Chemically Modified Nanopores and Nanochannels

Chemically Modified Nanopores and Nanochannels

Edited by

Mario Tagliazucchi

Universidad de Buenos Aires–CONICET, Buenos Aires, Argentina

Igal Szleifer

Northwestern University, Evanston, IL, United States

Table of Contents

Cover image

Title page

Copyright

List of Contributors

About the Editors

Preface

Acknowledgments

1. Introduction to Chemically Modified Nanochannels and Nanopores

Abstract

1.1 Types of Channels and Pores

1.2 Chemical Modification

1.3 Transport Experiments

References

2. Theoretical Basis for Structure and Transport in Nanopores and Nanochannels

Abstract

2.1 Fundamental Concepts of Thermodynamics and Transport

2.2 Solution of Transport Equations

Appendix I Calculation of the Conductance of a Nanopore by Finite Elements

Appendix II Symbols Used in This Chapter

References

3. Single Ion Track-Etched Nanochannels for Analytical Applications

Abstract

3.1 Introduction

3.2 Resistive Pulse Sensing

3.3 Sensing via Current–Voltage Characteristics (or I–V Characteristics for Sensing)

3.4 Conclusions and Outlook

References

4. Biomimetic Smart Nanopores and Nanochannels

Abstract

4.1 Biological Nanopores

4.2 Biomimetic Smart Nanopores

4.3 Conclusions and Outlook

References

5. Chemically Modified Nanopores in Colloidal Crystals

Abstract

5.1 Colloidal Crystals as Nanoporous Materials

5.2 Preparation of Colloidal Nanoporous Materials

5.3 Aminated Colloidal Nanopores

5.4 Sulfonated Colloidal Nanopores

5.5 Spiropyran-Modified Colloidal Nanopores

5.6 Colloidal Nanopores Modified With Chiral Moieties

5.7 Calixarene-Modified Colloidal Nanopores

5.8 Polymer Brush-Modified Colloidal Nanopores

5.9 Aptamer-Modified Colloidal Nanopores

5.10 Summary

References

6. Advanced Modeling of Ion Transport in Polymer and Polyelectrolyte-Modified Nanochannels and Nanopores

Abstract

6.1 Introduction

6.2 Formulation of the Molecular Theory

6.3 Structure of Nanopores and Nanochannels Modified by Polymers and Polyelectrolytes

6.4 Conductance of Polyelectrolyte-Modified Nanopores and Nanochannels

6.5 Protein Binding into Nanochannels and Applications in Biosensing

6.6 Conclusions and Outlook

Appendix I Symbols Used in This Chapter

References

Index

Copyright

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List of Contributors

O. Azzaroni,     Universidad Nacional de La Plata–CONICET, La Plata, Argentina

E. Fullwood,     University of Utah, Salt Lake City, UT, United States

E. Green,     University of Utah, Salt Lake City, UT, United States

W. Guo,     Chinese Academy of Sciences, Beijing, P.R. China

Q. Kang,     Chinese Academy of Sciences, Beijing, P.R. China

G. Pérez-Mitta,     Universidad Nacional de La Plata–CONICET, La Plata, Argentina

J. Selden,     University of Utah, Salt Lake City, UT, United States

I. Szleifer,     Northwestern University, Evanston, IL, United States

M. Tagliazucchi,     Universidad de Buenos Aires–CONICET, Buenos Aires, Argentina

M.E. Toimil-Molares,     GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany

C. Trautmann,     GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany

I. Zharov,     University of Utah, Salt Lake City, UT, United States

About the Editors

Mario Tagliazucchi

Mario Tagliazucchi was born in Buenos Aires, Argentina. He received his degree in Chemistry from the University of Buenos Aires (Argentina) in 2004 and obtained his PhD in Chemistry from the same university in 2009 under the supervision of Prof. Ernesto J. Calvo. From 2010 to 2015, he was a postdoctoral fellow at the Non-equilibrium Research Center at Northwestern University (United States), where he performed theoretical studies in the area of chemically modified nanopores and nanochannels working with Profs. Igal Szleifer and Emily Weiss. Since 2015, he is a Staff Scientist of CONICET (Science and Technology Council of Argentina). He has been awarded with CONICET-FUDETEC and Fulbright fellowships.

Igal Szleifer

Igal Szleifer was born in Buenos Aires, Argentina. He received his degree in Chemistry from the Hebrew University of Jerusalem (Israel) and his PhD in Chemistry from the same university, working with Prof. Avinoam Ben-Shaul. Igal Szleifer is currently the Christina Enroth-Cugell Professor of Biomedical Engineering at Northwestern University (United States) and he is a Professor of Chemistry, Chemical and Biological Engineering and Medicine. His work concentrates on the development of theoretical approaches to understand the coupling that exists between molecular organization and function. His studies on molecular modeling of complex multicomponent systems have applications in a range of systems ranging from responsive materials to biophysics. The understanding of the complexity of chemical reactions, physical interactions and their role in biological and biomimetic environments is at the center of his research interests.

Preface

The field of nanopores and nanochannels, a major area in modern nanotechnology, has emerged from the confluence of different research areas and technologies, which include (but are not limited to) membrane science, nanofluidics, nanopore (bio)analytics, nanoporous materials, and biological pores and channels. The confluence of such diverse areas required the participation of researchers from very different backgrounds and expertise, which makes this field a truly interdisciplinary enterprise. Historically, the first generations of nanopore membranes and single solid-state nanochannels and nanopores were used as prepared, without further chemical functionalization. However, researchers soon discovered the amazing potential of surface chemical modification to improve the transport properties of nanopores and nanochannels. Chemical functionalization allows controlling the degree of charge and hydrophobicity of the channels and it creates a handle to direct the transport of small ions, polymeric chains, and large particles. Chemical functionalization also has the ability to make pores and channels responsive to external stimuli, such as changes of pH, ionic strength, illumination, and the presence of analytes in solution. In summary, the area of chemically modified nanopores is driven by the promise of improved applications and fueled by the broad availability of tools for surface modification that chemists have been developing for decades to modify planar surfaces.

The link between chemical functionalization and transport properties is the key to design applications based on chemically modified nanochannels and nanopores. This book is built around this link, as it aims to equip the reader with the fundamental tools necessary to understand transport in these systems, as well as to examine the current state of the field by discussing examples in the recent literature. We have included two introduction chapters. The first one is focused on the experimental techniques used to prepare, chemically modify, and measure the transport properties of nanopores and nanochannels. The second introduction chapter discusses the theoretical basis necessary to understand transport, with special emphasis on the effects of surface charge. The following three chapters provide a closer look at nanopore and nanochannel systems of interest, both single channels and membranes with multiple pores. In particular, Chapters 3, Single Ion Track-Etched Nanochannels for Analytical Applications, and 4, Biomimetic Smart Nanopores and Nanochannels, discuss single nanochannels prepared by the ion-track-etch technique. Chemical modification of these channels is analyzed in terms of their applications in bioanalysis (chapter: Single Ion Track-Etched Nanochannels for Analytical Applications, by Omar Azzaroni and coworkers) and the ability to mimic the transport properties of biological systems (chapter: Biomimetic Smart Nanopores and Nanochannels, by Wei Guo and coworkers). Chapter 5, Chemically Modified Nanopores in Colloidal Crystals, by Ilya Zharov and coworkers, is focused on nanoporous membranes prepared by colloidal assembly and illustrates how chemical modification can tune the transport and separation behavior of these membranes. Finally, in Chapter 6, Advanced Modeling of Ion Transport in Polymer and Polyelectrolyte-Modified Nanochannels and Nanopores, we present new theoretical tools developed to model chemically modified nanochannels and nanopores. These tools are well suited to model these systems, as they explicitly consider the molecular properties of the chemical species attached to their inner walls. As a whole, this is the first book about nanopores and nanochannels that is strongly focused on chemical modification and their effects on transport, both from the theoretical and practical point of views. While the book has a chemical focus, a strong background in chemistry is not assumed, so we believe this work will be useful and enjoyable to researchers of diverse backgrounds, namely anyone interested in making, modifying, and using chemically modified nanopores and nanochannels in filtration membranes, sensors, or other emerging applications.

Acknowledgments

We thank our families for their constant support, patience, and encouragement. This book is dedicated to them.

We also thank our collaborators and coworkers in the field of nanopores and nanochannels for sharing their enthusiasm with us, bringing us interesting questions and problems, and making our work even more enjoyable than it is usually is. We are especially grateful to the authors of Chapters 3, 4, and 5—without their contribution this book would not exist.

Igal Szleifer insists on also dedicating this book to his coauthor, Mario Tagliazucchi. Despite Mario’s reluctance to take additional credit, he took over the bulk of the work when Prof. Szleifer suffered a stroke in October 2015. If not for Mario’s hard work and dedication, this book would never have become a reality. Igal will be forever grateful. Mario Tagliazucchi also wants to dedicate this book to the memory of his father, Jorge.

1

Introduction to Chemically Modified Nanochannels and Nanopores

M. Tagliazucchi,    Universidad de Buenos Aires–Conicet, Buenos Aires, Argentina

Abstract

The last decades have seen unprecedented advances in the preparation, functionalization, and characterization of nanopores and nanochannels. This introduction chapter briefly reviews aspects related to the fabrication of different types of pores and channels, their chemical functionalization, and the measurement of their transport properties.

Keywords

Polymer membrane; mesoporous material; nanochannel; nanopore; conductance; cyclic voltammetry; surface chemical modification

Chapter Outline

1.1 Types of Channels and Pores 1

1.2 Chemical Modification 5

1.2.1 Covalent Modification 5

1.2.2 Non-Covalent Modification 9

1.2.3 Co-condensation 12

1.3 Transport Experiments 13

1.3.1 Conductance Measurements 13

1.3.2 Electroactive Probe Measurements 14

1.3.3 Concentration-Driven Transport 19

References 19

1.1 Types of Channels and Pores

Broadly speaking, the field of chemically modified nanochannels and nanopores embraces several different technologies and materials which share some key aspects. In this book, we will specifically focus on materials and devices that: (1) comprise a single or an array of nanochannels or nanopores with diameters in the range 1–1000 nm, (2) are chemically modified in order to confer functionality and responsiveness, and (3) serve as a medium for selective transport for diverse applications (filtration, sensing, separation, etc.). Fig. 1.1 shows microscopy images of solid-state nanopores and nanochannels that fulfil these criteria. We excluded from this list materials exhibiting porosity at the molecular scale, such as zeolites and metal-organic frameworks. Table 1.1 summarizes some properties of the systems in Fig. 1.1.

Figure 1.1 Microscopy images of different types of nanopores and nanochannels: (A) top-view Scanning Electron Microscopy (SEM) image of nanochannels in track-etched poly(ethylene terephthalate) (PET) membrane; (B) top-view Transmission Electron Microscopy (TEM) image of single nanopore in an ultrathin silicon oxide membrane; (C) SEM image of a colloidal nanopore membrane (upper panel: top view, lower panel: lateral view, the inset in the upper panel shows that the nanopores are formed from the voids in the fcc lattice); (D) top-view SEM image of a mesoporous silica membrane; (E) optical (upper panel) and SEM (lower panel) image of a borosilicate nanopipette; (F) top-view SEM image of a microporous silicon membrane; (G) top-view SEM image of a nanochannel alumina membrane. Source: Adapted from (A) Wen, L.; Tian, Y.; Ma, J.; Zhai, J.; Jiang, L., Construction of Biomimetic Smart Nanochannels with Polymer Membranes and Application in Energy Conversion Systems. Phys. Chem. Chem. Phys. 2012, 14, 4027–4042, (B) Storm, A.J.; Chen, J.H.; Ling, X.S.; Zandbergen, H.W.; Dekker, C., Fabrication of Solid-State Nanopores with Single-Nanometre Precision. Nat. Mater. 2003, 2, 537–540, (E) An, S.; Stambaugh, C.; Kim, G.; Lee, M.; Kim, Y.; Lee, K., et al., Low-Volume Liquid Delivery and Nanolithography Using a Nanopipette Combined with a Quartz Tuning Fork-Atomic Force Microscope. Nanoscale 2012, 4, 6493–6500, (F) Velleman, L.; Shearer, C.J.; Ellis, A.V.; Losic, D.; Voelcker, N.H.; Shapter, J.G., Fabrication of Self-Supporting Porous Silicon Membranes and Tuning Transport Properties by Surface Functionalization. Nanoscale 2010, 2, 1756–1761, and (G) Lee, W.; Ji, R.; Gosele, U.; Nielsch, K., Fast Fabrication of Long-Range Ordered Porous Alumina Membranes by Hard Anodization. Nat. Mater. 2006, 5, 741–747; (D) courtesy of G. Soler-Illia’s Lab.

Table 1.1

Typical Dimensions and Membrane Materials for the Nanopore and Nanochannel Systems Shown in Fig. 1.1

The systems in Fig. 1.1 are very diverse in their physical and chemical properties. Depending on the aspect ratio (i.e., L/R, where R and L are the radius and length, respectively) they can be classified either as pores (L/R of order unity) or channels (L/R much larger than one). It is also important to note that some of the systems in Fig. 1.1 are single-pore (or single-channel) systems and others contain multiple nanopores (or nanochannels). In the latter case, channels may be either well-ordered or randomly distributed. Regarding their radial dimensions, porous materials are classified by IUPAC into micropores (R<2 nm), mesopores (2 nm<R<50 nm), and macropores (R>50 nm). These definitions are widely used for materials (e.g., porous silicon and mesoporous silica, Fig. 1.1D and F) but not for nanofabricated pores (e.g., e-beam drilled pores, Fig. 1.1B). When discussing pores in different systems is, therefore, important to consider the context: micropipettes have micrometer-sized openings, but pores in microporous silicon are smaller than 2 nm.

The systems shown in Fig. 1.1 are as follows:

1. Track-etched polymer membranes (Fig. 1.1A): They are prepared by irradiation of polymeric membranes with high-energy heavy ions (such as U and Bi). Due to their high energy, these ions are not stopped by the membrane but go through it, producing the degradation of the membrane in the form of a latent track. This latent track is then chemically etched in a highly alkaline solution order to produce very high aspect-ratio nanochannels.¹,² The etching procedure can be controlled in order to produce different nanochannel shapes (cylindrical,³ conical,⁴ cigar-shaped,⁵ etc.). Membranes containing multiple nanochannels are used for filtration and are commercially available, for example, polycarbonate (PC) membranes from Whatman (Nucleopore and Cyclopore) and PC, polyimide (PI), and polyester membranes from it4ip (ipPore). The ion-track technology has been extended in order to stop heavy-ion bombardment immediately after the impact of the first heavy ion,⁶ which enables the fabrication of single ion-channel membranes. Due to their long aspect ratio and control over channel shape and size, single ion channels prepared by the track-etched technique are one of the most versatile and popular platforms for the creation of nanochannel devices. Chemical modification of single ion channels prepared by this method and their applications are discussed in Chapter 3, Single Ion Track-Etched Nanochannels for Analytical Applications, and Chapter 4, Biomimetic Smart Nanopores and Nanochannels.

2. Electron- or ion-beam sculpted solid-state channels (Fig. 1.1B): This technique involves preparing a thin free-standing silicon oxide (SiO2) or silicon nitride (Si3N4) membrane using microfabrication techniques. The membrane is then milled with a highly focused electron⁷,⁸ or ion beam.⁹ In a related preparation technique,¹⁰ holes of a few tens of nanometer are prepared using electron-beam lithography and reactive-ion etching. Then, the as-drilled holes are shrunk by heating them with an electron beam.

3. Nanoporous colloidal films (Fig. 1.1C): These films are constructed by self-assembling monodisperse silica microparticles into a face-centered cubic (fcc) lattice.¹¹ The octahedral and tetrahedral voids of the lattice form an ordered three-dimensional (3D) network of interconnected pores. The pore size is given by the voids among spheres and, thus, it can be tuned by the size of the silica colloids (see inset in the top panel of Fig. 1.1C). The silanol groups on the surface of the particles enable chemical functionalization, as Zharov et al. and coworkers describe in Chapter 5, Chemically Modified Nanopores in Colloidal Crystals.

4. Mesoporous materials (Fig. 1.1D): These materials are prepared by combining a sol-gel process for the formation of the inorganic phase and self-assembled supramolecular aggregates as the removable template.¹²–¹⁶ The sol-gel process is a wet-chemistry route to prepare metal oxides from small molecules in solution. Templating species (e.g., block copolymers or surfactants) are added to the precursor solution and form a self-assembled organic template, around which the metal oxide is formed and structured. The precursor solution is then deposited onto the substrate (silicon, glass, etc.) by dip- or spin-coating. Finally, the film is treated with a thermal ramp in order to remove the solvent, cross-link the inorganic material, and remove the organic template. The resulting mesoporous film consists of a network of well-ordered interconnected pores, whose geometry depends on the template molecule and the synthetic conditions.

5. Glass nanopipettes (Fig. 1.1E): Glass nanopipettes are glass capillaries terminated in a nanometric size hole. The fabrication of micropipettes (with openings in the micrometer range) using laser pulling of quartz or glass capillaries is a standard and well-established procedure. Nanopipettes are also prepared by laser pulling,¹⁷ although the method may be technically challenging and, thus, some modified protocols have been developed to improve reproducibility. For example, in some cases, the tip of a micropipette is melted and resealed and then etched or polished until a nanopore of the desired size is formed.¹⁸,¹⁹

6. Porous silicon (Fig. 1.1F): Porous silicon membranes are prepared by electrochemical oxidation of silicon in HF solutions.¹⁷,¹⁸ Microporous silicon has potential applications as a membrane material²⁰ and it is also widely studied due to its interesting optical and electronic properties.²¹

7. Anodized alumina (Fig. 1.1G): The electrochemical oxidation (anodization) of aluminum in acidic medium yields an aluminum oxide (alumina) layer with channels self-organized into well-ordered hexagonal arrays.²² The aluminum substrate supporting the porous alumina film can be etched after the anodization step in order to obtain free-standing nanochannel membranes. This method allows the fabrication of very well ordered arrays of nanochannels with very high aspect ratios.²²,²³ Nanochannel alumina membranes with different channel radii are commercially available, for example, from Anopore (Anodisc).

1.2 Chemical Modification

Chemical modification is necessary in order to confer the native surface of the materials in Table 1.1 with desired surface properties (wetting behavior, surface charge), functionality (responsiveness, catalytic activity, biological affinity) or to reduce undesired interactions that may lead to fouling and clogging. An important exception is that of templated mesoporous oxide materials, for which the composition of the membrane can be tailored during synthesis using co-condensation reactions,¹³,¹⁵ thus incorporating the desired functionalities. Chemical functionalization of nanochannels is, in many cases, a multistep synthetic process, where a first chemical reaction introduces chemical groups onto the inner surface of the channels that serve to attach the molecules of interest in a following step. In this section, we will discuss the methods available to modify native surfaces of nanochannels/nanopores for some of the systems in Table 1.1. These methods can be widely classified into covalent chemistry (chemical reactions leading to the formation of covalent bonds), non-covalent assembly, and co-condensation synthesis of mesoporous oxides. Chapters 3, Single Ion Track-Etched Nanochannels for Analytical Applications, 4, Biomimetic Smart Nanopores and Nanochannels, and 5, Chemically Modified Nanopores in Colloidal Crystals, will provide examples of more complex synthetic chemistries that can be performed on nanopore and nanochannel surfaces following the functionalization of the native surface.

1.2.1 Covalent Modification

1.2.1.1 Silica Surfaces

Many of the nanopore/nanochannel systems discussed above have silica surfaces: colloidal crystals based on self-assembled silica spheres, mesoporous silica, glass pipettes, and single pores drilled in SiO2 ultrathin membranes. Silica surfaces also exists as a native oxide layer on SiN²⁶ and can be deposited as well on nanochannel membranes of other materials via atomic layer deposition.²⁷

Silica surfaces are terminated in a combination of siloxane groups, Si–O–Si and silanol groups, Si–OH.²⁸,²⁹ Silanols are classified into isolated silanols (whose Si maintains three bonds with the underlying silica structure), bridged or vicinal silanols (isolated silanols located on neighboring Si atoms, so they that can interact through hydrogen bonds), and germinal silanols (whose Si atoms have two hydroxyl groups and two bonds to the bulk silica). The surface density of each of these types of silanols is variable and depends on the type and degree of hydroxylation of the silica surface. For example, infrared studies indicate that a fully hydroxylated silica has a total surface density of 4.6 hydroxyls/nm², of which 25% are isolated, 62% bridged or vicinal, and 13% are germinal.²⁸,³⁰ On the other hand, acid–base titration of planar³¹ and mesoporous³² silica has suggested that 20% of the silanols are isolated and bridged and the remaining 80% are germinal.

Silanol groups can behave both as weak acids

(1.1)

and as weak bases.

(1.2)

Despite being