cover_image

Table of Contents

Related Titles

Title Page

Copyright

PF: Preface

List of Contributors

Part I: Self Assembly

Chapter 1: Yoctoliter-Sized Vessels as Potential Biological Models

1.1 Introduction

1.2 Cavities on Glass Plates and Gold Surfaces

1.3 Preparation and Confirmation of Rigid Yoctowell Cavity

1.4 Molecular Sorting

1.5 Yoctowell-Based Molecular Recognition Events

1.6 Conclusion

Acknowledgments

References

Chapter 2: Switchable Host–Guest Interactions of Supramolecular Rings and Cages

2.1 Introduction

2.2 Host–Guest Chemistry

2.3 Switching in Supramolecular Systems

2.4 Natural Paragons

2.5 Types of External Input and Methods for Analysis

2.6 Conclusion

References

Part II: NanoMaterials

Chapter 3: Tailored Graphene-Type Molecules by Chemical Synthesis

3.1 Introduction

3.2 Synthetic Concepts toward Expanded PAHs – Nanographenes

3.3 Conclusion and Outlook

References

Chapter 4: Analyzing the Surface Area Properties of Microporous Materials

4.1 Introduction

4.2 Microporous Materials

4.3 Porosity

4.4 Porous Materials and Calculating Surface Areas

4.5 Summary

Acknowledgments

References

Chapter 5: Nanostructured Materials Based on Core-Substituted Naphthalene Diimides

5.1 Introduction

5.2 Synthesis of Novel cNDI Derivatives

5.3 Electron Transfer

5.4 Supramolecular Self-Assembly of cNDI

5.5 Conclusion

Acknowledgments

References

Chapter 6: Metal Phosphides: From Chemist's Oddities to Designed Functional Materials

6.1 Introduction

6.2 Bulk Metal Phosphides: A Long History

6.3 White Phosphorus for the Low-Temperature Synthesis of Metal Phosphide Nanoparticles

References

Chapter 7: “Artificial Supermolecule”: Progress in the Study of II–V Colloidal Semiconductor Nanocrystals

7.1 Introduction

7.2 Optical Properties of II–V Nanocrystals

7.3 Synthesis of II–V Nanocrystals

7.4 Conclusions and Outlook

References

Chapter 8: Luminescent Dendrimers

8.1 Introduction

8.2 Intrinsic Photochemical and Photophysical Properties of Organic Dendrimers

8.3 Energy Transfer and Energy Upconversion in Multichromophoric Dendrimers

8.4 Dendrimers as Ligands for Metal Ions

8.5 Self-Assembly

8.6 Dendrimers as Photoswitchable Hosts

8.7 Conclusion and Perspectives

References

Chapter 9: Fabrication of Ultramicroporous Silica Membranes for Pervaporation and Gas Separation

9.1 Ultramicroporous Silica Membranes

9.2 MxOy–Silica Membrane

9.3 Hybrid Organic-Silica Membranes

9.4 Perspectives in the Fabrication and Application of Silica Membranes

References

Chapter 10: New Directions in the Fight against Cancer: From Metal Complexes to Nanostructured Materials

10.1 Introduction

10.2 Metal Complexes in Cancer Treatment

10.3 Nanostructured Materials in Cancer Treatments

References

Part III: Molecular Machinery

Chapter 11: Molecular Rotors: Imaging Intracellular Viscosity

11.1 Introduction

11.2 Theoretical Background

11.3 Biological Applications of Molecular Rotors

11.4 Conclusions and Outlook

Acknowledgments

References

Chapter 12: Surface-Functionalized Inorganic Colloidal Nanocrystals in Functional Nanocomposite Materials for Microfabrication

12.1 Introduction

12.2 Colloidal Nanocrystals: Properties, Synthesis, and Surface Functionalization

12.3 NC-Based Nanocomposites for Microfabrication

12.4 Conclusions and Future Perspectives

References

Chapter 13: Fluorescence Sensing of Temperature and Oxygen with Fullerenes

13.1 Introduction

13.2 Thermally Activated Delayed Fluorescence: Fundamental Aspects

13.3 Sensing Applications

13.4 Conclusions and Future Perspectives

Acknowledgments

References

Chapter 14: Going beyond Glucose Sensing with Boronic Acid Receptors

14.1 Introduction

14.2 Indicator Displacement Assays for the Detection of Sugars

14.3 Glucose Sensing with Boronic Acid Receptors

14.4 Solution-Phase Sensor Arrays with Boronic-Acid-Appended Bipyridinium Salts

14.5 Carbohydrate-Active Enzyme Assays

14.6 Boronic-Acid-Appended Bipyridinium Salts at Work – NOVOSIDES

14.7 Conclusions and Perspectives

Acknowledgments

References

Chapter 15: Design of Novel Iridium Complexes to Obtain Stable and Efficient Light-Emitting Electrochemical Cells

15.1 Brief History of Electroluminescence and Optoelectronic Devices

15.2 Light-Emitting Electrochemical Cells: Motivation and Definition

15.3 Ionic Transition-Metal Complexes Based on Ir(III) Metal Core for LECs

15.4 Strategies to Design Iridium(III) Complexes for Highly Efficient LECs

15.5 Strategies to Design Iridium(III) Complexes for Highly Stable LECs

15.6 Outlook and Conclusions

Acknowledgments

References

Chapter 16: Photochemically Driven Molecular Devices and Machines

16.1 Introduction

16.2 Switches and Logic Gates

16.3 Molecular Machines

16.4 Conclusions

Acknowledgments

References

Related Titles

Pignataro, Bruno (ed.)

New Strategies in Chemical Synthesis and Catalysis

2012

ISBN: 978-3-527-33090-4

Garcia-Martinez, Javier/ Serrano-Torregrosa, Elena (eds.)

The Chemical Element

Chemistry's Contribution to Our Global Future

2011

ISBN: 978-3-527-32880-2

Pignataro, Bruno (ed.)

Ideas in Chemistry and Molecular Sciences

Advances in Synthetic Chemistry

2010

ISBN: 978-3-527-32539-9

Pignataro, Bruno (ed.)

Ideas in Chemistry and Molecular Sciences

Where Chemistry Meets Life

2010

ISBN: 978-3-527-32541-2

Pignataro, Bruno (ed.)

Ideas in Chemistry and Molecular Sciences

Advances in Nanotechnology, Materials and Devices

2010

ISBN: 978-3-527-32543-6

Title Page

Preface

In addition to the traditional core areas of chemistry, the international trends record a growing development of those areas of chemistry that are multi- and cross-disciplinary, dealing more and more with recent challenges and opportunities in chemistry.

The aim of the most advanced meetings in chemistry is often to have a better quality of life for all people and to showcase knowledge, advanced products, and services that improve the efficiency of chemical professionals, the local and global environment, and our well-being. The central subject is chemistry, technology, and our global society for future “health” and sustainability. As shown in the last conference of the European Association for Chemical and Molecular Sciences—3rd EuCheMs Chemistry Congress in Nuremberg (29 August to 2 September 2010)—chemistry is considered “a creative force” and the scientists are convinced that it will give shape to the future.

A particular trend of the general roadmap of chemistry (see, for instance, the document “Chemistry: Developing Solutions in a Changing World” produced by EuCheMs) is related to the fact that the advancement in molecular design and its control becomes more and more finished. Chemists engineer their synthetic products more and more on the molecular scale exploiting and guiding in an increasing controlled way not only the strong bond but also the weak bonds (π–π interaction, metal–ligand coordination, hydrogen bonds, hydrophobic interactions, van der Waals interactions, etc.). This often also aims to close the gap between synthetic and natural products. Nature, in fact, still has a lot of things to teach us for preparing useful chemical systems. This even if we must here stress the fact that those systems chemists can create may have characteristics or properties that are present or not in nature!

Present efforts are directed at overcoming self-assembling and obtaining a control on the kinetic instability of the covalent architectures going from the self-assembling to the far-from-equilibrium self-organization. This is in order to have molecular superstructures with particular well-defined conformations and, therefore, functions.

In agreement with another current development in chemistry, the advancements in understanding the phenomena and behaviors at the molecular level continue to increase the tendency to look, in a more and more different way, to the properties and reactions of the chemical systems. This helps to throw further bridges between Chemistry and other disciplines such as Molecular Biology, Electronics, or Material Science. The power of the synthetic methods in order to obtain, for example, new functional nanoparticles is now well documented and the products of such synthetic efforts embrace a large spectrum of sophisticated applications such as gene transfection, catalysis, lithium storage, or sensors and, in general, materials science and technology for a variety of applications.

In addition, learning also from the behavior of green plants, a research line is developing molecular photovoltaic devices having power conversion efficiencies of the order of 10%. This brings us closer to identifying “environmentally friendly” solutions for the world energy problem.

Another very important international trend follows from the fact that new discoveries and technological advancements improve our capacity to obtain better and better spatial, temporal, and energy resolutions. This is for one of these quantities alone or for these quantities in combination. In various fields we are close to the achievement of physical limits. One of the most astonishing recent achievements, which exploit these improved capacities, is, for instance, that reported by Paul Corkum, who launched at Ottawa the attosecond science. These researches have shown that we can measure electronic orbitals and we might film the orbital modification during a photochemical reaction. This area of research then passes from the femtochemistry led by Ahamed Zewail, allowing for the production of movies of the rupture and formation of chemical bonds, to this type of measures where theory and experiment are more and more interwoven. In addition, today we have the ability to measure smaller and smaller weights or other physical quantities. Indeed, picojoules, piconewtons, fractions of nanometer, femtograms, femtoamperes, and kilodaltons are quantities that are measured in our laboratories with always increasing facility and reliability.

Moreover, ongoing from the nanoscopic to the macroscopic and to complex systems, the number of data that computers are able to manage continues to increase in a dramatic way. The impact of computational methods has become extraordinarily important in the development of science and technology. Simulations that were unthinkable a few years ago are now possible and allow us to start thinking about extremely complex predictions.

Just as a reference, in the frontier area with Life Sciences the challenges that chemists had sought a few years ago seem less and less ambitious and it appears more and more clear that chemistry plays an essential role in understanding life itself.

This book is placed in this international scenario. In particular, it represents one of the two books comprising contributions of selected scientists from the last edition of the European Young Chemist Award (EYCA 2010) presented during the 3rd EuChemS Chemistry Congress. It is aimed to cover the generic area of functional molecular and supramolecular materials, while the other encloses contributions from the area of synthetic chemistry and is entitled “New Strategies in Chemical Synthesis and Catalysis.”

As for EYCA 2010, it was the third time this Award has been given. The aim of EYCA is to showcase and recognize the excellent research being carried out by young scientists working in the chemical sciences. In particular, it is intended to honor and encourage younger chemists whose current research displays a high level of excellence and distinction. It seeks to recognize and reward younger chemists (less than 35 years old) of exceptional ability who show promise for substantial future achievements in chemistry-related research fields.

The applications presented by the best candidates during the two previous editions of the Award were so stimulating that together with Wiley, EuCheMs, SCI, RSC, and GDCh I decided to collect them into books. Thus, from the first edition of the Award was published the book “Tomorrow's Chemistry Today: Concept in Nanoscience, Organic Materials, and Environmental Chemistry” (Wiley 2009), and from the second edition the three books (Wiley 2010) entitled “Ideas in Chemistry and Molecular Sciences: Advances in Synthetic Chemistry,” “Ideas in Chemistry and Molecular Sciences: Where Chemistry Meets Life,” and “Ideas in Chemistry and Molecular Sciences: Advances in Nanotechnology, Materials and Devices.”

The work from this third edition of the Award was once more very stimulating and again pushed by Wiley, EuCheMs, SCI, RSC, and GDCh, I planned to collect the best contributions into two other books.

The scientific standing of the award applicants was undoubtedly very high and their research achievements are remarkable, especially in relation to their young age. A few figures help to substantiate this point. About 45% of the applicants have been chosen to give an oral contribution to the Nuremberg Congress. In the CV of the participants one can find that the candidates have about 60 papers in peer-reviewed international journals and are guiding a group of more than 20 PhDs and Post Docs, or their work got more than 1500 citations. The publication lists of most applicants proudly noted the appearance of their work in leading general science/chemistry journals such as Science, Nature, Angewandte Chemie, Journal of the American Chemical Society, and so on or the best niche journals in the fields of organic, inorganic, organometallic, physical, analytical, environmental, and medicinal chemistry. Several participants have been granted different prizes, have been invited to give lectures, and achieved further recognitions such as front-end covers, hot articles, or highlights in top journals. Moreover, reading the application documents it comes out clearly that many of the competitors have different scientific interests and do have very exciting ideas for their future work. Further support for the applications, and a testament to the very high quality of the competitors, was apparent from the comments contained in the often very effusive recommendation letters from a number of eminent scientists. A flavor of these from the applications received can be found in the guest editorial published by Chemistry: A European Journal (vol. 16 (2010), pp. 13888–13893), where I reported many other details of the quality of the participants and of the whole Award Competition.

This is the pool from which I fished the contributors of this book.

In fact, the book gives an account of the most recent results of research in self-assembly, nanomaterials, and molecular machinery, based on a selection by leading young scientists. The authors provide the state of the art in their field of research and the perspective or preview of the future research directions.

The content covers some of the aspects of the international chemical research highlighted above. The title reflects the fact that we are now able almost to see the molecules at work: they self-assemble, self-organize, and give rise to functional nanomaterials, thin films, and then to more complex systems such as molecular machinery and devices.

The book is divided into three parts even if in some cases the content of one part may overlap that of another. In summarizing the contents of the book, some points of the various chapters are reported below.

Part I, Self-Assembly, consists of two chapters. In Chapter 1, yoctoliter-sized vessels are discussed as potential biological models and it is shown how scientists have attained an astonishing degree of control over the noncovalent bond and associated thermodynamics. In this chapter, yoctowells formed by a template-directed strategy are inspected as surface-functionalized materials for studying molecular interactions.

Chapter 2 deals with switchable host–guest interactions of supramolecular rings and cages. This reminds us that supramolecular interactions span a wide range of the energy scale from fractions of a kilojoule per mole (weak van der Waals attractions) to hundreds of kilojoules per mole (strong ligand–metal bonds in coordination compounds). This latter fact shows that the border between what concerns covalent compounds and supramolecular compounds is somewhat fuzzy and that supramolecular assemblies should not be described by using as a unique criterion the strengths of binding of the particular building blocks. While the structure, formation, and thermodynamic and kinetic properties of supramolecular host–guest compounds have been described by a number of leading scientists over the past years in great detail, as the authors said, the scope of this chapter is merely limited to a selection of systems in which the host, the guest, or both can respond to external stimuli such as light, pH, and so on, triggering the uptake inside or the release from the host central cavity.

In Part II, the contributions on nanomaterials are reported.

Chapter 3 deals with tailored graphene-type molecules by chemical synthesis. Nanographenes are not only the subject of fundamental studies at the interface between synthetic, physical, organic, and theoretical chemistry but also are advanced functional materials for advanced organic and optoelectronic devices, in which graphene acts as the charge-transporting phase. In this chapter, a tour through a fascinating class of large extended aromatic compounds, namely, polycyclic aromatic hydrocarbons (PAHs), is made. As illustrated by carefully selected examples, the authors have seen the enormous potential of new preparative methodologies, such as intramolecular adaptations of the Lewis-acid-mediated cyclodehydrogenation, photochemical cyclization of stilbene derivatives, and a whole library of transition-metal-catalyzed, cross-coupling reactions, for the construction of various graphene-like systems. As pointed out by the same authors, the results reported are very encouraging for future research efforts leading to reliable surface-assisted reactions for the preparation of defect-free graphene structures with tailored properties, which can be performed under conditions compatible with standard metal-oxide-semiconductor fabrication processes thus enabling nanographene-based molecular electronics at an industrial level.

In Chapter 4, the surface area properties of microporous materials have been analyzed in connection with a wide range of applications from the field of energy to H2 storage, CO2 capture and sequestration, and gas separation.

Chapter 5 investigates the development of core-substituted naphthalene diimides as tunable redox and photoactive components for molecular self-assembly. This chapter clearly shows how subtle is the border between supramolecular chemistry and nanomaterials.

Chapter 6 deals with metal phosphide nanoparticles. As the authors recall, these MxPy materials exhibit remarkable properties compared with that of their metal counterparts as far as it concerns important fields such as those of catalysis (Ni2P), optic devices (InP), magnetism (FexP), and lithium batteries (NixPy, VPx, etc.). The chapter focuses on one of the few synthetic pathways offering a good control of the shape, size, and nanoparticle composition for a wide variety of metals. It makes use of white phosphorus (P4) as a stoichiometric “P” donor atom that is reacted with metal nanoparticles in solution and in mild conditions.

In Chapter 7, the progress in the study of II–V colloidal semiconductor nanocrystals (NCs) is reported. In particular, it deals with the concept of artificial supermolecule. From this chapter one can understand that by altering the quantum dot (QD) size and/or their chemical compositions, the fluorescence emission may be adjusted from the near ultraviolet (UV), throughout the visible, and into the near-infrared (NIR) spectrum. As reminded by the authors, the quantum confinement effect becomes prominent when charge carriers (electrons and holes) are confined by potential barriers to small regions less than the de Broglie wavelength of the charge carriers or, equally, when the NC diameter is less than twice the exiton Bohr radius in the bulk entity. Continuing to quote the authors, in 1982 Fojtik and Weller designated NCs showing such size quantization effects in the case of zero-dimensional materials. Chemists sometimes identify the zero-dimensional QD as a quite large molecule and therefore they may use the term artificial supermolecule. Owing to their unique tunable optical properties, colloidal luminescent NCs or QDs are very promising as fluorescent tags, electroluminescent devices, photoluminescent materials, photovoltaic cells, and optics and laser applications. Moreover, since the great success of the hot-injection method for the preparation of colloidal semiconductor NCs, a new trend in the research of II–V semiconductors has prospered concerning synthesis, property investigation, and device designs. High-quality cadmium phosphide NCs with emission bridging the blue-visible/IR gap have been synthesized.

Part II includes three other chapters.

On the basis of the very large development of dendrimer chemistry, which was possible by the great advances in synthetic strategies and analytical tools, Chapter 8 briefly discusses some fundamental concepts concerning photophysical processes in dendrimers and how these studies can validate the possibility of using these macromolecules as light-harvesting antennae, systems for energy upconversion, ligands of metal ions, substrates for self-assembly, or photoswitchable hosts.

Also, in connection with the fact that the approaching technology platforms for green fuel production require advanced molecular-separation processes for recovering liquid biofuels (biomethane, hydrogen), Chapter 9 reviews the state of the art and gives the perspectives for the fabrication and utilization of ultramicroporous silica membranes for gas-separation and pervaporation processes.

Chapter 10 reports on how nanotechnology can revolutionize both in vitro and in vivo cancer diagnostics, improving drug delivery in anticancer therapy. This chapter gives a historical approach to the development of metal-based drugs and hybrid materials consisting of nanostructured materials and metal complexes for anticancer therapy.

Part III consists of six chapters dealing with molecular machinery.

Chapter 11 is connected to the fact that the rate of diffusion of a species is of fundamental importance in the processes nurturing life since living organisms have evolved a complex intracellular machinery that relies on diffusion as the rate-determining step to bring chemicals together to meet the biological requirements. Thus, any changes in viscosity at both the cellular and the organism level can have catastrophic consequences, and many such changes can be directly linked to disease and malfunction in humans. This chapter shows the recent investigations using fluorescent molecular rotors as accurate tools to measure in vivo and in vitro viscosity in a wide range of biological environments, including those within a living cell.

In Chapter 12, the authors show the potential of chemically synthesized and organic-coated NCs in creating functional materials to be effectively integrated in systems and devices on the mesoscale. They have highlighted how the advancement of chemical routes in synthesizing NCs with unique optoelectronic properties and surface chemistry, together with their effective manipulation as macromolecules, has endorsed the increase in strategies for patterning them in mesostructures with defined properties on multiple length scales.

Chapter 13 gives an overview of the application of fullerene as a fluorescent sensor for oxygen and temperature, mainly in connection with the fact that there is a distinct lack of dual sensors covering high temperatures (above 70 °C) and ultralow oxygen concentrations (parts per billion).

Boronic acids and their tremendous potential as molecules at work in various fields of chemistry in the past 60 years is the subject of Chapter 14. Going beyond glucose sensing, this chapter addresses the problem of achieving selectivity for glucose with boronic acid receptors in solution-phase sensor arrays. These powerful sensor arrays have been established for neutral and anionic carbohydrates under physiological conditions. Finally, the use of these probes in novel, label-free fluorescent assays for carbohydrate-modifying enzymes demonstrates boronic acid molecules at work in a future biotechnology application.

In Chapter 15, different strategies to design iridium ionic transition-metal complexes (Ir-iTMCs) for highly efficient and stable light-emitting electrochemical cell (LEC) devices have been described. Indeed, the obtained results confirm that iTMC-based LECs are a promising technology for lighting applications. Nevertheless, these findings have been obtained by using different iTMCs in LECs. Hence, the main target for the future is to join all these strategies in only one iTMC.

The systems described in Chapter 16 show that, in the frame of supramolecular photochemistry, the design and construction of nanoscale devices able to perform useful light-induced functions can be attempted. Switches, logic gates, or molecular machines (threading–dethreading motions, molecular shuttles) are discussed there.

The readership of the book is aimed at the advanced and specialists level. It should be relevant to both readers from academia and industry since it deals with fundamental contributions and possible applications. I feel the audience that needs this book consists of chemists and also physicists and engineers interested in nanoscience, nanotechnology, materials, and devices.

As I have done for the other books in this series, I cannot finish this preface without acknowledging all the authors and all the persons who helped and supported me in the project. I thank Prof Giovanni Natile, Prof Francesco De Angelis, Prof Luigi Campanella who, as Presidents of the Italian Chemical Society and/or EuCheMs representatives, strongly encouraged me during the years in this activity. And of course, I thank all those Societies (see the book cover) that motivated and supported the book.

Palermo

Bruno Pignataro

January 2012

List of Contributors

Angela Agostiano
Università di Bari
Dipartimento di Chimica
via Orabona 4
70126 Bari
Italy
and
CNR-IPCF Sez. Bari
c/o Dipartimento di Chimica
Università di Bari
via Orabona 4
70126 Bari
Italy
Carlos Baleizinlineo
Technical University of Lisbon
Centro de Química-Física
Molecular and Institute of Nanoscience and Nanotechnology
Instituto Superior Técnico
Av. Rovisco
1049-001 Lisboa
Portugal
Mário N. Berberan-Santos
Technical University of Lisbon
Centro de Química-Física
Molecular and Institute of
Nanoscience and Nanotechnology
Instituto Superior Técnico
Av. Rovisco
1049-001 Lisboa
Portugal
Giacomo Bergamini
Università di Bologna
Dipartimento di Chimica
via Selmi 2
40126 Bologna
Italy
Sheshanath V. Bhosale
RMIT University
School of Applied Sciences
GPO Box 2476V
Melbourne Vic. 3001
Australia
Vittorio Boffa
Aalborg University
Section of Chemistry
Sohngaardsholmsvej 57
Aalborg 9000
Denmark
Cédric Boissière
UPMC Laboratoire de Chimie de la Matière Condensèe de Paris
Collège de France
CNRS
11 place Marcelin Berthelot
75231 Paris
France
Sophie Carenco
UPMC Laboratoire de Chimie de la Matière Condensèe de Paris
Collège de France
CNRS
11 place Marcelin Berthelot
75231 Paris
France
and
Ecole Polytechnique
Laboratoire Hétéroéléments et Coordination
CNRS
Route de Saclay
91128 Palaiseau cedex
France
Guido H. Clever
Georg-August University Göttingen
Institute for Inorganic Chemistry
Tammannstr. 4
37077 Göttingen
Germany
Rubén D. Costa
Friedrich-Alexander-Universität Erlangen-Nürnberg
Physical-Chemistry
Egerlandstraß e 3
Erlangen 91058
Germany
Maria Lucia Curri
Università di Bari
CNR-IPCF Sez. Bari
c/oDipartimento di Chimica
via Orabona 4
70126 Bari
Italy
Matthieu Demange
Ecole Polytechnique
Laboratoire Hétéroéléments et Coordination
CNRS
Route de Saclay
91128 Palaiseau cedex
France
Alexander Eychmüller
TU Dresden
Physical Chemistry/Electrochemistry
Bergstr. 66b
01062 Dresden
Germany
Xinliang Feng
Max Planck Institute for Polymer Research
Ackermannweg 10
55128 Mainz
Germany
Santiago Gómez-Ruiz
Universidad Rey Juan Carlos
Departamento de Química Inorgánica y Analítica
E.S.C.E.T, Calle Tulipán s/n, 28933 Móstoles (Madrid)
Spain
Stephen G. Hickey
TU Dresden
Physical Chemistry/Electrochemistry
Bergstr. 66b
01062 Dresden
Germany
Chiara Ingrosso
Università di Bari
Dipartimento di Chimica
via Orabona 4
70126 Bari
Italy
and
Università di Bari
CNR-IPCF Sez. Bari
c/o Dipartimento di Chimica
via Orabona 4
70126 Bari
Italy
and
CNR-IMM Sez Lecce
Via per Monteroni
presso Campus Universitario
Palazzina A3
73100 Lecce
Italy
Milan Kivala
Max Planck Institute for Polymer Research
Ackermannweg 10
55128 Mainz
Germany
Marina K. Kuimova
Imperial College London
Chemistry Department
Exhibition Road
South Kensington SW7 2AZ
UK
Steven J. Langford
Monash University
School of Chemistry
Wellington Road
Clayton VIC-3800
Australia
Nicolas Mézailles
Ecole Polytechnique
Laboratoire Hétéroéléments et Coordination
CNRS
Route de Saclay
91128 Palaiseau cedex
France
Shiding Miao
Hefei University of Technology
School of Chemical Engineering
Tunxin Road 193
Hefei 230009
China
and
TU Dresden
Physical Chemistry/Electrochemistry
Bergstr. 66b
01062 Dresden
Germany
Clément Sanchez
UPMC Laboratoire de Chimie de la Matière Condensée de Paris
Collège de France
CNRS
11 place Marcelin Berthelot
75231 Paris
France
Alexander Schiller
Friedrich-Schiller-University Jena
Chemical and Earth Sciences
Institute for Inorganic and Analytical Chemistry
Humboldtstrasse 8
07743 Jena
Germany
Serena Silvi
Università di Bologna
Dipartimento di Chimica
via Selmi 2
40126 Bologna
Italy
Marinella Striccoli
Università di Bari
CNR-IPCF Sez. Bari
c/o Dipartimento di Chimica
via Orabona 4
70126 Bari
Italy
Abbie Trewin
The University of Liverpool
Department of Chemistry
Crown Street
Liverpool L69 7ZD
UK
Bradley E. Wilman
Monash University
School of Chemistry
Wellington Road
Clayton VIC-3800
Australia

Part I

Self Assembly

Chapter 1

Yoctoliter-Sized Vessels as Potential Biological Models

Sheshanath V. Bhosale, Bradley E. Wilman, and Steven J. Langford

Molecular assemblies are ubiquitous in nature as they are involved in the reversible formation of a wide variety of complex biological structures. An understanding of such molecular assemblies and the associated noncovalent interactions that connect complementary interacting molecular entities to surfaces is of central concern to structural biochemistry. Self-assembly on solid or colloidal surfaces is also emerging as a new strategy in chemical synthesis, with the potential of generating wholly synthetic structures for form or function with dimensions of 1–102 nm [1].

Synthetically, nanostructures are manufactured by three different methods:

1. Controlled formation of covalent bonds
2. Through polymers
3. By molecular self-assembly.

Methods 1 and 2 have the distinct advantage of providing more accurate structures and analytics of the resulting nanostructures as they are less dynamic; however, they are often linked with a substantial experimental expenditure. The construction of discrete, well-defined nanostructures using molecular self-assembly has demonstrated how we, as scientists, have attained an astonishing degree of control over the noncovalent bond and associated thermodynamics. Two approaches are likely for further development of this field: solution-based and surface-derived functional systems utilizing molecular self-assembly [2]. This chapter investigates the development of the so-called yoctowells as a surface-functionalized material for studying molecular interactions.

1.1 Introduction

Among the biological processes known, photosynthesis is one of the most important. Photoactive molecules, brought together within a protein matrix with precise distance and orientation to facilitate an electron transfer process over 3 nm, are the key to the initial stages of photosynthetic reactions and hence life (Figure 1.1). By consuming carbon dioxide and liberating oxygen, photosynthesis has transformed the world into a hospitable environment. For decades, scientists have been fascinated by the photosynthetic reaction center (PRC) and its ability to transduce solar energy into electrical energy. There have been many approaches to identifying the factors that govern electron transfer, from small molecule dyads to large multichromophoric systems. One such approach, as highlighted recently by Matile and coworkers [3], makes use of core-substituted naphthalene diimides along a rigid-rod scaffold to generate a proton gradient across a lipid membrane. An earlier work by Moore and Gust [4] had introduced such a phenomenon by the application of a porphyrin–cartonoid–quinone conjugated system across a bilayer.

Figure 1.1 Model of a bacterial photosynthetic reaction center (PRC) for light-induced charge separation.

1.1

Chemists have been successful in the synthesis, isolation, and analysis of molecular machinery, but the mimicry of processes performed by natural systems, which have been developed over long-term evolutionary processes, still requires much attention. To gain understanding in this field, three general strategies have been employed in the past two decades for the preparation, entrapment, and ordering of molecules on a variety of surfaces: (i) lithographic [5], (ii) embossing [6, 7], and (iii) chemical-deposition methods [8, 9], that is, self-assembled monolayers (Figure 1.2).

Figure 1.2 Model of the three general strategies (a) ordering of dye molecules in zeolite L channels, constructed by a lithographic method, (b) laser-assisted embossing producing zeptoliter cavities, which are used for growth of semiconductor molecules, and (c) self-assembled yoctowells are constructed by chemical deposition by applying two-step template strategy.

1.2

Lithographic techniques have been employed to prepare many elegant examples such as hydrophilic pores of zeolite L crystals that have a diameter of 7.5 Å and are, as a result, able to include thousands of hydrated molecules such as electron-conducting methyl viologen or energy-transporting oligophenyl derivatives, which are thin enough to enter the gaps. Lithography is a destructive rather than constructive technique that still has problems at low-nanometer-level spatial resolutions, and as such problems can exist in establishing the precise intermolecular distances and number of molecules in each individual gap. Laser-assisted embossing on amorphous silicon can be used to form nanoscaled wells on the zeptoliter scale (1 zl = 10−21 l); these wells can be prepared in diameters as small as 50 nm. They can also be used as reaction vessels for the preparation of simple growth of inorganic salts and semiconducting nanocrystals with controlled sizes. Finally, the self-assembled containers formed by a template-directed strategy are the focus of this chapter.

1.2 Cavities on Glass Plates and Gold Surfaces

The chemical-deposition method has been demonstrated through the early work of the Sagiv group, in which molecules were covalently attached as Langmuir-Blodgett film (LB) monolayers on glass plates as carriers [10, 11]. Typically, trichlorooctadecylsilane is attached to the glass surface followed by the introduction of cyanine dyes with long alkyl chain substituents. However, problems experienced with the orientation of the dye molecules and with respect to the glass surface not being uniform limited this research from further development.

The preparation of gaps in monolayers was explored a decade ago by the group of Fuhrhop [12]. Typically, the monolayer of mercaptodiamido bolas was templated around a steroid or porphyrin moiety tightly bound parallel to the gold(I) surface, leading to gaps in the monolayers. Formation of the gaps was characterized by cyclic voltammogram techniques [13, 14]. This work demonstrated that 1,2-trans-cyclohexanediols and glucose can be actively sequestered from bulk water. Furthermore, there was a strong discrimination between 1,2-cis- and 1,2-trans-cyclohexanediols within the gaps. Later developments used citrate gold particles, which led to better reproducibility [15, 16]. Later research transferred this technology to colloidal silica as a means of offering more information through fluorescence measurements [17].

1.3 Preparation and Confirmation of Rigid Yoctowell Cavity

The silicate particles developed by van Blaaderen and Vrij [18] were produced in 1–10 g scales by hydrolysis of tetraethoxysilane with aqueous ammonia in ethanol in the presence of 3-aminopropyltriethoxysilicate (Figure 1.3a). Colloidal silica nanoparticles with a mean diameter of 100 nm were suitable for the self-assembly process. “Yoctowells” were constructed by a two-step procedure involving covalent attachment of an activated meso-(tetra-m-benzoic acid) porphyrin 1 with ethyl chloroformate followed by the reaction of diamido bolaamphiphiles (depending on choice) around 1, leading to small wells of yoctoliter (10−24 l) size (Figure 1.3b) [17]. The wells had a diameter similar in width to 1 and height corresponding to the bola length. A total of 1500 yoctowells per particle or 20% surface coverage was a typical value.

Figure 1.3 (a) Schematic showing yoctowell preparation on amino-functionalized silica particles, (b) structures used for preparation and size-exclusion study, and (c) discrimination study to confirm rigidity of the wells using fluorescence quenching.

1.3

1.3.1 Confirmation of Rigid Gaps

The gaps formed were confirmed by a discriminative fluorescence quenching assay in which the level of quenching of 1 was monitored as a function of the size of the quenching agent. For example, in the presence of 2, which is of the same dimension as 1 (diameter ∼2.2 nm), strong fluorescence quenching was observed. In the case of 3 (diameter ∼3.6 nm), little fluorescence change was observed, inferring that size exclusion is possible as a result (Figure 1.3c). This also inferred that the integrity of the yoctowell was maintained throughout the experiment. Later, this was found to be a result of intermolecular hydrogen bonding between the bola.

The chemical versatility offered by the fabrication technique means that the walls of the yoctowells can be made using different phobicity as well as designed to include biological models (Figure 1.4). For example, bolas containing an alkyl chain produce hydrophobic wells, oligoethylene (OEG) chains produce hydrophilic wells, and triglycide bolas produce a peptidic internal environment [17, 19, 20].

Figure 1.4 Models of the yoctowells hydrophobic (right), hydrophilic made up with rigid OEG walls (middle), and peptidic walls made up of triglycinyl bola (left).

1.4

1.4 Molecular Sorting

The rigidity and integrity of the yoctowell described through size-exclusion studies led to the formation of a molecular sorting protocol, where taking advantage of the slow and irreversible adsorption process of the included molecule could lead to the addition of a separate molecule (or more) through noncovalent and/or electrostatic forces [17]. The power of the sorting process was demonstrated through the preparation of porphyrin stacks in the order A, B, and C and A, C, and B within the yoctowells (Figure 1.5) [19].

Figure 1.5 Model of the sorted molecules A, B, C, and D within yoctowell.

1.5

Taking this further, a heterotrimeric system comprising C60 was also prepared by taking advantage of π-electronic donor–acceptor interactions. The capping of the pores with anionic porphyrin showed the preclusion of C60, demonstrating the importance of the sequential addition (Figure 1.6) [21]. The hydrophobic bolaamphiphile that forms the walls of these specific wells are made up of four important regions. The hydrophobic region stabilizes the fullerene within the pore via dispersion interactions and π − π interactions between the fullerene and the bottom porphyrin 1. Approximately 10 Å above the bottom porphyrin 1, a ring of methylammonium groups is used for capping the pore with the tetrasulfonate 4 using electrostatic interactions. The third region bearing polyether groups solubilizes the outer sphere of the silica particle in aqueous solution.

Figure 1.6 (a) Model of a yoctowell containing a trimeric (porphyrin–fullerene–porphyrin) stack, (b) UV–vis absorption spectroscopy trimeric dyes (1 ⊃ C604) within the pores of nanoscale dimensions, and (c) lotus fruit depicts this phenomenon well.

1.6

The importance of the chemistry associated with the introduction of methylammonium groups around the periphery of the yoctowell is demonstrated in this next example. A judicial choice of the position of the ammonium groups by limiting the length of the bola and inclusion of an anionic acceptor leads to a series of molecular dyads for studying photo-induced charge separation [17]. The anionic quinone 8 and the Mn(III) anionic porphyrin 4, which were added to the bulk water solution, were bound at the rim of the gap (Figure 1.7). Quenching of the bottom porphyrin fluorescence was observed depending on the distance; addition of a large excess of smaller quinone had no effect, indicating efficient capping [17, 22]. On excitation of the base porphyrin 1, transient emission spectroscopy gives faster decay times of 0.028, 0.035, and 0.042 ns with varying amplitudes of 70 − 60%, when the anionic quinone is fixated at a distance of 5, 10, and 15 Å, respectively [22].

Figure 1.7 Model of two different dyes of different oxidation potentials.

1.7

1.5 Yoctowell-Based Molecular Recognition Events

Considerable work had shown that yoctowells could be used to immobilize a series of different substrates including phenols (tyrosine, o-hydroquinone), carbohydrates (glucose, cellobiose, ascorbic acid), benzene, cyclohexane (1,2-trans-diol, 1,2-trans-diamine, 1,2-trans-dicarboxylate) and that these samples do not equilibrate with bulk water volumes over long periods as a result of “immobilized hydration water,” which stick to the walls of the hydrophobic yoctowells and cause a nanocrystallization event within the yoctowell [23]. To understand this inclusion phenomenon further, yoctowells comprising hydrophobic and hydrophilic walls have been used to investigate the discrimination of neurotransmitters [24], namely, dopamine, adrenaline, noradrenaline, tyramine, and serotonin in aqueous solution [25]. Findings have revealed that the hydrophobic yoctowells efficiently included most neurotransmitters; however, serotonin, which has a different overall structure, had little binding (Figure 1.8). In contrast, hydrophilic wells were shown to be more discriminant and weaker binders.

Figure 1.8 Excitation of bottom porphyrin 1 leads to fluorescence output (a), insertion of a quencher (Q) into the yoctowell causes fluorescence quenching (b), blocking of the yoctowell by a neurotransmitter that does not interfere with the fluorescence output of 1 and inhibits quenching by Q indicates an efficiency of binding (c).

1.8

Hydrophobic yoctowells act as a size- and stereoselective kinetic trap for a range of solutes in water and offer exceptional means to study water-soluble molecules in these systems [23]. To check the hypothesis of “hydrophobic kinetic trapping” and also to apply the yoctowells for single polar molecules, yoctowells with tetraethyleneglycol walls were constructed. The new yoctowells bearing tetraethyleneglycol walls (Figure 1.9a) are similar to crown ethers, meaning oligoamines such as spermine, polylysine, and the rigid tricyclic tetraamine tobramycin are able to stick to the walls with binding constants on the order of > 103 M−1 at physiological pH (Figure 1.9). Titration of the filled oligoamine yoctowells with naphthoquinone 2-sulfonate failed to displace the guests. However, hydrophobic yoctowells containing only flexible OEG-head groups on the outer surface were shown not to bind oligoamines to any appreciable amount [20].

Figure 1.9 Yoctowells made up of oligoethylene bola and including a quinone that quenches bottom porphyrin fluorescence (a), entrapment of oligoamines (spermine, polylysine, and tobramycin) replaces quinone and binds tightly inside the cavity leading to fluorescence (b).

1.9

1.6 Conclusion

Yoctowell-recognition systems are likely to contribute to a new generation of bioinspired materials in biotechnology and nanotechnology, high-throughput identification screening systems, and provide a new approach toward energy-transduction systems [26]. Furthermore, the ability to form informative nanoscale assemblies will be vital to advances in the development of novel sensors and techniques for medical, biochemical, industrial, and environmental applications. One may apply these yoctowells to instances of sorting of two or more molecules leading to controlled release.

Acknowledgments

This work was supported by the Australian Research Council for support under the Discovery program (DP0878756). S.V.B. is grateful to the ARC for an APD fellowship.

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Chapter 2

Switchable Host–Guest Interactions of Supramolecular Rings and Cages

Guido H. Clever

2.1 Introduction