Edited by

Bruno Pignataro

Discovering the Future of MolecularSciences

Related Titles

Pignataro, B. (ed.)

Molecules at WorkSelfassembly, Nanomaterials, MolecularMachinery

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Pignataro, B. (ed.)

New Strategies in ChemicalSynthesis and Catalysis

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Ideas in Chemistry andMolecular SciencesAdvances in Synthetic Chemistry

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Tomorrow’s Chemistry TodayConcepts in Nanoscience, OrganicMaterials and Environmental ChemistrySecond edition

2009

ISBN: 978-3-527-32623-5

Edited byBruno Pignataro

Discovering the Future of Molecular Sciences

Editor

Prof. Bruno PignataroUniversita di PalermoDipartimento di Fisica e ChimicaViale delle Scienze ed. 1790128 PalermoItaly

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V

Contents

Preface XIIIList of Contributors XXI

Part I Advanced Methodologies 1

1 Supramolecular Receptors for the Recognition of Bioanalytes 3D. 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 inLive Cell Imaging 7

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

1.4 Functionalized Vesicles for the Recognition of Bioanalytes 14

1.4.1 Polydiacetylene Based Chromatic Vesicles 15

1.4.1.1 PDA Based Receptors for Biological Phosphate 15

1.4.1.2 PDA Based Receptors for Lipopolysaccharide 20

1.4.1.3 PDA Based Receptors for Oligonucleotides and Nucleic Acids 21

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 31Olalla Vazquez

2.1 Introduction 31

2.2 Historical Outline: The Central Dogma 32

2.3 Intermolecular Interaction between the Transcription Factors and theDNA 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

VI Contents

2.3.3 General Aspects of the Intermolecular Interactions between the TFsand 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 theDNA 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 TheirUse as Specific dsDNA Sensors 53

2.6 Outlook 56

Acknowledgments 56

References 56

3 Structural Analysis of Complex Molecular Systems by High-Resolutionand Tandem Mass Spectrometry 63Yury 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 ArtificialMultichromophoric Systems 91Elisabetta 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 UnifiedApproach 96

4.4 Experimental Detection of Quantum Coherence 100

4.5 Electronic Coherence Measured by Two-Dimensional PhotonEcho 104

4.6 Future Perspectives and Conclusive Remarks 110

Acknowledgments 111

References 111

Contents VII

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

5.1 Introduction 1155.2 Theoretical Limits 1165.3 Bulk Semiconductors 1175.4 Semiconductor Quantum Dots 1185.4.1 Lead Chalcogenides 1205.5 Carrier Dynamics 1215.5.1 Carrier Multiplication 1215.5.2 Relaxation 1215.6 Ultrafast Techniques 1245.6.1 Pump-Probe 1245.6.2 Photoluminescence 1265.6.3 Relaxation Times 1265.7 Quantum Efficiency 1265.7.1 Quantum Yield Arguments 1285.7.2 Experimental Considerations 1295.8 Ligand Exchange and Film Studies 1305.9 Conclusions 133

Acknowledgments 133References 133

6 Micro Flow Chemistry: New Possibilities for SyntheticChemists 137Timothy Noel

6.1 Introduction 1376.2 Characteristics of Micro Flow – Basic Engineering Principles 1386.2.1 Mass Transfer – the Importance of Efficient Mixing 1386.2.2 Heat Transfer – the Importance of Efficient Heat Management 1406.2.3 Multiphase Flow 1426.3 Unusual Reaction Conditions Enabled by Microreactor

Technology 1446.3.1 High-Temperature and High-Pressure Processing 1446.3.2 Use of Hazardous Intermediates – Avoiding Trouble 1456.3.3 Photochemistry 1476.4 The Use of Immobilized Reagents, Scavengers, and Catalysts 1496.5 Multistep Synthesis in Flow 1526.6 Avoiding Microreactor Clogging 1546.7 Reaction Screening and Optimization Protocols in

Microreactors 1576.8 Scale-Up Issues – from Laboratory Scale to Production Scale 1576.9 Outlook 160

References 161

VIII Contents

7 Understanding Trends in Reaction Barriers 165Israel Fernandez Lopez

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 FunctionalFuture 191Haralampos 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

8.3.2.1 Shrink-Wrapping Effect 199

8.3.2.2 Hydrothermal and Ionic Thermal Synthesis 200

8.3.2.3 Novel Templates: XO3 and XO6-Templated POMs 200

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 Tubesand Inorganic Cells 208

8.6.3 Controlled POM-Based Oscillations 210

8.7 Conclusions and Perspectives 212

References 212

Contents IX

9 Molecular Metal Oxides for Energy Conversion and EnergyStorage 217Andrey Seliverstov, Johannes Forster, Johannes Tucher, KatharinaKastner, and Carsten Streb

9.1 Introduction to Molecular Metal Oxide Chemistry 2179.1.1 Polyoxometalates – Molecular Metal Oxide Clusters 2179.1.2 Principles of Polyoxometalate Redox Chemistry 2199.1.3 Principles of Polyoxometalate Photochemistry 2199.1.4 POMs for Energy Applications 2219.2 POM Photocatalysis 2219.2.1 The Roots of POM-Photocatalysis Using UV-light 2219.2.2 Sunlight-Driven POM Photocatalysts 2229.2.2.1 Structurally Adaptive Systems for Sunlight Conversion 2229.2.2.2 Optimized Sunlight Harvesting by Metal Substitution 2239.2.2.3 Visible-Light Photocatalysis – Inspiration from the Solid-State

World 2249.2.3 Future Development Perspectives for POM Photocatalysts 2259.3 Energy Conversion 2259.3.1 Water Splitting 2259.3.2 Water Oxidation by Molecular Catalysts 2269.3.2.1 Water Oxidation by Ru- and Co-Polyoxometalates 2269.3.2.2 Polyoxoniobate Water Splitting 2279.3.2.3 Water Oxidation by Dawson Anions in Ionic Liquids 2279.3.2.4 On the Stability of Molecular POM-WOCs 2289.3.3 Photoreductive H2-Generation 2299.3.4 Photoreductive CO2-Activation 2299.4 Promising Developments for POMs in Energy Conversion and

Storage 2319.4.1 Ionic Liquids for Catalysis and Energy Storage 2319.4.1.1 Polyoxometalate Ionic Liquids (POM-ILs) 2319.4.1.2 Outlook: Future Applications of POM-ILs 2339.4.2 POM-Based Photovoltaics 2349.4.3 POM-Based Molecular Cluster Batteries 2349.5 Summary 235

References 235

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

10.1 General Introduction 24310.1.1 Silylenes 24310.1.2 Bissilylenes 24410.1.3 Silylene Transition Metal Complexes 24510.2 Synthesis and Catalytic Applications of Silylene Transition Metal

Complexes 24610.2.1 Bis(silylene)titanium Complexes 246

X Contents

10.2.2 Bis(silylene)nickel Complex 24810.2.3 Pincer-Type Bis(silylene) Complexes (Pd, Ir, Rh) 25410.2.4 Bis(silylenyl)-Substituted Ferrocene Cobalt Complex 26010.2.5 Silylene Iron Complexes 26310.3 Conclusion and Outlook 267

References 268

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

11.1 Introduction 27511.2 Nickel-Based Methodologies for Halide Exchanges 27811.3 Recent Advances in Palladium-Catalyzed Aryl Halide Exchange

Reactions 28011.4 The Versatility of Copper-Catalyzed Aryl Halide Exchange

Reactions 28411.5 Conclusions and Perspectives 290

References 292

12 Nanoparticle Assemblies from Molecular Mediator 295Marie-Alexandra Neouze

12.1 Introduction 29512.2 Assembly or Self-assembly 29612.3 Nanoparticles and Their Protection against Aggregation or

Agglomeration 29712.3.1 Finite-Size Objects 29712.3.2 Protection against Aggregation 29812.4 Nanoparticle Assemblies Synthesis Methods 29812.4.1 Interligand Bonding 29912.4.1.1 Noncovalent Linker Interactions and Self-assembly 29912.4.1.2 Covalent Molecular Mediators 30312.4.1.3 Noncovalent versus Covalent Interaction 30512.4.2 Template Assisted Synthesis 30612.4.3 Deposition of 2D Nanoparticle Assemblies: Monolayers, Multilayers,

or Films 30712.4.3.1 Layer-by-Layer Deposition 30812.4.3.2 Langmuir-Blodgett Deposition 31012.4.3.3 Evaporation Induced Assembly 31112.4.3.4 Bubble Deposition 31312.4.4 Pressure-Driven Assembly 31412.5 Applications of Nanoparticle Assemblies 31412.5.1 Plasmonics 31412.5.1.1 Plasmonic Nanostructures 31612.5.1.2 Sensoric 31712.5.1.3 Signal Amplification/Surface-Enhanced Raman Scattering 31812.5.2 Interacting Super-Spins/Magnetic Materials 319

Contents XI

12.5.3 Metamaterials 32112.5.4 Catalysis/Electrocatalysis 32212.5.5 Water Treatment/Photodegradation 32212.6 Conclusion 323

References 324

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

13.1 Introduction 32913.2 Porous Organic Molecular Crystals 33013.2.1 Porous Organic Molecules 33013.2.2 Porous Organic Cages 33113.2.3 Simulation of Porous Organic Molecular Crystals 33613.2.4 Applications for Porous Molecular Crystals 33813.3 Porous Amorphous Molecular Materials 33813.3.1 Synthesis of Porous Amorphous Molecular Materials 33913.3.1.1 Synthesis of Amorphous Cage Materials by Scrambling Reactions and

Freeze-Drying 34013.3.2 Simulation of Porous Amorphous Molecular Materials 34213.4 Summary 344

References 344

14 Electrochemical Motors 349Gabriel Loget and Alexander Kuhn

14.1 Inspiration from Biomotors 34914.2 Chemical Motors 35014.3 Externally Powered Motion 35314.4 Asymmetry for a Controlled Motion 35514.5 Bipolar Electrochemistry 35614.6 Asymmetric Motors Synthetized by Bipolar Electrochemistry 35814.7 Direct Use of Bipolar Electrochemistry for Motion

Generation 36314.8 Conclusion and Perspectives 372

References 373

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

15.1 Introduction 37915.2 Dendrimers 38015.2.1 Azobenzene at the Periphery 38015.2.2 Azobenzene at the Core 38415.3 Molecular Devices and Machines 38715.3.1 Switching Rotaxane Character with Light 388

XII Contents

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

15.4 Conclusion 395References 395

Index 399

XIII

Preface

This book is the last of the series based on The European Young Chemist Award(EYCA) competition and it reports on some of the latest hits of chemistry by youngexcellence.

The EYCA is indeed aimed to showcase and recognize the excellent researchbeing carried out by young scientists (less than 35 years old) working in thechemical sciences. In particular, it is intended to honour and encourage youngerchemists whose current research displays a high level of excellence and distinction.It seeks to recognize and reward younger chemists of exceptional ability who showpromise for substantial future achievements in chemistry-related research fields.

The inaugural award was bestowed during the first European ChemistryCongress, which took place at the ELTE Convention Centre in Budapest in 2006,while the second and the third were in 2008 and 2010 during the same conferencesin Torino (Italy) and Nurnberg (Germany), respectively.

The quality of the young chemists competitors was so high that I decidedin all these cases to edit books collecting their contributions. Thus always withWiley-VCH as Publisher and under the patronage of the major European Chemi-cal Societies and the European Association for Chemical and Molecular Sciences(EuCheMS) and of the Italian Chemical Society (SCI) as sponsors I edited thefollowing books: Tomorrow’s Chemistry Today-Concepts in Nanoscience, OrganicMaterials and Environmental Chemistry (2nd Ed. 2009); Ideas in Chemistry andMolecular Sciences-Advances in Synthetic Chemistry (2010); Ideas in Chemistryand Molecular Sciences-Where Chemistry Meets Life (2010); Ideas in Chem-istry and Molecular Sciences-Advances in Nanotechnology, Materials and Devices(2010); Molecules at Work-Self-assembly, Nanomaterials and Molecular Machinery(2012); New Strategies for Chemical Synthesis and Catalysis (2012).

The fourth European Young Chemist Award was presented in Prague (CzechRepublic) during the fourth EuCheMS Chemistry Congress (2012).

As it occurred for all the previous awards, the scientific quality of the youngchemists competitors was again outstanding.

Just to give an idea of their scientific level and therefore of the expected qualityof the chapters in the book, I am delighted and proud to report some very shortstatements extracted from the supporting letters of some of the competitors of theawards invited by me to contribute to this book.

XIV Preface

‘‘In my experience, it will be very difficult to find a scientist of this age with betterpersonality and higher capacities than him’’; ‘‘He has done stellar work’’; ‘‘She isa superb scientist with the skills to perform incredibly difficult experiments andto model results based on theory. She has shown the ability to imagine innovativeideas for new research directions’’; ‘‘I consider him among the most brilliantEuropean chemists of his generation’’; ‘‘The best way to define to him is as trulyexceptional’’; ‘‘I believe he is one of the leaders of the actual generation of EuropeanChemists’’; ‘‘I can qualify him without hesitation as the best PhD student I hadso far in my career’’; ‘‘He is a rising star in the field of chemistry’’; ‘‘He is rapidlybeing recognized worldwide as one of the leading young European chemists’’. ‘‘Hehas pioneered a number of new research strands. I consider the candidate to beone of the top, if not the top, person I have mentored’’.

Two among the authors of the chapters have got the ERC starting grant and someof them got different awards. Much of the scientific production of all the authorsis in high-quality Journals with some of the competitors having papers in Nature,Science, Chem. Rev., Angew. Chem., JACS and other important Journals.

After the brief genesis of the book and the above points on the scientific qualityof the authors, let me spend some words about its content.

The book is divided into two parts: ‘‘Advanced methodologies’’ and ‘‘Materials,Nanoscience and Nanotechnologies’’.

In the first part there are various collected contributions ranging from analyticalmethodologies involving recognition issues or mass spectrometry to the area ofstudies involving electronic energy transfer and pump and probe methodologies aswell as micro flow chemistry or advanced calculation methodologies.

The first chapter, entitled ‘‘Supramolecular receptors for the recognition of bio-analytes’’ by Amilan Jose Devadoss (in collaboration with Prof Alexander Schillerand Dr Amrita Ghosh), reports on fluorogenic and chromogenic supramolecularsensors for the recognition of important bioanalytes and their applications invarious biological studies. Studies conducted by the author and examples fromother researchers are considered. Thus, promising examples for the recogni-tion of bioanalytes like pyrophosphate, nucleoside triphosphates, carbohydrates,lipopolysaccharides and nucleic acids are described. Metal complexes with chro-mogenic or luminescent motif (mainly of the Zn(II) type), new color- andfluorescence-based polydiacetylene vesicle systems and boronic acids have been theconsidered receptors. Potential application in biological cell staining, drug delivery,and molecular logic functions has also been summarized. In agreement with theauthors I believe that this chapter will inspire new advancement in the researcharea of bioanalytes recognition and in the discovery of molecular sciences in thefuture.

To the same broad area of research than that by Devadoss et al. belongs the nextcontribution by Olalla Vazquez. The title is ‘‘Methods for DNA recognition’’. Owingto the paramount importance of DNA for life, the focus is however here on themolecular bases of double stranded DNA (dsDNA) recognition. Special emphasisis placed on recognizing the most relevant conformation under physiologicalconditions: the so- called B-form of dsDNA. The interaction of natural transcription

Preface XV

factors (TFs) with the DNA, gene expression, and the current developments inthe design and preparation of synthetic dsDNA binders are considered. As tothis last items, within the discussion on the Metallo-DNA and Polypyrroles andbis(benzamidine) binders, I like to mention that a schematic representation of thecytotoxic pathway of the famous cisplatin and the simple explanation of the celldeath is reported. In conclusion, I feel that the chapter, in some aspect, tries toprovide a contribution to yet incompletely answered important questions in thefield, like those pushed by the author: ‘‘How do the large and diverse number ofDA-binding proteins recognize their specific binding sites? Which are the rulesthat govern how proteins bind to DNA sequences?’’

The next chapter by Yury Tsybin is dedicated to the astonishing advances inhigh resolution and tandem MS applied to structure analysis of complex molecularsystems. In this chapter, following the presentation of the basic principles in massspectrometry (MS), the Fourier Transform Mass Spectrometer that gives superiorresolving power and mass accuracy among all types of mass spectrometers isintroduced. Then the configuration and working principles of some modernMS variants, namely, Orbitrap Fourier Transform MS (Orbitrap FTMS), IonCyclotron Resonance FTMS (ICR FTMS) and Time of Flight FTMS (TOF FTMS)are described with particular emphasis on the first two because of their widerspread and commercial availability compared to TOF FTMS. This part of thechapter is followed by two sections with a discussion on the applications of highresolution MS and tandem mass spectrometry (MS/MS) in the analysis of complexmixtures or biological samples. The study of peptides and proteins with theemerging field of native mass spectrometry (which aims at preserving the solutionphase protein–ligand interactions) and petroleomics (comprehensive molecularstructure analysis of crude oils and complex petroleum fractions by high-resolutionFTMS ) are, for example, research areas that should benefit greatly from thesemethodologies. Great effort is made by the author to give suggestions on how toimprove the actual performance of the available instrumentation in order to copewith the always increasing demand for analytical chemistry.

The next contribution by Elisabetta Collini is entitled ‘‘Coherent electronic energytransfer in biological and artificial multichromophoric systems’’ and deals withelectronic energy transfer (EET), a phenomenon that is important for efficientlight-harvesting in photosynthesis, the development of fluorescence-based sensortechnologies, and improvements in solar cell design. In particular the chapter, wellbalanced between introductory theorethical problems and experimental studies,focuses on the involvement of quantum-coherence in this type of phenomenon andprovides some basis to allow to answer the two following fundamental questionsoutlined by the author: ‘‘To what extent such coherences are really relevant for theefficiency and the mechanism of biological and artificial EET processes? Wouldit be possible to implement quantum interference effects to control and optimizeenergy transfer pathways?’’ After an introductory part in which the author brieflytalks of the EET phenomenon, the meaning of electronic coherence in energytransfer, the theorethical interpretation of the energy migration, what mentionedabove is done by first presenting the developments of new ultrafast spectroscopy

XVI Preface

experiments and then describing and discussing some experimental studies oncoherent electronic energy transfer in two multichromophoric systems: a light-harvesting antenna isolated from a marine cryptophyte alga and the conjugatedpolymer MEH-PPV (poly[2-methoxy,5-(2′-ethyl-hexoxy)-1,4-phenylenevinylene.

The next chapter is provided by Danielle Buckley and is entitled ‘‘UltrafastStudies of Carrier Dynamics in Quantum Dots for Next Generation Photovoltaics’’.It is pointed out here that first generation devices suffer from losses in efficiencybecause of different causes, while second generation devices make them moreappealing because of the lower material and manufacturing costs. Third generationphotovoltaics (PVs), also referred to as next generation PVs, aims to correct one ormore efficiency losses found in first and second generation devices as well as tolower the costs. Next generation approaches to achieve these improvements includeutilizing multi-junction cells, intermediate band cells, hot-carriers, multiple excitongeneration (MEG), and spectrum conversion. After some introductory sectionstalking of concepts that are needed to understand carrier dynamics in quantumdots, this chapter focuses on ultrafast studies of quantum dots that have thepotential to contribute to the development of hot carrier and MEG cells. Theseinclude transient absorption (TA), time-resolved terahertz spectroscopy (TRTS),and time-resolved photoluminescence (TRPL). In each case ultrafast pulses areused to excite or ‘pump’ a sample with energy at or above the band gap andthe subsequent probe or resulting emission provides information about carrierdynamics. Some issues on the chemistry of the quantum dots used in the thirdgeneration PVs are also reported. The overall situation described in the chaptersuggests a rapid advancement of quantum dot PV devices.

In the next chapter by Timothy Noel entitled ‘‘Micro Flow Chemistry: NewPossibilities For Synthetic Chemists’’ the new possibility for synthetic chemistsoffered by micro flow chemistry are presented. Starting from a introduction ofthe basic engineering principles of micro flow, this chapter gives an overview ofthe most important advantages of micro flow chemistry for the organic syntheticchemist with respect to traditional batch techniques. Thus it is stressed thatunusual reaction conditions far from the common laboratory practices such ashigh temperatures and high pressures or the use of hazardous intermediates,are enabled by microreactor technology. Also, scale-up problems that have tobe considered to go from laboratory scale to production scale and the reactionscreening and the optimization protocols in microreactors are issues considered inthis contribution. The chapter ends with a section where the author says how hesees the field evolving in the near future.

On the basis of recent contributions from the author’s laboratories and selectedhighlights from the Houk and Bickelhaupt research groups, the next chapter byIsrael Fernandez Lopez is entitled ‘‘Understanding trends in reactions barriers’’and contributes to an old challenge for chemists: the need to control the reactivityof molecules.

In the chapter, the author demonstrates the good performance of the combinedactivation strain (ASM) model/ energy decomposition analysis (EDA) methodto explore and understand trends in reactivity in various fundamental types of

Preface XVII

reactions in organic chemistry such as Pericyclic Reactions (Double Group TransferReactions, Alder-ene Reactions, 1,3-Dipolar Cycloaddition Reactions, Diels-AlderReactions) Nucleophilic Substitutions and Additions, SN2 Reactions, NucleophilicAdditions to Arynes, as well as Unimolecular Processes.

The second Part of the book provides contributions on a series of materials goingfrom polyoxometalates (POMs) to other metal complexes. Nanoparticle assembliesand porous molecular solids are two other considered themes. The two last chaptersdeal with molecular machines and motors. Nanoscience and nanotechnology issuesare often reported in most of these chapters.

The first chapter in this Part is provided by Haralampos N. Miras and is dedicatedto the science of molecular metal oxides or POMs. These molecular systems haveattracted the attention of research groups over the years, because of their plethoraof unique archetypes with applications ranging from catalysis and medicine tomolecular electronics, magnetism, energy, and so on. The chapter shows that aftera period in which the discovery of new architectures was connected to serendipityit is now possible to design and control to an important extent both the structure aswell as the function of the systems. This is achieved essentially by combining theuse of new techniques like ESI/MS and the new synthetic approaches discussed inthe chapter. The new discoveries and developments in the area has led to a varietyof unprecedented architectures and the emergence of intriguing properties andnew phenomena, paving the route for the engineering of materials with innovativefunctionalities. On the other hand, the capability of a real control over the self-assembly processes of these complex chemical systems opens the door for furtherdiscoveries towards a well-established and directed functional future as it is writtenin the title of this contribution.

Again, the second chapter in this Part, by Andrey Seliverstov, Johannes Forster,Johannes Tucher, Katharina Kastner and Carsten Streb, deals with POMs. Let mestart the comments on this contribution stressing that, as outlined by the authors,the POMs possess, among others, a great capacity to incorporate a wide range ofheterometals into the cluster shell, thus giving access to a large number of clusterderivatives with tunable physicochemical properties.

In this chapter the focus is on the immense potential of these systems forthe development of new energy conversion and storage systems. The authorsoutline first the electrochemical and photochemical activity of POMs and thenthe applications are considered. Thus treated themes are: the POM photocatalysisand the conversion of light into chemical reactivity; the energy conversion and thesplitting of water into oxygen and hydrogen; the oxidation of water to molecularoxygen and protons by using POMs; the photoreductive H2-generation or thephotoreductive CO2-activation always exploiting POMs. In the second part of thechapter the authors describe the important role of POM ionic liquids (POM-ILs)in the area and after that they report a section on POM-based photovoltaics wherethe discussion is centered on the fact that POM anions have been employed asredox active components for the assembly of photoelectrical cells for sunlight toelectricity conversion. A final section is dedicated to POM-based molecular clusterbatteries.

XVIII Preface

The next chapter is provided by Shigeyosh Inoue and is entitled ‘‘The nextgeneration of silylene ligands for better catalysts’’.

In this chapter after a brief general introduction on silylene (that can beconsidered as the heavier analog of carbene), bis(silylene), and silylene transitionmetal complexes, the author reports on the synthesis and catalytic applications ofsilylene transition metal complexes. Ti, Ni, Pd, Ir, Rh as well as Fe containingcomplexes have been considered in these respects. The key of the game is that theligand is always used to modulate the electronic properties of the transition metal.Also, steric effect may be obviously operative when bulky ligands are considered.In agreement with the author I believe that ‘‘although a broad range of fascinatingachievements have been recently disclosed, this research area is still unexplored,and more fascinating advances will be made in the near future’’.

The next chapter is provided by Alicia Casitas and is entitled ‘‘Halide ExchangeReactions Mediated by Transition Metals’’. Here the author, after having outlinedthe practical importance of the halide exchange reactions in various fields, gives anoverview of the history and developments of these types of reactions with particularemphasis to the nickel-, palladium-, and copper-mediated reactions. The need toimprove the actual situation in order to have milder and more environmentallybenign type of reactions and the need to have more efficient and practical syntheticmethods are underlined.

The next chapter by Marie-Alexandra Neouze Gauthey is entitled ‘‘Nanoparticleassemblies from molecular mediator’’ and is dedicated to the synthesis andapplications of nanoparticle assembly. As to the synthesis, the following methodsare reviewed: (i) inter-ligand bonding, where a molecule is introduced between thenanoparticles and will remain in the final material; (ii) template-assisted method,where the template molecules will force the organization of the nanoparticles;(iii) deposition of 2D assemblies, where the interaction with a surface helps toorganize the nanoparticle assembly; and (iv) pressure driven assemblies. Then thechapter deals with some applications of such materials. For this reason, plasmonicnanostructures for sensing, communication or signal enhancement, magneticnanostructures, metamaterials, as well as catalysis are considered.

The next chapter is provided by Shan Jiang in collaboration with Andy Cooperand Abbie Trewin and is entitled ‘‘Porous molecular solids’’. This contributiondeals with microporous materials that have pore sizes smaller than 2 nm andare of strong interest as they have potential applications in separations, gasstorage, catalysis, sensors, and drug delivery. Porous organic molecular crystalsand Porous amorphous molecular materials are both considered. For the first typeof systems, porous organic molecules like the well-known calixarenes or otherchemical systems are first reviewed. Then an overview is done on the porousorganic cage molecules developed by the Cooper’s research group and preparedby cycloimination condensation reactions. The work done in other groups is alsoreported. This is followed by a section dedicated to simulation issues in order toshow how useful molecular modeling and simulation tools to design and rationalizethe properties of these systems are. A further section deals with applications. As tothe amorphous systems, the problems of synthesis and simulation are again taken

Preface XIX

into account underlining the fact that obviously here they are more challenging withrespect to the crystalline systems. In all cases, the structure activity connectionsand the success since now obtained on the synthetic control of the structures ofthese systems are highlighted and discussed.

The next contribution is provided by Gabriel Loget and Alexander Kuhn andis entitled ‘‘Electrochemical Motors.’’ Here, some examples of moving objectsare first presented. Thus, examples of biomotors, chemical motors such as self-electrophoretic swimmers and bubble-propelled swimmers or externally poweredmotors (which do not need a fuel molecule for the movement like the magnetically-propelled swimmers) are briefly discussed. It is then noted that, because ofmorphological or chemical reasons as well as being introduced by an electric ormagnetic field, some form of asymmetry is always present in all the reported cases.Thus the authors state and show that asymmetry is crucial for the generation ofcontrolled motion; the key concept for the propulsion of particles is asymmetry.Because bipolar electrochemistry, a phenomenon known for a long time and origi-nally used in industrial application for electrolysis or batteries, intrinsically providesa break of symmetry, which can be induced on any kind of conducting object, itis an appealing alternative to the existing mechanisms for motion generation. Thechapter is then dedicated to show the potentiality of this methodology and describedifferent strategies that, by using bipolar electrochemistry, can trigger differenttypes of motion.

The last chapter by Massimo Baroncini and Giacomo Bergamini is entitled‘‘Azobenzene in Molecular and Supramolecular Devices and Machines’’ and givesa contribution to the design of synthetic nanomachines able to carry out movementsat the molecular and supramolecular scale triggered by external stimuli. In thereported examples, azobenzene moieties are part of molecular and supra-moleculararchitectures in which photoisomerization controls molecular movements andnanoscale interactions.

According to the authors the results described show that ‘‘molecular andsupramolecular systems capable of performing large-amplitude controlled mechan-ical movements upon light stimulation can be obtained by careful incrementaldesign strategies, the tools of modern synthetic chemistry, and the paradigms ofsupramolecular chemistry, together with inspiration from natural systems.’’

The book is aimed at advanced and specialist researchers. It should be relevantfor both readers from academia and industry as it will deal with fundamentalcontributions as well as possible applications. The contributions come essentiallyfrom academia researchers. The audience I feel need this book is Chemists inAdvanced Methodologies, Materials, Nanoscience, Nanotechnologies, and Chemi-cal Synthesis areas. The audience with an occasional need for this book should bethat of Physicists and Engineers.

I am not aware of books that can compete with the proposed one for the peculiarityof being a book written with the contributions of top-level young chemists. All thechapters are written in a clear and simple way and all try to give perspectives forthe future.

XX Preface

Going to the conclusions and in connection with these crucial times I would liketo say what one of the fourth EuCheMS Congress attendees told me at the end ofthe event: Future is done! And one can probably be more optimistic by lookingat the creativity shown by this generation of scientists and their ability to developinterdisciplinary and collaborative projects with such a high degree of innovation.Putting everything together I really thing that the book helps in discovering at leasta part of the future of the Molecular Science.

I cannot finish this preface without acknowledging the various institutions andpeople that supported the EYCA rendering possible this new book: the ItalianConsiglio Nazionale dei Chimici (CNC) and the Italian Chemical Society (SCI)and their Presidents, Roberto Zingales and Vincenzo Barone, for sponsoring theAward; the Symposia Chairs and Experts involved in the selection of finalists; theJury for their availability for this hard task; my coworkers for their continuoushelp; Francesco De Angelis, Sergio Facchetti and Nineta Majcen for the help andencouragement; the local organizers with Pavel Drasar for the support; the EYCN,EuCheMS and the fourth EuCheMS Chemistry Congress for their patronage.

Universita di Palermo Bruno PignataroPalermo, Italy

XXI

List of Contributors

Massimo BaronciniUniversita di BolognaDipartimento di Chimica‘‘G. Ciamician’’via Selmi 2I-40126 BolognaItaly

Giacomo BergaminiUniversita di BolognaDipartimento di Chimica‘‘G. Ciamician’’via Selmi 2I-40126 BolognaItaly

Danielle BuckleyUniversity of Colorado BoulderDepartment of Chemistry andBiochemistryBoulder, CO 80309USA

Alicia Casitas MonteroMax-Planck-Institut furKohlenforschungDepartment of OrganometallicChemistryKaiser-Wilhelm-Platz 145470 Mulheim an der RuhrGermany

and

Max-Planck-Institut furKohlenforschungKaiser-Wilhelm-Platz 145470 Mulheim an der RuhrGermany

Elisabetta ColliniUniversita di PadovaDipartimento di ScienzeChimichevia Marzolo 135131 PadovaItaly

Andrew I. CooperThe University of LiverpoolDepartment of ChemistryCrown StreetLiverpool L69 7ZDUK

Israel Fernandez LopezUniversidad Complutense deMadridDepartamento de QuımicaOrganicaFacultad de Ciencias QuımicasAvda. Complutense s/n28040 MadridSpain

XXII List of Contributors

Johannes ForsterFriedrich-Alexander-UniversityErlangen-NurembergDepartment of Chemistry andPharmacyInorganic Chemistry IIEgerlandstr. 191058 ErlangenGermany

Amrita GhoshUniversity of BielefeldDepartment of InorganicChemistryUniversitatsstraße 25Fakultat fur ChemieD-33501 BielefeldGermany

Shigeyoshi InoueInstitut fur ChemieAnorganische ChemieTechnische Universitat BerlinStraße des 17. Juni 135Sekr. C2D-10623 BerlinGermany

Shan JiangThe University of LiverpoolDepartment of ChemistryCrown StreetLiverpool L69 7ZDUK

D. Amilan JoseFriedrich Schiller University JenaFaculty of Chemistry and EarthSciencesInstitute for Inorganic andAnalytical ChemistryHumboldtstrasse 8D-07743 JenaGermany

and

Department of ChemistryNational Institutes of TechnologyKurukshetraHaryana-136119ThanesarIndia

Katharina KastnerFriedrich-Alexander-UniversityErlangen-NurembergDepartment of Chemistry andPharmacyInorganic Chemistry IIEgerlandstr. 191058 ErlangenGermany

and

University of UlmInstitute of Inorganic Chemistry IAlbert-Einstein-Allee 1189081 UlmGermany

Alexander KuhnUniversite de BordeauxISM, ENSCBPUMR 525516 Avenue Pey Berland33607 PessacFrance

Gabriel LogetUniversity of California-IrvineDepartment of ChemistryIrvineCalifornia 92697United States

List of Contributors XXIII

Haralampos N. MirasThe University of GlasgowSchool of ChemistryGlasgow G12 8QQUK

Marie-Alexandra Neouze GautheyInstitute of Materials ChemistryVienna University of TechnologyGetreidemarkt 9/1651060 ViennaAustria

and

Interdisciplinary Laboratory onNanometric and SupramolecularOrganization (LIONS)CEA SaclayDSM, IRAMISNiMBE 91191Gif-sur-Yvette CedexNote de PalaiseauFrance

Timothy NoelEindhoven University ofTechnologyMicro Flow Chemistry andProcess TechnologyDepartment of Chemistry andChemical EngineeringDen Dolech 2 (STW 1.48)5612 AZ, EindhovenThe Netherlands

Alexander SchillerFriedrich Schiller University JenaFaculty of Chemistry and EarthSciencesInstitute for Inorganic andAnalytical ChemistryHumboldtstrasse 8D-07743 JenaGermany

Andrey SeliverstovFriedrich-Alexander-UniversityErlangen-NurembergDepartment of Chemistry andPharmacyInorganic Chemistry IIEgerlandstr. 191058 ErlangenGermany

and

University of UlmInstitute of Inorganic Chemistry IAlbert-Einstein-Allee 1189081 UlmGermany

Carsten StrebFriedrich-Alexander-UniversityErlangen-NurembergDepartment of Chemistry andPharmacyInorganic Chemistry IIEgerlandstr. 191058 ErlangenGermany

and

University of UlmInstitute of Inorganic Chemistry IAlbert-Einstein-Allee 1189081 UlmGermany

XXIV List of Contributors

Abbie TrewinThe University of LiverpoolDepartment of ChemistryCrown StreetLiverpool L69 7ZDUK

Yury O. TsybinBiomolecular Mass SpectrometryLaboratoryInstitute of Chemical Sciencesand EngineeringEcole Polytechnique Federale deLausanneav. Forel 1015 LausanneSwitzerland

Johannes TucherFriedrich-Alexander-UniversityErlangen-NurembergDepartment of Chemistry andPharmacyInorganic Chemistry IIEgerlandstr. 191058 ErlangenGermany

and

University of UlmInstitute of Inorganic Chemistry IAlbert-Einstein-Allee 1189081 UlmGermany

Olalla VazquezUniversidade de Santiago deCompostelaDepartment of OrganicChemistryCruz Gallastegui 15-4A36001 PontevedraSpain

1

Part IAdvanced Methodologies

Discovering the Future of Molecular Sciences, First Edition. Edited by Bruno Pignataro.c© 2014 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2014 by Wiley-VCH Verlag GmbH & Co. KGaA.

3

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

Detection, identification, and imaging of specific analytes are of broad interest inchemical as well as in biological science. In this regard, molecular sensors playinnumerable roles such as in the detection of biological molecules, hazardousmaterials, and warfare agents, in high-throughput screenings, monitoring bio-chemical processes, intelligent drug delivery, and molecular logic devices. Thischapter focuses on fluorogenic and chromogenic supramolecular sensors for therecognition of important bioanalytes and their applications in various biologicalstudies. A significant amount of literature is available related to this research area[1]. However, our aim is to review the research work carried out by us and selectedimportant examples by others.

1.1Introduction

Molecular recognition is a basic phenomenon in biological processes. The principleof molecular recognition is the specific interaction between a chemical entity anda target molecule. They are often complementary in their geometric and electronicfeatures [2]. The idea of molecular recognition was first described by Emil Fischer in1894, who proposed that enzyme and substrate fit together like ‘‘lock-and-key’’ [3].The recognition mechanism is mediated mainly by supramolecular interactionssuch as hydrogen bonding, ion-pairing, hydrophobic interactions, and dipolarassociations [4]. Several examples for these mechanisms exist in nature, for example,deoxyribonucleic acid (DNA) protein, ribonucleic acid (RNA) ribosome, and antigenantibody recognition. Researchers have shown great interest in the design ofartificial systems to mimic these biological recognition processes. In this regard,the concept of supramolecular chemistry provides a route to design such sensormaterials according to the technical needs [2]. In fact, supramolecular methodshave already been proven to be very successful for biomolecule detection. However,developing new methods capable of detecting trace amounts of biologically relevantanalytes, such as anions, nucleic acid, enzymes, microorganisms, and proteins inwater, is still a demanding task. Apart from detecting methods, the biggest obstacle

Discovering the Future of Molecular Sciences, First Edition. Edited by Bruno Pignataro.c© 2014 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2014 by Wiley-VCH Verlag GmbH & Co. KGaA.

4 1 Supramolecular Receptors for the Recognition of Bioanalytes

is identifying suitable receptor systems that are sensitive to specific analytes orfamilies of analytes under physiological conditions.

Great advances have been made in the signaling of small target molecules, suchas inorganic anions and metal ions [5, 6]. However, it is still difficult to designhighly selective and sensitive receptors for complex bioanalytes, such as nucleosidepolyphosphates, proteins, nucleic acids, and complex carbohydrates in water.A large number of active research groups around the world, including those of A. D.Hamilton, A. Das, A. Schiller, B. D. Smith, B. Koenig, B. Singaram, C. M. Niemeyer,C. Schmuck, E. V. Anslyn, I. Hamachi, J. L. Sessler, J. -L. Reymond, J. Yoon, J. W.Steed, K. Severin, P. A. Gale, P. Jr. Anzenbacher, R. Jelinek, S. Matile, S. Shinkai, T.D. James, T. Schrader, W. Nau, and many more contributed toward the developmentof novel supramolecular receptors for the recognition of important bioanalytes.

Fluorescent and colorimetric receptors for binding to bioanalytes are of enormousimportance [7]. Fluorescent sensors are crucial as they generally allow detectionof the analyte present in (ultra)trace amounts and offer possibilities for the useas a biological cell imaging reagent. In contrast, chromogenic sensors with visualdetection have an edge over others as they allow naked eye detection without theuse of any sophisticated instrumentation.

1.2Bioanalytes

It is essential to know the important functions of the target analytes, so that onecan design a suitable receptor for them. Our interest and main focus of this chapterlies in pyrophosphate (PPi), nucleoside triphosphates (NTPs), phosphorylatedproteins, and peptides, nucleic acids (DNA and RNA), lipopolysaccharides (LPSs),and carbohydrates. These analytes are ubiquitous in nature; phosphates andits derivatives dominate the living world. Most of the coenzymes are esters ofphosphoric or pyrophosphoric acid; the principal reservoirs of biochemical energyare phosphates. Many intermediary metabolites are phosphate esters.

PPi (P2O74− (Figure 1.1) is an essential intermediate in biochemical syntheses

and degradation reactions [8]. PPi is one of the important products of adenosine-5′-triphosphate (ATP) hydrolysis under cellular conditions, and the detection ofPPi has been investigated as a real-time DNA sequencing method [9]. Recently,signaling of PPi has become an important issue in cancer research. Patients withcalcium pyrophosphate dihydrate disease (CPPD) have also been shown to have ahigh synovial fluid PPi level [10].

NTPs (Figure 1.1), such as ATP, cytidine triphosphate (CTP), uridine triphosphate(UTP), are widespread in living systems and crucial for various cellular functions[11]. Among all NTPs, recognition studies of ATP are well known. ATP is producedmainly in mitochondria and used as an universal energy source for various cellularevents. It is also involved in enzymatic processes as a reactive substrate. For example,ATP serves as a phosphate donor in kinase catalyzed protein phosphorylation andalso acts as an extracellular signaling mediator [12]. Adenosine-5′-diphosphate