Strategy 341

10.3.2 Duplexes Containing One Alternative Metal–Ligand Base Pair with Identical Ligands 342

10.3.3 Duplexes Containing One Alternative Metal–Ligand Base Pair with Different Ligands 359

10.4 Duplexes Containing Multiple Metal Complexes 362

10.5 Metal-Containing, Ligand-Modified Nucleic Acid Triplexes 367

10.6 Summary and Outlook 367

References 372

11 Interaction of Biomimetic Oligomers with Metal Ions 379

Galia Maayan

11.1 Introduction 380

11.2 Single-Stranded Oligomers in Which Metal Coordination Templates, or Templates and Nucleates the Formation of an Abiotic Helix 381

11.3 Folded Oligomers in Which Metal Coordination Nucleates the Formation of an Abiotic Single-Stranded Helix 384

11.4 Folded Oligomers in Which Metal Coordination Enhances Secondary Structure and Leads to Higher-Order Architectures 393

11.4.1 Metal Coordination in Folded Aromatic Amide Oligomers 394

11.4.2 Metal Coordination in Peptidomimetic Foldamers 396

11.5 Concluding Remarks 402

References 402

12 Applications of Metallofoldamers 407

Yan Zhao

12.1 Introduction 407

12.2 Metallofoldamers in Molecular Recognition 409

12.3 Metallofoldamers as Sensors for Metal Ions 414

12.4 Metallofoldamers as Dynamic Materials 419

12.5 Conclusions and Outlook 429

References 429

Index 433

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