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Discovering the Future of Molecular Sciences

Bruno Pignataro (Editor)
ISBN: 978-3-527-33544-2
440 pages
August 2014
Discovering the Future of Molecular Sciences (3527335447) cover image
A glimpse into the future of the European chemistry research landscape.
Fifteen top contributions have been selected for this single volume covering areas of chemistry and materials science. The broad range is presented in an approachable and readable manner equally appropriate for non-specialists on the topic. The overview of intriguing topics includes chemical synthesis and advanced methodologies as well as materials, nanoscience and nanotechnologies.
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Preface XIII

List of Contributors XXI

Part I Advanced Methodologies 1

1 Supramolecular Receptors for the Recognition of Bioanalytes 3
D. Amilan Jose, Amrita Ghosh, and Alexander Schiller

1.1 Introduction 3

1.2 Bioanalytes 4

1.3 Metal Complexes as Receptors for Biological Phosphates 6

1.3.1 Fluorescent Zn(II) Based Metal Complexes and Their Applications in Live Cell Imaging 7

1.3.2 Chromogenic Zn(II)-Based Metal Receptors and Their Applications in Biological Cell Staining 9

1.4 Functionalized Vesicles for the Recognition of Bioanalytes 14

1.4.1 Polydiacetylene Based Chromatic Vesicles 15

1.5 Boronic Acid Receptors for Diol-Containing Bioanalytes 23

1.6 Conclusion and Outlook 25

Acknowledgment 26

References 26

2 Methods of DNA Recognition 31
Olalla Vázquez

2.1 Introduction 31

2.2 Historical Outline: The Central Dogma 32

2.3 Intermolecular Interaction between the Transcription Factors and the DNA 33

2.3.1 The Structure of DNA and Its Role in the Recognition 34

2.3.2 DNA Binding Domains of the TF 36

2.3.3 General Aspects of the Intermolecular Interactions between the TFs and the DNA 40

2.4 Miniature Versions of Transcription Factors 42

2.4.1 Synthetic Modification of bZIP Transcription Factors 43

2.4.2 Residue Grafting 44

2.4.3 Conjugation in Order to Develop DNA Binding Peptides 45

2.5 Intermolecular Interaction Between Small Molecules and the DNA 46

2.5.1 General Concepts 46

2.5.2 Metallo-DNA Binders: From Cisplatin to Rh Metallo-Insertors 50

2.5.3 Polypyrroles and Bis(benzamidine) Minor Groove Binders and Their Use as Specific dsDNA Sensors 53

2.6 Outlook 56

Acknowledgments 56

References 56

3 Structural Analysis of Complex Molecular Systems by High-Resolution and Tandem Mass Spectrometry 63
Yury O. Tsybin

3.1 Dissecting Molecular Complexity with Mass Spectrometry 63

3.2 Advances in Fourier Transform Mass Spectrometry 67

3.3 Advances in Mass Analyzers for FT-ICR MS 70

3.4 Advances in Mass Analyzers for Orbitrap FTMS 72

3.5 Applications of High-Resolution Mass Spectrometry 73

3.6 Advances in Tandem Mass Spectrometry 78

3.7 Outlook: Quo vadis FTMS? 81

3.8 Summary and Future Issues 86

Acknowledgments 88

References 88

4 Coherent Electronic Energy Transfer in Biological and Artificial Multichromophoric Systems 91
Elisabetta Collini

4.1 Introduction to Electronic Energy Transfer in Complex Systems 91

4.2 The Meaning of Electronic Coherence in Energy Transfer 94

4.3 Energy Migration in Terms of Occupation Probability: a Unified Approach 96

4.4 Experimental Detection of Quantum Coherence 100

4.5 Electronic Coherence Measured by Two-Dimensional Photon Echo 104

4.6 Future Perspectives and Conclusive Remarks 110

Acknowledgments 111

References 111

5 Ultrafast Studies of Carrier Dynamics in Quantum Dots for Next Generation Photovoltaics 115
Danielle Buckley

5.1 Introduction 115

5.2 Theoretical Limits 116

5.3 Bulk Semiconductors 117

5.4 Semiconductor Quantum Dots 118

5.4.1 Lead Chalcogenides 120

5.5 Carrier Dynamics 121

5.5.1 Carrier Multiplication 121

5.5.2 Relaxation 121

5.6 Ultrafast Techniques 124

5.6.1 Pump-Probe 124

5.6.2 Photoluminescence 126

5.6.3 Relaxation Times 126

5.7 Quantum Efficiency 126

5.7.1 Quantum Yield Arguments 128

5.7.2 Experimental Considerations 129

5.8 Ligand Exchange and Film Studies 130

5.9 Conclusions 133

Acknowledgments 133

References 133

6 Micro Flow Chemistry: New Possibilities for Synthetic Chemists 137
Timothy Nöel

6.1 Introduction 137

6.2 Characteristics of Micro Flow – Basic Engineering Principles 138

6.2.1 Mass Transfer – the Importance of Efficient Mixing 138

6.2.2 Heat Transfer – the Importance of Efficient Heat Management 140

6.2.3 Multiphase Flow 142

6.3 Unusual Reaction Conditions Enabled by Microreactor Technology 144

6.3.1 High-Temperature and High-Pressure Processing 144

6.3.2 Use of Hazardous Intermediates – Avoiding Trouble 145

6.3.3 Photochemistry 147

6.4 The Use of Immobilized Reagents, Scavengers, and Catalysts 149

6.5 Multistep Synthesis in Flow 152

6.6 Avoiding Microreactor Clogging 154

6.7 Reaction Screening and Optimization Protocols in Microreactors 157

6.8 Scale-Up Issues – from Laboratory Scale to Production Scale 157

6.9 Outlook 160

References 161

7 Understanding Trends in Reaction Barriers 165
Israel Fernández López

7.1 Introduction 165

7.2 Activation Strain Model and Energy Decomposition Analysis 166

7.2.1 Activation Strain Model 166

7.2.2 Energy Decomposition Analysis 167

7.3 Pericyclic Reactions 168

7.3.1 Double Group Transfer Reactions 168

7.3.2 Alder-ene Reactions 173

7.3.3 1,3-Dipolar Cycloaddition Reactions 174

7.3.4 Diels-Alder Reactions 178

7.4 Nucleophilic Substitutions and Additions 179

7.4.1 SN2 Reactions 179

7.4.2 Nucleophilic Additions to Arynes 180

7.5 Unimolecular Processes 181

7.6 Concluding Remarks 183

Acknowledgments 184

References 184

Part II Materials, Nanoscience, and Nanotechnologies 189

8 Molecular Metal Oxides: Toward a Directed and Functional Future 191
Haralampos N. Miras

8.1 Introduction 191

8.2 New Technologies and Analytical Techniques 192

8.3 New Synthetic Approaches 196

8.3.1 The Building Block Approach 197

8.3.2 Generation of Novel Building Block Libraries 198

8.3.3 POM-Based Networks 201

8.4 Continuous Flow Systems and Networked Reactions 203

8.5 3D Printing Technology 205

8.6 Emergent Properties and Novel Phenomena 206

8.6.1 Porous Keplerate Nanocapsules – Chemical Adaptability 207

8.6.2 Transformation of POM Structures at Interfaces – Molecular Tubes and Inorganic Cells 208

8.6.3 Controlled POM-Based Oscillations 210

8.7 Conclusions and Perspectives 212

References 212

9 Molecular Metal Oxides for Energy Conversion and Energy Storage 217
Andrey Seliverstov, Johannes Forster, Johannes Tucher, Katharina Kastner, and Carsten Streb

9.1 Introduction to Molecular Metal Oxide Chemistry 217

9.1.1 Polyoxometalates – Molecular Metal Oxide Clusters 217

9.1.2 Principles of Polyoxometalate Redox Chemistry 219

9.1.3 Principles of Polyoxometalate Photochemistry 219

9.1.4 POMs for Energy Applications 221

9.2 POM Photocatalysis 221

9.2.1 The Roots of POM-Photocatalysis Using UV-light 221

9.2.2 Sunlight-Driven POM Photocatalysts 222

9.2.3 Future Development Perspectives for POM Photocatalysts 225

9.3 Energy Conversion 225

9.3.1 Water Splitting 225

9.3.2 Water Oxidation by Molecular Catalysts 226

9.3.3 Photoreductive H2-Generation 229

9.3.4 Photoreductive CO2-Activation 229

9.4 Promising Developments for POMs in Energy Conversion and Storage 231

9.4.1 Ionic Liquids for Catalysis and Energy Storage 231

9.4.2 POM-Based Photovoltaics 234

9.4.3 POM-Based Molecular Cluster Batteries 234

9.5 Summary 235

References 235

10 The Next Generation of Silylene Ligands for Better Catalysts 243
Shigeyoshi Inoue

10.1 General Introduction 243

10.1.1 Silylenes 243

10.1.2 Bissilylenes 244

10.1.3 Silylene Transition Metal Complexes 245

10.2 Synthesis and Catalytic Applications of Silylene Transition Metal Complexes 246

10.2.1 Bis(silylene)titanium Complexes 246

10.2.2 Bis(silylene)nickel Complex 248

10.2.3 Pincer-Type Bis(silylene) Complexes (Pd, Ir, Rh) 254

10.2.4 Bis(silylenyl)-Substituted Ferrocene Cobalt Complex 260

10.2.5 Silylene Iron Complexes 263

10.3 Conclusion and Outlook 267

References 268

11 Halide Exchange Reactions Mediated by Transition Metals 275
Alicia Casitas Montero

11.1 Introduction 275

11.2 Nickel-Based Methodologies for Halide Exchanges 278

11.3 Recent Advances in Palladium-Catalyzed Aryl Halide Exchange Reactions 280

11.4 The Versatility of Copper-Catalyzed Aryl Halide Exchange Reactions 284

11.5 Conclusions and Perspectives 290

References 292

12 Nanoparticle Assemblies from Molecular Mediator 295
Marie-Alexandra Neouze

12.1 Introduction 295

12.2 Assembly or Self-assembly 296

12.3 Nanoparticles and Their Protection against Aggregation or Agglomeration 297

12.3.1 Finite-Size Objects 297

12.3.2 Protection against Aggregation 298

12.4 Nanoparticle Assemblies Synthesis Methods 298

12.4.1 Interligand Bonding 299

12.4.2 Template Assisted Synthesis 306

12.4.3 Deposition of 2D Nanoparticle Assemblies: Monolayers, Multilayers, or Films 307

12.4.4 Pressure-Driven Assembly 314

12.5 Applications of Nanoparticle Assemblies 314

12.5.1 Plasmonics 314

12.5.2 Interacting Super-Spins/Magnetic Materials 319

12.5.3 Metamaterials 321

12.5.4 Catalysis/Electrocatalysis 322

12.5.5 Water Treatment/Photodegradation 322

12.6 Conclusion 323

References 324

13 Porous Molecular Solids 329
Shan Jiang, Abbie Trewin, and Andrew I. Cooper

13.1 Introduction 329

13.2 Porous Organic Molecular Crystals 330

13.2.1 Porous Organic Molecules 330

13.2.2 Porous Organic Cages 331

13.2.3 Simulation of Porous Organic Molecular Crystals 336

13.2.4 Applications for Porous Molecular Crystals 338

13.3 Porous Amorphous Molecular Materials 338

13.3.1 Synthesis of Porous Amorphous Molecular Materials 339

13.3.2 Simulation of Porous Amorphous Molecular Materials 342

13.4 Summary 344

References 344

14 Electrochemical Motors 349
Gabriel Loget and Alexander Kuhn

14.1 Inspiration from Biomotors 349

14.2 Chemical Motors 350

14.3 Externally Powered Motion 353

14.4 Asymmetry for a Controlled Motion 355

14.5 Bipolar Electrochemistry 356

14.6 Asymmetric Motors Synthetized by Bipolar Electrochemistry 358

14.7 Direct Use of Bipolar Electrochemistry for Motion Generation 363

14.8 Conclusion and Perspectives 372

References 373

15 Azobenzene in Molecular and Supramolecular Devices and Machines 379
Massimo Baroncini and Giacomo Bergamini

15.1 Introduction 379

15.2 Dendrimers 380

15.2.1 Azobenzene at the Periphery 380

15.2.2 Azobenzene at the Core 384

15.3 Molecular Devices and Machines 387

15.3.1 Switching Rotaxane Character with Light 388

15.3.2 Light-Controlled Unidirectional Transit of a Molecular Axle through a Macrocycle 391

15.4 Conclusion 395

References 395

Index 399

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Bruno Pignataro is Professor of Physical Chemistry at the University of Palermo. He received his degree in chemistry in 1995 from the University of Catania and his PhD in materials science five years later. He has chaired the European Young Chemist Award in 2006, 2008, 2010 and 2012. He has authored more than 100 scientific publications and leads a group working in the fields of nanoscience, nanotechnology, electronics and biotechnology.
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