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Supramolecular Chemistry on Surfaces 2D Networks and 2D Structures
Explore the cutting-edge in 2D chemistry on surfaces and its applications
In Supramolecular Chemistry on Surfaces: 2D Networks and 2D Structures, expert chemist Neil R. Champness delivers a comprehensive overview of the rapidly developing field of two-dimensional supramolecular chemistry on surfaces. The book offers explorations of the state-of-the-art in the discipline and demonstrates the potential of the latest advances and the challenges faced by researchers in different areas.
The editor includes contributions from leading researchers that address new spectroscopic methods which allow for investigations at a sub-molecular level, opening up new areas of understanding in the field. Included resources also discuss important supramolecular strategies, like hydrogen-bonding, van der Waals interactions, metal-ligand coordination, multicomponent assembly, and more. The book also provides:
- A thorough introduction to two-dimensional supramolecular chemistry on surfaces
- Comprehensive explorations of the characterization and interpretation of on-surface chemical reactions studied by ultra-high resolution scanning probe microscopy
- Practical discussions of complexity in two-dimensional multicomponent assembly, including explorations of coordination bonds and quasicrystalline structures
- In-depth examinations of covalently bonded organic structures via on-surface synthesis
Perfect for polymer chemists, spectroscopists, and materials scientists, Supramolecular Chemistry on Surfaces: 2D Networks and 2D Structures will also earn a place in the libraries of physical and surface chemists, as well as surface physicists.
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Veröffentlichungsjahr: 2021
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Table of Contents
Cover
Title Page
Copyright
Preface
1 Two-Dimensional Supramolecular Chemistry on Surfaces
References
2 Characterisation and Interpretation of On-Surface Chemical Reactions Studied by Ultra-High-Resolution Scanning Probe Microscopy
2.1 Introduction
2.2 SPM Under UHV Conditions
2.3 Practical Steps in Accomplishing Sub-Molecular Imaging
2.4 Interpretation of Sub-Molecular Contrast at the Single Bond Level
2.5 Characterising On-Surface Reactions with ncAFM
2.6 Conclusions
Acknowledgements
References
3 Complexity in Two-Dimensional Multicomponent Assembly
3.1 Introduction
3.2 Two-Component Self-Assembled Systems
3.3 Three-Component Systems
3.4 Four-Component Systems
3.5 Summary and Perspectives
References
4 Complexity in Two-Dimensional Assembly: Using Coordination Bonds
4.1 Introduction
4.2 Asymmetric Linkers
4.3 Multiple Types of Linkers
4.4 Multiple-Level (Hierarchical) Interaction
4.5 Multiple Binding Modes
4.6 Summary and Outlook
References
5 Complexity in Two-Dimensional Assembly: Quasicrystalline Structures
5.1 History
5.2 Random Tilings
5.3 Quasicrystalline Tilings
References
6 Using Self-Assembly to Control On-Surface Reactions
6.1 Introduction
6.2 Mediating On-Surface Reaction Selectivity
6.3 Mediating On-Surface Reaction Pathway
6.4 Mediating On-Surface Reaction Site
6.5 Brief Summary and Perspective
Acknowledgement
References
7 Covalently Bonded Organic Structures via On-Surface Synthesis
7.1 Introduction
7.2 Dehalogenation
7.3 Dehydrogenation
7.4 Dehydration Reaction
7.5 Other Reactions
7.6 Conclusion and Perspectives
References
8 Hybrid Organic-2D TMD Heterointerfaces: Towards Devices Using 2D Materials
8.1 Introduction
8.2 Atomic Structures
8.3 Surface Functionalisation of 2D TMDs by Organics
8.4 Fundamental Electronic Properties
8.5 Applications in Devices: Organic-2D TMD p–n Heterojunctions
8.6 Conclusion
Acknowledgements
References
9 Surface Self-Assembly of Hydrogen-Bonded Frameworks
9.1 Introduction
9.2 Carboxylic Acid Supramolecular Synthons
9.3 Imide-Melamine Supramolecular Synthons
9.4 From Hydrogen-bonding Synthons to Covalently-organic Frameworks
9.5 Heteromolecular Hydrogen-bonding Synthons
Conclusions
References
Index
End User License Agreement
List of Illustrations
Chapter 1
Figure 1.1 Examples of two-dimensional supramolecular chemistry on surfaces ...
Chapter 2
Figure 2.1 Outline of SPM image acquisition and examples of molecular charac...
Figure 2.2 Overview of the setup and procedure for generating a suitable sur...
Figure 2.3 Key results in understanding intermolecular bond resolution in nc...
Figure 2.4 Examples mapping the local electrostatic field, and chemical iden...
Figure 2.5 ncAFM characterisation of the synthesis of 2D graphene structures...
Figure 2.6 Details of on-surface cyclisation reactions where products and re...
Figure 2.7 Examples of characterisation of bond order and chemical structure...
Chapter 3
Scheme 3.1 On-surface fabrication of multicomponent self-assembled systems....
Figure 3.1 Host–guest chemistry using intrinsically porous building blocks. ...
Figure 3.2 Two-component self-assembly using hydrogen-bonded host-networks. ...
Figure 3.3 Stimulus responsive two-component host–guest systems. (a) Molecul...
Figure 3.4 Guest-induced phase transitions in self-assembled monolayers. (a)...
Figure 3.5 Two-component self-assembled systems exhibiting a high degree of ...
Figure 3.6 Two-component self-assembly using fluorophilic interactions betwe...
Figure 3.7 Host–guest architectures based on surface-confined 2D-COFs. (a) S...
Figure 3.8 Two-component non-host–guest type architectures. (a) Molecular st...
Figure 3.9 Three-component architectures made from two-component host and a ...
Figure 3.10 Three-component architecture from a two-component host and a che...
Figure 3.11 Three-component architectures made from a single component host ...
Figure 3.12 Three-component architectures: site-selective guest adsorption. ...
Figure 3.13 Three-component architectures: site-selective guest adsorption. ...
Figure 3.14 Three-component architectures: site-selective guest adsorption. ...
Figure 3.15 Non-host–guest type three-component architectures. (a) Molecular...
Figure 3.16 Four-component architectures based on DBA derivatives. (a) Molec...
Figure 3.17 Four-component architectures based on PTCDI–melamine. (a) A sche...
Figure 3.18 Four-component non-host–guest architectures. (a) A schematic sho...
Chapter 4
Scheme 4.1 Four categories of complexity discussed in this work.
Scheme 4.2 Molecular linkers in the selected examples.
Figure 4.1 (a) STM images showing the formation of the metal–organic Sierpiń...
Figure 4.2 (a) STM image (up) and structural model (bottom) of a fourth gene...
Figure 4.3 (a) STM topograph (100 nm × 100 nm) of the rosette structures for...
Figure 4.4 (a) An overview STM image (100 nm × 100 nm) showing the two-compo...
Figure 4.5 (a) The mixture of three molecular linkers 5a, 5b, and 6. (b) STM...
Figure 4.6 (a) STM image showing the two Fe(TMA)
4
stereoisomers on the Cu(10...
Figure 4.7 (a) High-resolution STM image of (3.4.6.4) semi-regular titling (...
Figure 4.8 Mixture of 1D supramolecular chains and three-way junctions inter...
Figure 4.9 2D porous MOFs. (a) STM topograph showing well-ordered hexagonal ...
Figure 4.10 (a) Chemical structure of 11 and twofold and threefold Cu–pyridy...
Figure 4.11 Comparison of the real-space arrangement and reciprocal pattern ...
Figure 4.12 STM images of the 2D-MOFs assembled at different ratios of [9]/[...
Figure 4.13 (a) STM image of the dodecagonal quasicrystal MOF assembled on A...
Chapter 5
Figure 5.1 Complex but periodic self-assembled structures. (a) 4,4″-dichloro...
Figure 5.2 Structure of
p
-terphenyl-3,5,3′,5′-tetracarboxylic acid (TPTC, pa...
Figure 5.3 STM image of TPTC at the graphite/nonanoic acid interface (a). Pa...
Figure 5.4 STM image of TMA assembled on Ag(111). The ratio of COOH to COO
−
...
Figure 5.5 Large-scale (600 Å × 600 Å) STM image of TMA granular alloy phase...
Figure 5.6 STM image of a self-assembled monolayer of ferrocenecarboxylic ac...
Figure 5.7 Illustration of cyclic hydrogen bonding forming the regular penta...
Figure 5.8 High-resolution image of FcCOOH on Au(111), with structural model...
Figure 5.9 STM image of FcCOOH on Au(111) with pentagonal tiles superimposed...
Figure 5.10 (a) A 1-D section of the spatial correlation function shows long...
Figure 5.11 (a) Chemical structure of the molecule
para
-quaterphenyl-dicarbo...
Figure 5.12 A large-scale STM image of a Eu/qdc metal–organic coordination n...
Chapter 6
Figure 6.1 (a) Possible dehydrocyclisation and coupling reaction pathways of...
Figure 6.2 (a) STM image of the self-assembly structure of the aryl–alkyne o...
Figure 6.3 (a) Generated supramolecular chiral catalyst via the self-assembl...
Figure 6.4 (a) Two pathways for Ullmann reactions of BBP on Ag(111). (b–e) F...
Figure 6.5 Structure of (a) 1-octadecanethiol (C18) and (b) 1-adamantanethio...
Figure 6.6 (a) Major reaction pathways for furfural hydrogenation on Pd cata...
Figure 6.7 (a) Schematic diagram of the assembly filled with thiols; (b) thr...
Figure 6.8 (a–c), STM images of R1/R2-LD FePc/Ag(110): (a) as-deposited, (b)...
Figure 6.9 Sequential evolution of the Ullmann coupling of BBP molecules on ...
Chapter 7
Figure 7.1 STM images showing the initial steps of the tip-induced on-surfac...
Figure 7.2 Thermal-induced Ullmann reactions of TPP derivatives. (a–c) High-...
Figure 7.3 Hierarchical growths following sequential thermal activation. (a)...
Figure 7.4 Substrate influence in Ullmann reaction. (a) Chemical structure o...
Figure 7.5 (a) STM and nc-AFM images of
trans
-cumulene (D-1) and
cis
-cumulen...
Figure 7.6 (a) Homocoupling and heterocoupling of phenylacetylene (PA) and i...
Figure 7.7 Dehydrogenation coupling between benzylic groups. (a) Molecular s...
Figure 7.8 Linear alkane polymerisation on Au(100) surface. (a) Monolayer of...
Figure 7.9 (a) High catalytic activity of extra row of gold atoms in (1×3)-A...
Figure 7.10 Aryl–aryl dehydrogenation coupling on surface. (a) Optimised geo...
Figure 7.11 (a) Reaction scheme for the polymerisation of DBPM into (3,1)-GN...
Figure 7.12 (a) Schematic illustration of the bottom-up fabrication of armch...
Figure 7.13 Stereoselective synthesis of diene moieties on Cu(110) surface. ...
Figure 7.14 Glaser coupling reaction on surfaces. (a) Small size covalently ...
Figure 7.15 (a) Proposed reaction steps of dehydrogenation of DATP molecules...
Figure 7.16 (a) Imine formation via on-surface condensation reaction of benz...
Figure 7.17 (a) The experiment procedure of solid–vapour interface Schiff-ba...
Figure 7.18 (a) Imidisation condensation reaction pathway between PTCDA and ...
Figure 7.19 (a) Conversion of PDBA into boroxines network at room temperatur...
Figure 7.20 (a) General reaction scheme of diboronic acid self-condensation ...
Figure 7.21 (a) NDCA self-assembly structure on Cu(111). (b) C–Cu–C organome...
Figure 7.22 (a) STM image of 2D network formation via cyclocondensation of T...
Figure 7.23 (a) 1,4-Triazole products obtained on Cu(111) at room temperatur...
Figure 7.24 Electrostatic catalysis of a Diels–Alder reaction. The stages en...
Figure 7.25 On-surface Bergman-like cyclisation reactions of various enediyn...
Figure 7.26 (a) STM image of TAPP molecules self-assemble structure on Cu(11...
Figure 7.27 The σ-bond metathesis of silylated alkynes with aromatic carboxy...
Figure 7.28 (a) Diacetylene polymerisation initiated by a STM tip at designa...
Chapter 8
Figure 8.1 Atomic structures of monolayer TMDs. (a) Overview of the transiti...
Figure 8.2 1H/1T tilting pattern in PtSe
2
monolayer and the selective adsorp...
Figure 8.3 The selective adsorption of DBT molecules on MoS
2
nanoclusters. (...
Figure 8.4 Surface engineering with vacancies. (a) Functionalisation of MoS
2
Figure 8.5 Covalent functionalisation through phase engineering. (a) A gener...
Figure 8.6 Schematic of three types of ELAs at the interface between semicon...
Figure 8.7 Schematics showing energy level alignments at heterointerfaces. (...
Figure 8.8 Liquid–solid phase transformation. (a) A schematic model of the a...
Figure 8.9 DFT calculations of the charge transfer and the dipole moment at ...
Figure 8.10 Energy levels and transport properties tuned by the molecular do...
Figure 8.11 Electronic properties of the 1D intrinsic/p-doped interface dete...
Figure 8.12 Electronic screening at organic/2D TMD interface. (a) Schematic ...
Figure 8.13 Summary of the calculated PTCDA-substrate distances (
d
) and HOMO...
Figure 8.14 A pentacene/MoS
2
photovoltaic device. (a) Schematic structure of...
Chapter 9
Figure 9.1 (a) and (c) Schematic representations of trimesic acid hydrogen b...
Figure 9.2 (a) STM image of a typical area of TPTC network at the nonanoic a...
Figure 9.3 (a) Schematic representation of a section of the random rhombus t...
Figure 9.4 (a) STM image of a TPTC framework self-assembled using commercial...
Figure 9.5 (a) STM image of three molecular chains of NTCDI adsorbed on Ag/S...
Figure 9.6 (a) A schematic of the PTCDI-melamine junction, showing the tripl...
Figure 9.7 (a) and (c) STM images of 1,3,5-
tris(4-iodophenyl)benzene
(
TIPB
) ...
Figure 9.8 (a) Views of the molecular structure of Mn
12
O
12
(O
2
CCH
3
)
16
(H
2
O)
4
; ...
Figure 9.9 C
60
entrapment in a (SAdam)
2
-PTCDI-melamine framework on Au(111),...
Figure 9.10 (a) AFM image of a honeycomb arrangement of trimesic acid framew...
Figure 9.11 (a) STM image showing the hydrogen-bonded array formed by 1,4-be...
Figure 9.12 (a) and (d) Zn-tetra-TP and tetra-AP tectons used in two-dimensi...
Guide
Cover Page
Table of Contents
Title Page
Copyright
Preface
Begin Reading
Index
End User License Agreement
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Supramolecular Chemistry on Surfaces
2D Networks and 2D Structures
Edited by Neil R. Champness
Editor
Prof. Neil R. ChampnessUniversity of BirminghamSchool of ChemistryEdgbastonB15 2TT BirminghamUnited Kingdom
Cover Image: Reproduced from “On-surface chemical reactions characterised by ultrahigh resolution scanning probe microscopy” A. Sweetman, N.R. Champness, and A. Saywell. Chem. Soc. Rev., 2020, 49, 4189–4202, with permission from The Royal Society of Chemistry.
All books published by WILEY-VCH are carefully produced. Nevertheless, authors, editors, and publisher do not warrant the information contained in these books, including this book, to be free of errors. Readers are advised to keep in mind that statements, data, illustrations, procedural details or other items may inadvertently be inaccurate.
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Print ISBN: 978-3-527-34491-8ePDF ISBN: 978-3-527-81668-2ePub ISBN: 978-3-527-81670-5oBook ISBN: 978-3-527-81669-9
Preface
The field of supramolecular chemistry has developed from its inception to now influence thinking, strategies, and application across the chemical and materials sciences. Whilst remarkable progress has been made in many fields, the need to interface supramolecular systems to the real world has spurred interest in performing supramolecular chemistry on surfaces. The goal of studying supramolecular self-assembly processes has in turn engendered new ideas, new concepts, and ultimately a new field of study.
Interestingly, this fresh research focus has brought together experts from many different backgrounds creating new interdisciplinary connections, notably between synthetic chemists and physicists. Surface-based supramolecular chemistry is a truly multidisciplinary field. Indeed, the field has rapidly developed and the original focus on hydrogen-bonded systems has been joined by the exploitation of other supramolecular interactions. Similarly, some researchers have moved towards using self-assembly processes that enable the formation of covalent bonds and hence robust chemical systems, such as nanoscale graphenes.
These studies rely on characterisation techniques, particularly scanning-probe microscopies, that enable molecular, and even submolecular, resolution. Not only do such approaches result in visually inspiring images they also allow appreciation of supramolecular structures with a level of detail that is rarely achievable in traditional supramolecular chemistry. In turn, this has led to the discovery of complex quasi-crystalline arrays and highly complex arrangements. These fascinating structures spark the imagination and move beyond much that has been achieved in supramolecular chemistry.
All these remarkable developments and new avenues of research have spurred increasing attention to how these systems may be exploited in devices operating at the single-molecule level. The interaction between the surface and those absorbed molecules allows direct interaction between molecular systems and the macroscopic world and has led to increasing interest in developing devices, particularly employing electronic properties. Thus, the field is developing from simple curiosity and structural fascination towards applications.
It is timely to evaluate progress in the field and to appreciate where the focus has been and where it is going. Hence, this collection surveys the field from the point of view of experts who have devoted their endeavours to develop this new area of science. I am grateful to all those authors for their excellent contributions and for so clearly expounding their vision of the research area. I hope that the chapters contained herein will inspire the many researchers in the field but also those who currently sit around the periphery of this activity whether chemist, physicist, or the next generation of scientist.
BirminghamApril 2021 Neil R. Champness
1Two-Dimensional Supramolecular Chemistry on Surfaces
Neil R. Champness
University of Birmingham, School of Chemistry, Edgbaston, Birmingham B15 2TT, UK
Supramolecular chemistry represents one of the central themes of modern chemical sciences. Crossing traditional boundaries of chemistry, materials science, biology, and physics, the field of supramolecular chemistry affords opportunities to create new molecules and materials, with far reaching implications for many and diverse applications. The significance of supramolecular chemistry lies behind two Nobel Prizes, 1987 [1] and 2016 [2–4], and is now not only a field in its own right but is also a central underpinning theme in almost any area of chemistry. The primary principle of supramolecular chemistry is the use of non-covalent interactions to create and control self-assembled structures. A large range of interactions is available to the supramolecular chemist to influence and control self-assembly processes. From hydrogen bonds [5–7] and halogen bonds [8, 9] to π-interactions [10, 11], coordination bonds [12, 13] and the mechanical bond [2, 3, 14–16], interactions of different strengths and varying degrees of geometrical preferences are available to design and create structures. When in its infancy, supramolecular chemistry focussed predominantly on synthetic strategies in combination with understanding the fundamental properties of the non-covalent interactions employed. Over recent years, the field has developed to such an extent that it is now commonplace to focus effort towards applications and these range across a vast spectrum. Supramolecular chemistry is so wide-ranging that its relevance can be applied to diverse fields, from biology [17, 18] and medicine [18, 19] to new materials [20, 21] and energy-related applications [22, 23].
The origins of supramolecular chemistry lie in solution-based systems, using intermolecular interactions to create supermolecules. From these origins, supramolecular chemistry is now observed in most phases, notably in the solid-state, through crystal engineering [24, 25], in liquid crystals [26] and ionic liquids [27], and even in the gas phase [28]. It was only natural that supramolecular chemistry strategies would come to be applied to the two-dimensional (2D) environment of surfaces (Figure 1.1). This seemingly natural progression also raised a number of challenges to practitioners of the subject, not least in terms of appreciating this quite different environment and perhaps most importantly the different techniques that are used to characterise and interpret surface-based molecular systems.
Figure 1.1 Examples of two-dimensional supramolecular chemistry on surfaces discussed within this volume. (a) ncAFM image of a hydrogen-bonded naphthalene-1,4:5,8-tetracarboxylic diimide (NTCDI) island on a Ag:Si(111) – (√3 × √3) R30° surface acquired at 77 K. The image reveals sub-molecular details of the self-assembled structure; (b) STM image of self-assembled arrays of ferrocene-carboxylic acid (FcCOOH); each bright feature represents a separate FcCOOH molecule, which then assemble into pentamers highly reminiscent of a Penrose tiling arrangement; (c) Surface-assisted C–C coupling reaction used to prepare straight graphene nanoribbons from bianthryl monomers, including a STM image of nanoribbon, following cyclodehydrogenation at 400 °C, with partly overlaid molecular model (right in blue) and a density-functional theory model (bottom left in grey); (d) Schematic representation of a strategy used to prepare a multicomponent system using a ‘core–shell’ approach. Each colour represents a different molecular building block; (e) Schematic representation and STM image showing dibenzothiophene bound to the corner vacancy of a S-edge-terminated MoS2 nanocluster.
Source: Images reproduced with permission as follows: (a) Sweetman et al. [29]; (b) reproduced with permission from Springer Nature from Wasio et al. [30]; (c) reproduced with permission from Springer Nature from Cai et al. [31]; (d) Mali et al. [32]; (e) reprinted and adapted with permission from Tuxen et al. [33]. Copyright (2010) American Chemical Society.
Whereas the techniques applied to characterising solution phase, or solid-state, supramolecular systems are common across synthetic chemistry, for example, NMR spectroscopy, mass spectrometry, and X-ray diffraction, characterisation of surface-bound molecules is a quite distinct domain. The most common approaches to characterising molecular species on surfaces are scanning probe microscopies (SPM). Specifically, techniques such as scanning-tunnelling microscopy (STM) [34] and atomic force microscopy (AFM) [35] represent the dominant characterisation methods used in the analysis of surface-based supramolecular systems. These imaging microscopies can be, and often are, supplemented by other approaches, such as X-ray photoelectron spectroscopy (XPS), but SPM approaches provide invaluable insight into specific molecular arrangements allowing determination of the geometric structure of organic molecules with molecular resolution. More recently, the development of noncontact atomic force microscopy (ncAFM) [36] allows the characterisation of supramolecular systems with sub-molecular resolution [37]. The use of SPM characterisation techniques in itself presents opportunities, which are rarely available to those working in other phases, not least because such microscopies function at the molecular, or even sub-molecular, level and as a result information, both structural and electronic, can be gathered for individual molecules and defined self-assembled arrays. In comparison, techniques such as NMR spectroscopy or X-ray diffraction rely upon the signal from comparatively large numbers of molecules. Thus, the characterisation of surface-based supramolecular systems can give a detailed picture of the structures and even transformations between different arrangements with a high degree of resolution. The complexities, challenges, and advantages of different SPM techniques are discussed in more detail by Sweetman, Champness, and Saywell in this volume.
A further aspect of the detailed imaging with molecular resolution is that this allows characterisation of structures that would prove extremely challenging by any other technique. Using SPM techniques allows ready identification of defects within supramolecular arrays but intriguingly allows the study of extended structures, which do not possess long-range order, with molecular resolution. This approach has been applied to the study of random, entropically stabilised, rhombus tilings [29, 38, 39], a molecular Penrose tile [30], quasicrystalline structures [40], and fascinating assemblies that exhibit the structure of Serpiński triangles [41]. The complex issues with studying and characterising quasicrystalline 2D arrays are discussed in detail by Kandel in this book.
The study of supramolecular chemistry on surfaces probably began with early studies of hydrogen-bonded assemblies [42–44] but has spread to employ other non-covalent interactions including coordination bonds [45, 46] and weaker van der Waals interactions [47–49]. The use of different intermolecular interactions is discussed throughout chapters in this volume. In particular, Mali, Teyssandier, Bilbao, and De Feyter discuss the use of hydrogen bonds and van der Waals interactions to create complex structures whereas the application of coordination bonds is presented by Lin and Liu. It will become clear to the reader that the choice of intermolecular interaction influences the choice of experimental conditions used, including deposition conditions, use of ultra-high vacuum (UHV) or studies at the solid–solution interface, and even the nature of the surface employed for surface self-assembly. The interactions between surface, substrate, solution, and self-assembled array are all important in determining the subtle energetic balance between different products [50].
These studies have now developed further to create covalently linked structures including nanographenes [51, 52] and covalent-organic frameworks (COFs) [53]. All of these strategies present their own distinct advantages, and disadvantages, but importantly represent a broad palette for researchers to employ and explore. Weaker interactions such as hydrogen bonds, van der Waals interactions, and even coordination bonds, form reversibly and therefore facilitate the formation of well organised, and relatively defect-free, supermolecule structures over comparatively large areas. Creating larger defect free structures can be more challenging using covalent bonds although the use of reversibly-formed bonds such as imines [54] has been developed to aid in this respect. Nanographenes, where carbon–carbon bonds are an absolute requirement, present quite different challenges but remarkable advances have been made in this area. In this volume Peng, Xing, and Wu discuss the use of intermolecular interactions to control on-surface reactions and Wang, Zhang, and Chi present developments in the field of on-surface reactions to create covalently bonded systems.
Another major challenge that requires thought when one considers surface-based supramolecular chemistry are the reaction environment and conditions. Firstly, it is typical to use a surface that is atomically flat or at least close to atomically flat. This rather stringent requirement facilitates the use of SPM characterisation and simultaneously controls the introduction of surface-based reactive sites to the self-assembly process. Even though atomically flat surfaces are commonly used, it would be a mistake to consider the surface as an innocent bystander in the self-assembly process. Indeed, adsorption between the surface and the molecules involved in self-assembly is essential to allow the formation of a surface-bound or surface-supported, supramolecular structure [50]. A range of surfaces are available to researchers investigating such systems but some are more common than others, notably highly-oriented pyrolytic graphite (HOPG) and Au(111). However, in some areas of study, the surface plays an integral role in the reaction process providing active sites, such as metal atoms, which catalyse the formation of a specific product [55].
The other major aspect that influences the self-assembly process is the experimental conditions of the experiment. SPM techniques can be used in both UHV conditions or at the interface between surface and solution. These quite different conditions present both advantages and disadvantages depending on the specific molecules and reaction processes being investigated. For example, studying molecules and self-assembled aggregates in UHV conditions can lead to higher resolution imaging, in part because lower temperatures (below the freezing point of solvents) can be accessed. Additionally, ncAFM imaging specifically requires UHV conditions. However, the introduction of molecules to the surface typically involves sublimation, and hence heating of the sample. Sublimation is not always possible and thermal degradation is a significant impediment for complex molecules. Milder electrospray deposition techniques have been developed [56] but the use of this approach is not yet widespread. In contrast, studies at the solution-solid interface directly image self-assembled structures in the presence of solvent. In terms of preparative conditions, this approach is quite straightforward, simply imaging at the interface between a drop of solvent containing the molecules of interest and the substrate. Although this approach offers many advantages the choice of solvent, which is limited by the requirements for imaging, can clearly influence the self-assembly process, potentially with solvent molecules interacting or even co-adsorbing with the target species. Although images tend to have lower resolution than UHV studies, this is not always the case and remarkable examples of molecular resolution with AFM have been reported [49].
Ultimately, the possibilities that arise from the various approaches to create supramolecular structures suggest the possibility of creating molecular level devices and the application of 2D materials. The advances in this area are illustrated in the chapter by Huang and Wee where they discuss the rapidly advancing field that studies 2D transition metal dichalcogenides and their potential integration with organic molecules for multifunctional flexible devices.
This book brings together perspectives from research leaders in the field. It can be seen that across the breadth of the subject, there are many fascinating examples of applying supramolecular chemistry to the development of surface-based arrays. Whether through the direct implementation of hydrogen bonds, coordination bonds, or well-designed van der Waals interactions, or through the controlled formation of covalently-bonded arrays, it is clear that strategies for creating 2D arrays on surfaces are well developed. A theme that commonly arises throughout the contributions is that of complexity. It is not a surprise that this subject has become prominent in the field of surface-based supramolecular arrays when one considers the specificity of the SPM characterisation techniques employed for characterisation. When one applies a technique that affords molecular resolution, allowing detailed appreciation of extended frameworks, their complexity becomes all the more apparent, drawing the attention of researchers and hence becoming a focus for investigation. Remarkable discoveries have been made across the field and in turn, spur new endeavours. An emerging aspect of the field is the implementation of synthetic strategies towards new applications with electronic properties of new structures receiving notable attention. However, other directions of research are also emerging at the solid–solution interface, for example, applying the chirality of surface arrays. Exploiting the interplay between surface-based arrays and solution chemistry promises to be of significance in applications ranging from sensing to the interface with biological processes.
In summary, as is common for new areas of science, the field now stands at a crossroads. The origins of the field have been based on developing an underpinning methodology for both synthesis and characterisation and an appreciation of the many factors that affect surface-based supramolecular assembly. Increasingly, there is a focus on developing these fascinating 2D materials for specific applications and for their incorporation into devices. I am confident that all the authors of the other chapters will agree that there is a promising and bright future for the area of 2D chemistry on surfaces.
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2Characterisation and Interpretation of On-Surface Chemical Reactions Studied by Ultra-High-Resolution Scanning Probe Microscopy
Adam Sweetman1, Neil R. Champness2, and Alex Saywell3
1University of Leeds, School of Physics and Astronomy, Leeds LS2 9JT, UK
2University of Birmingham, School of Chemistry, Edgbaston, Birmingham B15 2TT, UK
3University of Nottingham, School of Physics and Astronomy, Nottingham NG7 2RD, UK
2.1 Introduction
The development of supramolecular chemistry on surfaces is reliant upon detailed characterisation at the molecular level. A variety of approaches have been employed to understand the detailed arrangement of molecules in self-assembled arrays but the dominant and typically most informative techniques are based upon scanning probe microscopy (SPM). In the main scanning-tunnelling microscopy (STM) [1] has been highly successful in establishing a detailed appreciation of the structure of supramolecular systems, often at the molecular level, but it can be helpful to supplement this approach with other techniques that allow an analysis of the chemical speciation or other structural features that STM cannot probe. For example, X-ray photoelectron spectroscopy (XPS) [2–5] allows investigation of the chemical composition of molecules within supramolecular arrays, and techniques such as X-ray standing wave (XSW) analysis [6] can probe the molecular conformations of adsorbed molecules. However, STM and atomic force microscopy (AFM) [7] are the most common techniques used to study surface-based supramolecular structures. Indeed, SPMs facilitate the characterisation of single molecules and assemblies of molecules, confined to a supporting substrate, on the molecular or sub-molecular level. The defining characteristic of all variants of SPM is the use of a probe to measure a specific probe–sample interaction over a grid of points, which is used to generate an ‘image’ of a well-defined spatial region of the surface; often resulting in resolution on the sub-Ångström level.
Conceptually, the probe is terminated with a single atom and it is the interaction between this atom and the molecule-substrate system which is measured. The origins of this probe–sample interaction determine the interpretation of the resulting image but commonly the information acquired provides a relatively simple pathway to understanding structural arrangements. Thus, the terminating atom at the apex of the probe is typically brought to within a few Ångström of the surface and, due to the strong distance dependence of the probe–surface interactions, the measured interaction is dominated by the position and properties of the single terminating atom. In both STM [1] and AFM [7], the current flow between the probe and sample or the probe–sample interaction force, respectively, are measured. In the majority of applications, the probe is either formed from a metal wire, sharpened mechanically or etched chemically, or an etched silicon tip. The resolution obtainable can be further improved when the apex of the tip is functionalised with a well-defined terminating species, such as CO [8], providing a probe with a defined size and known intermolecular chemistry. It is the localised nature of the probe–sample interaction measured by the probe, which gives rise to the high spatial resolution which allows the study of molecule-substrate systems on the atomic and molecular level.
A noteworthy feature of all SPM techniques is that the acquired data directly corresponds to real-space measurements, which allow an image of the surface to be produced. This is distinct from techniques such as X-ray crystallography and low-energy electron diffraction (LEED) where ensemble reciprocal space measurements are converted to produce a real-space structure. Such images of the surface, particularly of molecule-substrate systems, may often offer what appears to be an easily accessible view of molecular structure and/or reaction processes. However, great care should always be taken when interpreting the data acquired; the acquired data provides a wealth of information on the electronic and chemical structure of the system under study which is distinct from, although often related to, the topography of the adsorbed molecules.
This chapter seeks to provide a background to SPM studies of molecule-substrate systems and how they can be employed to understand self-assembled structures and in particular surface-based reaction processes. The chapter will focus on the underlying theory and experimental considerations that are required to conduct and interpret the investigation of on-surface synthesis reactions using high-resolution SPM methodologies. However, the specific examples discussed in this chapter also provide the underpinning concepts that can be applied to related areas of surface-based molecular assembly such as those discussed in the other chapters within this volume. The chapter provides details of the basic premise of SPM studies for molecule-substrate systems, including an overview of the experimental conditions (Section 2.2), and provides an in-depth discussion of the technical aspects of performing noncontact atomic force microscopy (ncAFM) experiments (Section 2.3). The physical processes underlying the probe–molecule interaction will be used as a basis for discussion of image interpretation (Section 2.4), and in the final section (Section 2.5) examples of on-surface reactions investigated by SPM will be given; focusing specifically on the formation of graphene structures (including graphene nanoribbons – GNRs) and cyclisation reactions (e.g. Bergman cyclisation).
2.2 SPM Under UHV Conditions
Although there are many examples of the implementation of SPM in ambient, liquid, and even electrochemical environments, here we specifically focus on the ultra-high vacuum (UHV) studies conducted at cryogenic temperatures (e.g. <5 K – achievable using liquid helium). A UHV environment is usually a vital prerequisite for the formation of atomically flat and clean substrates. All SPM techniques work optimally, with regards to the characterisation of molecular species, when large areas (>100 nm2) of flat surface are accessible. These large atomically flat regions facilitate sub-molecular and atomic resolution, which is in itself a prerequisite for the characterisation of on-surface chemical reactions.
Sample preparation under UHV conditions allows contaminant-free surfaces to be produced (simply by limiting exposure to contaminant species), offers accurate temperature control for sample preparation (with specific temperatures required to form certain surface reconstructions), and facilitates the use of the cleaning procedures described in Section 2.3. Typically UHV chambers allow pressures down to ∼10−10 mbar, and lower, to be obtained. Cryogenic SPM systems also allow samples to be cooled to <5 K (inhibiting both molecular diffusion and the progress of chemical reactions – required to study intermediate states of on-surface reactions).
There is however a disconnect between the use of UHV and the environment in which industrial scale, or even lab-based, chemical reactions often take place: specifically with regards to the environment in which solution-phase reactions are performed. In general, it is not possible to introduce solvents into UHV (as the high vapour pressure of many solvents renders them incompatible with a UHV environment), meaning that reactions investigated by SPM under UHV are studied in the absence of solvents. In addition, studying such molecule-substrate systems under UHV, as opposed to ambient conditions, gives rise to several challenges (including the inherent technical difficulties of simply moving samples around in a UHV environment). Most notable is the issue of transferring the molecules to a surface held in UHV. In the simplest case, a crucible loaded with the molecules under study can be introduced to the UHV system with subsequent thermal evaporation used to produce a sub-monolayer to multi-layer film upon the substrate. However, in many cases, the molecules may be non-volatile or thermally labile and in such cases, one of a variety of alternative techniques has to be employed [9].
There are several benefits in utilising UHV-SPM compared to other characterisation techniques. The molecules to be studied do not have to be crystalline (as is the case for some diffraction-based techniques) and only very small quantities of material are required for study by SPM (compared to, for example, nuclear magnetic resonance [NMR]). Combined with the exceptionally high spatial resolution offered by SPM, the technique has recently gained importance as a characterisation technique that can provide ‘real space’ characterisation of molecule-substrate systems, which both complements and enhances the chemical and structural characterisation offered by ensemble averaging techniques.
2.2.1 On-Surface Reactions
An obvious consideration with regards to characterisation utilising SPM techniques is that the molecules investigated have to be studied on a supporting substrate; prohibiting the study of solvent confined systems. The operational mechanics of SPM lend themselves to the study of systems confined to a 2D substrate and provide an invaluable technique for investigating chemical reactions upon, a potentially reactive and/or catalytic [10], surface (see reviews [10–15] and references therein). As the systems to be studied are on a substrate, this precludes the use of transmission electron microscopy (TEM) which can also be used in principle to provide atomic-level resolution, but is generally unsuitable for the study of molecule-substrate systems due to the thickness of the substrates required.
The major benefit of characterisation via SPM is the level of spatial resolution achievable (vertical resolution of less than 5 pm and sub-angstrom lateral resolution is routine). This is based upon sensitive measurements of the probe–substrate/molecule interaction (vide infra). As the probe plays a vital part in the measurements, one needs to consider its shape, and its electronic and chemical properties, as these can potentially give rise to a variety of ‘artefacts’ (Section 2.3 discusses this in detail). An additional benefit of confining a chemical reaction to a 2D plane is the potential to control reactions via different methodologies to those available in solution [16]. The technique has also been shown to allow different stages during the progression of a chemical reaction to be studied (i.e. initial, final, and even intermediate states) [13].
Two main variants of SPM have commonly been employed to study on-surface reactions; STM and AFM. In particular, a specific variant of AFM, ncAFM, provides a sub-molecular resolution that allows characterisation of the spatial position of chemical groups within a molecule, as well as facilitating not only the observation of single chemical bonds [8] but providing a methodology to distinguish the bond order (i.e. single, double, or triple carbon–carbon bond species) [17]. It is important to note that the specific aspects of ncAFM (discussed in detail throughout this chapter) provide sub-molecular resolution, and therefore, sub-molecular resolution ncAFM is part of the family of SPM techniques, it is not simply a mode of operation that can be applied to other SPM systems and requires, at least in the current implementation, a specific experimental set-up.
The level of sub-molecular resolution provided by ncAFM can be used to complement traditional characterisation techniques (e.g. NMR, GLC, LEED) and, for example, allows a level of single-molecule characterisation, which can aid in the structural determination of completely new species (typified by the role of ncAFM in the characterisation of a planar, proton-poor compound in combination with computational studies [18]) as well as distinguishing between the structure of asphaltenes (polycyclic aromatic hydrocarbons within crude oil; whose structural analysis is a tremendous challenge for non-spatially resolved techniques) [19].
2.2.2 Characterisation of Molecule-Substrate Systems via STM
There are many ‘flavours’ of SPM all designated by a confusing menagerie of acronyms, including but not limited to STM, ncAFM, KPFM (Kelvin probe force microscopy), and SNOM (scanning near-field optical microscopy). The archetypal example of this set of methods is STM. In common with all SPM methodologies, STM works by scanning a probe across a surface, in this case with an applied bias (relative to the probe – which is usually defined as grounded). The conducting tip (usually metallic) is moved in a straight line across a conducting/semi-conducting surface and the interaction between the probe and the tip measured (in the case of STM, the measured quantity is the magnitude of the current flow due to electrons tunnelling between the probe and the surface, or vice versa). Details of the concepts underpinning STM are given in several excellent textbooks [20, 21], but in summary, the salient points are: (i) the substrate is biased relative to the probe (typically in the range ±2 V), (ii) the resultant flow of electrons between the probe and the molecule/substrate is recorded, (iii) the magnitude of this tunnel-current (I) has an exponential dependence on the distance between the probe and the substrate/molecule, and (iv) the vertical probe position (z) can be varied in order to give a constant current as the probe is moved laterally across the surface (this feed-back mode is known as a constant-current operation) or (v) the vertical probe position is kept constant and the current is recorded at various lateral positions above the substrate/molecule, known as constant-height mode (see Figure 2.1).
An STM image is produced by obtaining a series of line scans (shown in Figure 2.1a), which are then combined to form a 2D image. In constant current mode, I is maintained at a fixed set-point, typically a few picoamperes, and the resultant image, therefore, shows the variation in z as the probe is scanned over the surface. In constant height mode, images will show the variation in I with tip position. It is important to note that the measured current, for a finite bias voltage, is proportional to the sum of the contributions for the local density of states (LDOS) from which tunnelling is possible [20, 21]; i.e. the measured current is related to the electronic structure of the molecule/substrate, and is not necessarily well correlated to the spatial position of the atomic nuclei. In this respect, the path of the probe in constant-current mode does not simply provide a topographic height but is better interpreted as a map of the LDOS. This issue manifests in the characterisation of molecules where molecular orbitals are often delocalised over the molecular species under study. Therefore, preventing the position of individual atoms, within similar chemical environments (e.g. conjugated aromatic carbons), from being resolved as they will often form part of the same feature observed within an STM image. However, in cases where electronic character is localised over specific chemical moieties, STM images may be compared (at least as an approximation) to the chemical structure of the molecule under study. An example of this is shown in Figure 2.1c where the structure of a brominated terfluorene molecule (α,ω-dibromoterfluorene [DBTF]) can be compared with a constant-current STM image [22]; features related to the peripheral Br atoms and central fluorene groups are visible. Such electronic structures are often compared with density functional theory (DFT) based simulations of STM images, which can help identify molecular structure and conformations [24].
While STM can provide sub-molecular resolution, it suffers, in common with all SPM techniques, with regards to the non-trivial interpretation of the acquired data. Although DFT studies used in conjunction with STM data often offer good agreement and provide a plausible interpretation of the results (in terms of a more complete appreciation of the expected LDOS), an overreliance on DFT can lead to potential pitfalls as calculating the energy and spatial distribution of molecular orbitals for surface adsorbed species can be challenging (specifically when taking into account hybridisation with electronic surface states). This is not to say that STM is not able to provide reliable and informative evidence with regards to the study of molecule-surface systems, but rather that it is best used in conjunction with complementary techniques to ensure robust characterisation of the structural, chemical, and electronic properties of the molecules under study.
Figure 2.1 Outline of SPM image acquisition and examples of molecular characterisation. (a) Schematic showing image acquisition via a series of line profiles in constant current operation of STM. (b) Operation of STM in constant-height mode. (c) Example of STM characterisation of a single DBTF molecule via STM [22] (Scale bar: 1 nm, VSample-bias = − 0.4 V, ISet-point
