STM Study of Terephthalic Acid Self-Assembly on Au(111): Hydrogen-Bonded Sheets on an Inhomogeneous Substrate

Recent Progress of Imaging Chemical Bonds by Scanning Probe Microscopy: A Review

In the past decades, the invention of scanning probe microscopy (SPM) as the versatile surface-based characterization of organic molecules has triggered significant interest throughout multidisciplinary fields. In particular, the bond-resolved imaging acquired by SPM techniques has extended its fundamental function of not only unraveling the chemical structure but also allowing us to resolve the structure-property relationship. Here, we present a systematical review on the history of chemical bonds imaged by means of noncontact atomic force microscopy (nc-AFM) and bond-resolved scanning tunneling microscopy (BR-STM) techniques. We first summarize the advancement of real-space imaging of covalent bonds and the investigation of intermolecular noncovalent bonds. Beyond the bond imaging, we also highlight the applications of the bond-resolved SPM techniques such as on-surface synthesis, the determination of the reaction pathway, the identification of molecular configurations and unknown products, and the generation of artificial molecules created via tip manipulation. Lastly, we discuss the current status of SPM techniques and highlight several key technical challenges that must be solved in the coming years. In comparison to the existing reviews, this work invokes researchers from surface science, chemistry, condensed matter physics, and theoretical physics to uncover the bond-resolved SPM technique as an emerging tool in exploiting the molecule/surface system and their future applications.

Enantiopure molecules form apparently racemic monolayers of chiral cyclic pentamers

Ultra-high vacuum scanning tunneling microscopy (UHV-STM) was used to investigate two related molecules pulse-deposited onto Au(111) surfaces: indoline-2-carboxylic acid and proline (pyrrolidine-2-carboxylic acid). Indoline-2-carboxylic acid and proline form both dimers and C5-symmetric "pinwheel" pentamers. Enantiomerically pure S-(-)-indoline-2-carboxylic acid and S-proline were used, and the pentamer structures observed for both were chiral. However, the presence of apparently equal numbers of 'right-' and 'left-handed' pinwheels is contrary to the general understanding that the chirality of the molecule dictates supramolecular chirality. A variety of computational methods were used to elucidate pentamer geometry for S-proline. Straightforward geometry optimization proved difficult, as the size of the cluster and the number of possible intermolecular interactions produced an interaction potential with multiple local minima. Instead, the Amber force field was used to exhaustively search all of phase space for chemically reasonable pentamer structures, producing a limited number of candidate structures that were then optimized as gas-phase clusters using density functional theory (DFT). The binding energies of the two lowest-energy pentamers on the Au(111) surface were then calculated by plane-wave DFT using the VASP software, and STM images predicted. These calculations indicate that the right- and left-handed pentamers are instead two different polymorphs.

Effects of Anion Coadsorption on the Self-Assembly of 11-Acryloylamino Undecanoic Acid on an Au(111) Electrode

11-acryloylamino undecanoic acid (AAUA) is a versatile polymerizable surfactant that has been applied to coat medical devices, and these applications can benefit from a fundamental understanding of its interaction with a metal substrate. Cyclic voltammetry and in situ scanning tunneling microscopy (STM) were used to examine the adsorption configuration of AAUA molecules on an ordered Au(111) electrode and their mutual interactions, as AAUA was adsorbed from a methanol dosing solution. In addition to the van der Waals force between the aliphatic groups, the hydrogen bonding between the carboxylic acid and acrylamide groups was also important to guide the spatial arrangement of AAUA admolecules on the Au electrode. The -COOH group of AAUA admolecule likely dissociated in neutral media to -COO-, which formed hydrogen bonds with H2PO4 - in phosphate buffer solution (PBS). This interaction between the AAUA admolecules and ions in the electrolyte resulted in different electrochemical characteristics observed in phosphate buffer solution (PBS) and potassium sulfate (K2SO4). Molecular-resolution STM imaging revealed distinctly different AAUA spatial structures on the Au electrode in PBS and K2SO4. Shifting the potential positively to 0.5 V (versus Ag/AgCl) led to lifting of the reconstructed Au(111) to the (1 × 1) phase and the dissolution of the ordered AAUA film, suggesting that the orientation of the AAUA admolecule was altered. The ordered AAUA adlayer could be partially recovered by shifting the potential negatively.

Procrystalline Self-Assembly of Desymmetrized Pentaphenylcyclopentadiene

The interplay between the molecular shape and the intermolecular interaction plays a decisive role in self-assembled structures. Recently, inherent randomness of low ordered assemblies, resulting from lack of short- and long-range periodicities, has attracted significant attention due to the unique structural, electronic, and mechanical properties. Here, we present procrystalline self-assemblies of pentaphenyl cyclopentadienyl derivatives on Ag(111) and Au(111) with scanning tunneling microscopy, operating at 4.3 K under ultrahigh vacuum conditions. Two examples, using 5-fold symmetric molecules substituted with methyl or fluorine groups, show that weak interactions, such as π-π stacking, CH-π interactions, and CH···F hydrogen bonding, play a pivotal role in formation of the procrystalline assembly. Our results may give insights into the intricate relationship between the molecular shape and the intermolecular interaction in the formation of non-crystalline assemblies.

Tensor renormalization group study of orientational ordering in simple models of adsorption monolayers

A simple lattice model of the orientational ordering in organic adsorption layers that considers the directionality of intermolecular interactions is proposed. The symmetry and the number of rotational states of the adsorbed molecule are the main parameters of the model. The model takes into account both the isotropic and directional contributions to the molecule-molecule interaction potential. Using several special cases of this model, we have shown that the tensor renormalization group (TRG) approach can be successfully used for the analysis of orientational ordering in organic adsorption layers with directed intermolecular interactions. Adsorption isotherms, potential energy, and entropy have been calculated for the model adsorption layers differing in the molecule symmetry and the number of rotational states. The calculated thermodynamic characteristics show that entropy effects play a significant role in the self-assembly of dense phases of the molecular layers. All the results obtained with the TRG have been verified by the standard Monte Carlo method. The proposed model reproduces the main features of the phase behavior of the real adsorption layers of benzoic, terephthalic, and trimesic acids on a homogeneous surface of metal single crystals and graphite.

Engineering Two-Dimensional Multilevel Supramolecular Assemblies from a Bifunctional Ligand on Au(111)

Herein, we demonstrate the supramolecular assemblies from a bifunctional ligand on Au(111), towards engineering two-dimensional (metal-) organic multilevel nanostructures. The bifunctional ligand employed, including two Br atoms and one carboxylic terminal, offers multiple bonding motifs with different configurations and binding energies. These bonding motifs are highly self-selective and self-recognizable, and thus afford the formation of subunits that contribute to engineering multilevel self-assemblies. Our scanning tunneling microscopy experiments, in combination with the density functional theory calculations, revealed various hydrogen, halogen and alkali-carboxylate bonding motifs dictating the different levels of the assemblies. The multilevel assembly protocol based on a judicious choice of multiple bonding motifs guarantees a deliberate control of surface-confined (metal-) organic nanostructures. Our findings may present new opportunities for the fabrication of complex two-dimensional (metal-) organic nanostructures with potential in applications of functionally diverse nanomaterials.

Successive Deprotonation Steering the Structural Evolution of Supramolecular Assemblies on Ag(111)

In this study, we demonstrate the structural evolution of a two-dimensional (2D) supramolecular assembly system, which is steered by the thermally activated deprotonation of the primary organic building blocks on a Ag(111) surface. Scanning tunneling microscopy revealed that a variety of structures, featuring distinct structural, chiral, and intermolecular bonding characters, emerged with the gradual thermal treatments. According to our structural analysis, in combination with density function theory calculations, the structural evolution can be attributed to the successive deprotonation of the organic building blocks due to the inductive effect. Our finding offers a facile strategy towards controlling the supramolecular assembly pathways and provides a comprehensive understanding of the 2D crystal engineering on surfaces.

Molecular Imaging of Viologen Adlayers and In Situ Monitoring Structural Transformations at Electrode-Electrolyte Interfaces

The effects of temperature and molecular concentration on the ordering of two-dimensional (2D) nanostructures have been investigated at the well-defined Au(111)-electrolyte interface. In comparison to the assembly of thiolated alkanes or hydrogen-bonded nonthiolated molecules, fabricating large aromatic thiolated molecules into a highly ordered adlayer on a surface remained a challenge. In this study, we demonstrated the importance of controlling the assembly conditions and procedures for the formation of ordered adlayers of redox-active viologen derivatives. The assembly conditions that were explored include the variation of molar concentration of assembly solutions, assembly time, and thermal annealing. We report that the optimal assembly conditions for creating highly ordered thiolated viologen derivatives on a Au(111)-(1 × 1) electrode surface are to limit the time in which the electrode is immersed in a deoxygenated 0.05 mM ethanolic viologen solution (preheated to 70 °C) to 45 s, followed by thermal annealing in absolute ethanol for 12 h. Highly ordered molecular adlayers were imaged by electrochemical scanning tunneling microscopy (STM), revealing the molecular packing of low-coverage adlayers. Furthermore, in situ STM combined with cyclic voltammetry (CV) allowed for the exploration of the structural transformation and potential limit of reductive and "oxidative" desorption of adlayers within the electrochemical potential range of the sample potential (E_S) from -0.95 V to -0.10 V vs SCE.

Current Progress and Future Directions in Gas-Phase Metal-Organic Framework Thin-Film Growth

Deposition of materials as a thin film is important for various applications, such as sensors, microelectronic devices, and membranes. There have been breakthroughs in gas-phase metal-organic framework (MOF) thin-film growth, which is more applicable to micro- and nanofabrication processes and also less harmful to the environment than solvent-based methods. Three different types of gas-phase MOF thin film deposition methods have been developed using chemical vapor deposition (CVD), atomic layer deposition (ALD), and physical vapor deposition (PVD)-CVD combined techniques. The CVD-based method basically converts metal oxide layers into MOF thin films by exposing the surface to ligand vapor. The ALD-based method allows growing MOF thin films following layer-by-layer (LBL) growth by sequentially exposing gas-phase metal and ligand precursors. The PVD-CVD method uses PVD for metal deposition and CVD for ligand deposition, which is similar to LBL growth. These gas-phase growth methods can broaden the use of MOFs in diverse areas. Herein, the current progress of gas-phase MOF thin film growth is discussed and future directions suggested.

Quantifying the Ultraslow Desorption Kinetics of 2,6-Naphthalenedicarboxylic Acid Monolayers at Liquid-Solid Interfaces

Kinetic effects in monolayer self-assembly at liquid-solid interfaces are not well explored but can provide unique insights. We use variable-temperature scanning tunneling microscopy (STM) to quantify the desorption kinetics of 2,6-naphthalenedicarboxylic acid (NDA) monolayers at nonanoic acid-graphite interfaces. Quantitative tracking of the decline of molecular coverages by STM between 57.5 and 65.0 °C unveiled single-exponential decays over the course of days. An Arrhenius plot of rate constants derived from fits results in a surprisingly high energy barrier of 208 kJ mol^-1 that strongly contrasts with the desorption energy of 16.4 kJ mol^-1 with respect to solution as determined from a Born-Haber cycle. This vast discrepancy indicates a high-energy transition state. Expanding these studies to further systems is the key to pinpointing the molecular origin of the remarkably large NDA desorption barrier.

Control of the deprotonation of terephthalic acid assemblies on Ag(111) studied by DFT calculations and low temperature scanning tunneling microscopy

This paper deals with the investigations of terephthalic acid (TPA) molecules deposited on a low reactive Ag(111) surface and studied using scanning tunneling microscopy (STM) at low temperature and DFT calculations. These investigations show that two deprotonation states energetically equivalent can be produced at the single molecule level. On self assemblies, the mobility of H atoms at 77 K favours the motion of created defects in the layer. STM observations and DFT calculations show that the most stable structures are obtained when only one hydrogen atom is removed from an O-HO bond and when these deprotonated molecules are located in adjacent TPA rows.

On-surface synthesis of gold–coronene molecular wires

Perchlorocoronene undergoes selective dehalogenation under the one-dimensional constraint by intermolecular interactions, resulting in the formation of gold–coronene wires on Au(111) surfaces.

Fluorinated carboxylic acids as powerful building blocks for the formation of bimolecular monolayers

We compare the ability of a prototypical dicarboxylic acid and its fluorinated analogue to act as molecular building blocks for the formation of self-assembled monolayers. Whilst fluorination is found to prevent homomolecular self-assembly, it greatly increases the ability of the carboxylic acid to act as a hydrogen bond donor for the formation of bimolecular networks.

Probing Molecular Nanostructures of Aromatic Terephthalic Acids Triggered by Intermolecular Hydrogen Bonds and Electrochemical Potential

Self-assembly provides unique routes to create supramolecular nanostructures at well-defined surfaces. In the present work, we employed scanning tunneling microscopy (STM) in combination with electrochemical techniques to explore the adsorption and phase formation of a series of aromatic carboxylic acids (ACAs) at Au(111)/0.1 M HClO₄. Specific goals are to elucidate the roles of electrochemical potential and directional hydrogen-bonding on the structures and orientation of individual ACAs that form nanoarchitectures. ACAs are prototype materials for supramolecular self-assemblies via stereospecific hydrogen bonds between neighboring molecules. In this study, we mainly focus on a special ACA, terephthalic acid (TPA), which is almost insoluble in water, making the assembly of this molecule from aqueous solution challenging. Depending on the applied electric field, TPA molecules form distinctly different, highly ordered adlayers on Au(111) triggered by directional intermolecular hydrogen bonds. At low electrochemical potentials, TPA molecules are planar oriented, forming a potentially infinite hydrogen-bonded adlayer without any observed domain boundaries. The increase of the electrode potential triggers the deprotonation of one carboxylic acid functional group of TPA; additionally, this is accompanied by an orientation change of molecules from planar to perpendicular. In contrast, structural "defects" and multiple domain boundaries were found at this positively charged surface. The assembled nanostructures of TPA are compared with other ACAs (trimesic acid, benzoic acid, and isophthalic acid), and corresponding adsorption models were built for all molecular adlayers, showing that intermolecular hydrogen-bonding plays a determining role in the formation of two-dimensional ACA nanostructures.

Controlling a Chemical Coupling Reaction on a Surface: Tools and Strategies for On-Surface Synthesis

On-surface synthesis is appearing as an extremely promising research field aimed at creating new organic materials. A large number of chemical reactions have been successfully demonstrated to take place directly on surfaces through unusual reaction mechanisms. In some cases the reaction conditions can be properly tuned to steer the formation of the reaction products. It is thus possible to control the initiation step of the reaction and its degree of advancement (the kinetics, the reaction yield); the nature of the reaction products (selectivity control, particularly in the case of competing processes); as well as the structure, position, and orientation of the covalent compounds, or the quality of the as-formed networks in terms of order and extension. The aim of our review is thus to provide an extensive description of all tools and strategies reported to date and to put them into perspective. We specifically define the different approaches available and group them into a few general categories. In the last part, we demonstrate the effective maturation of the on-surface synthesis field by reporting systems that are getting closer to application-relevant levels thanks to the use of advanced control strategies.

Self-assembly of 5,6-dihydroxyindole-2-carboxylic acid: polymorphism of a eumelanin building block on Au(111)

Investigating two-dimensional (2D) self-assembled structures of biological monomers governed by intermolecular interactions is a prerequisite to understand the self-assembly of more complex biomolecular systems. 5,6-Dihydroxyindole carboxylic acid (DHICA) is one of the building blocks of eumelanin - an irregular heteropolymer and the most common form of melanin which has potential applications in organic electronics and bioelectronics. By means of scanning tunneling microscopy, density functional theory and Monte Carlo calculations, we investigate DHICA molecular configurations and interactions underlying the multiple 2D patterns formed on Au(111). While DHICA self-assembled molecular networks (SAMNs) are dominated by the hydrogen bonding of carboxylic acid dimers, a variety of 2D architectures are formed due to the multiple weak interactions of the catechol group. The hydroxyl group also allows for redox reactions, caused by oxidation via O2 exposure, resulting in molecular rearrangement. The susceptibility of the molecules to oxidation is affected by their SAMNs architectures, giving insights on the reactivity of indoles as well as highlighting non-covalent assembly as an approach to guide selective oxidation reactions.

Recent Advances of Hierarchical and Sequential Growth of Macromolecular Organic Structures on Surface

The fabrication of macromolecular organic structures on surfaces is one major concern in materials science. Nanoribbons, linear polymers, and porous nanostructures have gained a lot of interest due to their possible applications ranging from nanotemplates, catalysis, optoelectronics, sensors, or data storage. During decades, supramolecular chemistry has constituted an unavoidable approach for the design of well-organized structures on surfaces displaying a long-range order. Following these initial works, an important milestone has been established with the formation of covalent bonds between molecules. Resulting from this unprecedented approach, various nanostructures of improved thermal and chemical stability compared to those obtained by supramolecular chemistry and displaying unique and unprecedented properties have been developed. However, a major challenge exists: the growth control is very delicate and a thorough understanding of the complex mechanisms governing the on-surface chemistry is still needed. Recently, a new approach consisting in elaborating macromolecular structures by combining consecutive steps has been identified as a promising strategy to elaborate organic structures on surface. By designing precursors with a preprogrammed sequence of reactivity, a hierarchical or a sequential growth of 1D and 2D structures can be realized. In this review, the different reaction combinations used for the design of 1D and 2D structures are reported. To date, eight different sequences of reactions have been examined since 2008, evidencing the intense research activity existing in this field.

2-D assembly of supramolecular nanoarchitectures on Mg(0001)

In this work, a Mg(0001) single crystal is used as a novel template to grow 2D supramolecular nano-architectures. By using scanning tunnelling microscopy (STM) and high-resolution X-ray photoemission spectroscopy (HR-XPS), the formation of either a homo-molecular or metal-organic network is reported for carboxylic or amino functionalized molecules, respectively.

Assembly of Robust Holmium-Directed 2D Metal-Organic Coordination Complexes and Networks on the Ag(100) Surface

We describe the formation of lanthanide-organic coordination networks and complexes under ultra-high-vacuum conditions on a clean Ag(100) surface. The structures comprise single Ho atoms as coordination centers and 1,4-benzenedicarboxylate (from terephtalic acid, TPA) as molecular linkers. Using low-temperature scanning tunneling microscopy, we find two different chiral phases of surface-supported metal-organic structures incorporating Ho atoms. Density functional theory calculations can explain the structure of both binding motifs and give possible reasons for their varying formation under the respective Ho/TPA ratios, as well as deposition and annealing temperatures. Metal-ligand interactions drive the formation of cloverleaf-shaped mononuclear Ho-TPA₄ complexes establishing supramolecular arrays stabilized through hydrogen bonding. A 2D lanthanide-organic reticulation is observed when changing the stoichiometry between the two building blocks. The combined insights from scanning tunneling microscopy and density functional theory reveal the relative stability, charge transfer, and bonding environment of both motifs.

Room-temperature surface-assisted reactivity of a melanin precursor: silver metal-organic coordination versus covalent dimerization on gold

The ability of catecholamines to undergo oxidative self-polymerization provides an attractive route for preparation of coatings for biotechnology and biomedicine applications. However, efforts toward developing a complete understanding of the mechanism that underpins polymerization have been hindered by the multiple catechol crosslinking reaction pathways that occur during the reaction. Scanning tunneling microscopy allows the investigation of small molecules in a reduced-complexity environment, providing important insight into how the intermolecular forces drive the formation of supramolecular assemblies in a controlled setting. Capitalizing on this approach, we studied the self-assembly of 5,6-dihydroxy-indole (DHI) on Au(111) and Ag(111) to investigate the interactions that affect the two-dimensional growth mechanism and to elucidate the behavior of the catechol group on these two surfaces. X-ray photoelectron spectroscopy, together with density functional theory and Monte Carlo modeling, helps unravel the differences between the two systems. The molecules form large ordered domains, yet with completely different architectures. Our data reveal that some of the DHI molecules deposited on Ag are in a modified redox state, with their catechol group oxidized into quinone. On Ag(111), the molecules are deposited in long-range lamellar patterns stabilized by metal-organic coordination, while covalent dimer pairs are observed on Au(111). We also show that the oxidation susceptibility is affected by the substrate, with the DHI/Au remaining inert even after being exposed to O2 gas.

Growth of regular nanometric molecular arrays on a functional 2D template based on a chemical guest-host approach

A regular 2D array of crown molecules, which would spontaneously self-assemble into disordered molecular clusters, is obtained by exploiting a guest-host process, based on the chemical affinity between amino and carboxylic groups on a gold surface. First a carboxylic organic template is formed, which then serves as a host for amino-functionalized crown molecules. The amino-carboxylic interaction thereby drives the formation of a monolayer of guest molecules, regularly distributed at the nanometer scale, preventing their aggregation in unordered clusters observed on a bare gold surface. This method, which can be applied to other guest molecules, represents a novel route to overcome the shape-matching requirements of the standard guest-host architectures. Furthermore, it is intrinsically selective, due to the chemical nature of the anchoring process.

Ubiquitous deprotonation of terephthalic acid in the self-assembled phases on Cu(100)

We performed an exhaustive study of terephthalic acid (TPA) self-assembly on a Cu(100) surface, where first-layer molecules display three sequential phase transitions in the 200–400 K temperature range, corresponding to different stages of molecular deprotonation.

Molecular adaptation in supramolecular self-assembly: brickwall-type phases of indacene-tetrone on silver surfaces

Different contrasts are observed via STM in brickwall phases of indacene-tetrone resulting from the adaptation on different epitaxial templates.

Supramolecular heterostructures formed by sequential epitaxial deposition of two-dimensional hydrogen-bonded arrays

Two-dimensional (2D) supramolecular arrays provide a route to the spatial control of the chemical functionality of a surface, but their deposition is in almost all cases limited to a monolayer termination. Here we investigated the sequential deposition of one 2D array on another to form a supramolecular heterostructure and realize the growth-normal to the underlying substrate-of distinct ordered layers, each of which is stabilized by in-plane hydrogen bonding. For heterostructures formed by depositing terephthalic acid or trimesic acid on cyanuric acid/melamine, we have determined, using atomic force microscopy under ambient conditions, a clear epitaxial arrangement despite the intrinsically distinct symmetries and/or lattice constants of each layer. Structures calculated using classical molecular dynamics are in excellent agreement with the orientation, registry and dimensions of the epitaxial layers. Calculations confirm that van der Waals interactions provide the dominant contribution to the adsorption energy and registry of the layers.

Self-assembly of melem on Au(111) and Ag(111): the origin of two different hydrogen bonding configurations

We studied the self-assembly of melem on the Au(111) and Ag(111) surfaces. By scanning tunneling microscopy imaging, we observed two different STM appearances of the melem molecule within the self-assembled nanostructure on Au(111), which resulted from the different intermolecular bonding configurations. Moreover, further DFT details including the intermolecular charge density difference and bonding energy were also obtained to compare the different natures of the intermolecular bonding configurations.

Ordered Superstructures of a Molecular Electron Donor on Au(111)

The molecular donor tetraphenyldibenzoperiflanthene (DBP) forms coverage-dependent superstructures on Au(111). At submonolayer coverage, the molecules align parallel to each other. They arrange in row-like structures, which exhibit a nearly rectangular primitive unit cell. By contrast, the molecular monolayer is characterized by a herringbone-type DBP arrangement spanned by an almost square unit cell containing two molecules. Both superstructures occur simultaneously in a narrow coverage range close to completion of the molecular monolayer. The adsorbate-substrate interaction is similar to other physisorbed molecular films on Au(111), but differs for the two adsorption phases as inferred from the different modification of the Au(111) surface reconstruction. Structural properties were consistently probed in real and reciprocal space by scanning tunneling microscopy and low-energy electron diffraction, respectively.

Coverage-Dependent Anchoring of 4,4'-Biphenyl Dicarboxylic Acid to CoO(111) Thin Films

We investigated the adsorption behavior of 4,4'-biphenhyl dicarboxylic acid (BDA) on well-ordered CoO(111) films grown on Ir(100) as a function of coverage and temperature using time-resolved and temperature-programmed infrared reflection absorption spectroscopy (TR-IRAS, TP-IRAS) in combination with density functional theory (DFT) and scanning tunneling microscopy (STM) under ultrahigh vacuum (UHV) conditions. To compare the binding behavior of BDA as a function of the oxide film thickness, three different CoO(111) film thicknesses were explored: films of about 20 bilayers (BLs) (approximately 5 nm), 2 BLs, and 1 BL. The two carboxylic acid groups of BDA offer two potential anchoring points to the oxide surface. At 150 K, intact BDA adsorbs on 20 BL thick oxide films in planar geometry with the phenyl rings aligned parallel to the surface. With decreasing oxide film thickness, we observe an increasing tendency for deprotonation and the formation of flat-lying BDA molecules anchored as dicarboxylates. After saturation of the first monolayer, intact BDA multilayers grow with molecules aligned parallel to the surface. The BDA multilayer desorbs at around 360 K. Completely different growth behavior is observed if BDA is deposited above the multilayer desorption temperature. Initially, doubly deprotonated dicarboxylates are formed by adopting a flat-lying orientation. With increasing exposure, however, the adsorbate layer transforms into upright standing monocarboxylates. A sharp OH stretching band (3584 cm^-1) and a blue-shifted CO stretching band (1759 cm^-1) indicate weakly interacting apical carboxylic acid groups at the vacuum interface. The anchored monocarboxylate phase slowly desorbs in a temperature range of up to 470 K. At higher temperature, a flat-lying doubly deprotonated BDA is formed, which desorbs and decomposes in a temperature range of up to 600 K.

On-surface synthesis of aligned functional nanoribbons monitored by scanning tunnelling microscopy and vibrational spectroscopy

In the blooming field of on-surface synthesis, molecular building blocks are designed to self-assemble and covalently couple directly on a well-defined surface, thus allowing the exploration of unusual reaction pathways and the production of specific compounds in mild conditions. Here we report on the creation of functionalized organic nanoribbons on the Ag(110) surface. C–H bond activation and homo-coupling of the precursors is achieved upon thermal activation. The anisotropic substrate acts as an efficient template fostering the alignment of the nanoribbons, up to the full monolayer regime. The length of the nanoribbons can be sequentially increased by controlling the annealing temperature, from dimers to a maximum length of about 10 nm, limited by epitaxial stress. The different structures are characterized by room-temperature scanning tunnelling microscopy. Distinct signatures of the covalent coupling are measured with high-resolution electron energy loss spectroscopy, as supported by density functional theory calculations.

On-surface synthesis, in which molecular units assemble and couple on a defined surface, can access rare reaction pathways and products. Here, the authors synthesize functionalized organic nanoribbons on the Ag(110) surface, and monitor the evolution of the covalent reactions by an unorthodox vibrational spectroscopy approach.

Self-assembled nanostructures of a di-carbonitrile molecule on copper single-crystal surfaces

A di-carbonitrile molecule prefers to form nanostructures by hydrogen bonds rather than coordination bonds on Cu(110) and Cu(100) at RT.

Molecular self-assembly of substituted terephthalic acids at the liquid/solid interface: investigating the effect of solvent

Self-assembly of three related molecules – terephthalic acid and its hydroxylated analogues – at liquid/solid interfaces (graphite/heptanoic acid and graphite/1-phenyloctane) has been studied using a combination of scanning tunnelling microscopy and molecular mechanics and molecular dynamics calculations. Brickwork-like patterns typical for terephthalic acid self-assembly have been observed for all three molecules. However, several differences became apparent: (i) formation or lack of adsorbed monolayers (self-assembled monolayers formed in all systems, with one notable exception of terephthalic acid at the graphite/1-phenyloctane interface where no adsorption was observed), (ii) the size of adsorbate islands (large islands at the interface with heptanoic acid and smaller ones at the interface with 1-phenyloctane), and (iii) polymorphism of the hydroxylated terephthalic acids’ monolayers, dependent on the molecular structure and/or solvent. To rationalise this behaviour, molecular mechanics and molecular dynamics calculations have been performed, to analyse the three key aspects of the energetics of self-assembly: intermolecular, substrate–adsorbate and solvent–solute interactions. These energetic characteristics of self-assembly were brought together in a Born–Haber cycle, to obtain the overall energy effects of formation of self-assembled monolayers at these liquid/solid interfaces.

Synthesis of new dithia[3.3]parapara- and metapara-cyclophane based tectons: toward an universal surface-confined 2D/3D molecular binding motif

A series of new paraphenylene-based 2D and 3D tectons has been designed for supramolecular self-assembly on both HOPG and Au. Several versatile chemical strategies have been developed to reach the target tectons, bearing either metaparacyclophane or paraparacyclophane cores, functionalized or not, allowing the obtention soon of more complex 3D tectons bearing functional unit such as chromophores. Moreover, preliminary STM results show that these compounds can successfully self-assemble both on HOPG and Au(111) substrates at liquid-solid interface, encouraging us in finding an universal surface-confined 2D/3D molecular binding motif. This feature combined with the preliminary results of the self-assembly on the plasmonic substrate Au(111) open-up opportunities in the field of Nanoscience.

Metal dependent motif transition in a self-assembled monolayer of bipyridine derivatives via coordination: An STM study

Low-dimensional molecular motifs with diversity developed via the on-surface chemistry are attracting growing interest for their potential in advanced nanofabrication. In this work, scanning tunneling microscopy was employed to investigate the in situ and ex situ metal coordinations between 4,4'-ditetradecyl-2,2'-bipyridine (bpy) and Zn(ii) or Cu(ii) ions at a highly oriented pyrolytic graphite (HOPG)/1-phenyloctane interface under ambient conditions. The results demonstrate that the bpy adopts a flat-lying orientation with its substituted alkyl chains in a tail-to-tail arrangement in a bpy monolayer. For the in situ coordination, the bpy/Zn(ii) and bpy/Cu(ii) complexes are aligned in edge-on fashions, wherein the bpy stands vertically on the HOPG surface and interdigitates at the alkyl chains. In the two-dimensional arrays of ex situ coordinated complexes, metal dependent motifs have been observed with Zn(ii) and Cu(ii), wherein the bipyridine moieties are parallel to the graphite surface. These results suggest that the desired on-surface coordination architectures may be achieved by the intentional selection of the metal centers.

On-Surface Domino Reactions: Glaser Coupling and Dehydrogenative Coupling of a Biscarboxylic Acid To Form Polymeric Bisacylperoxides

Herein we report the on-surface oxidative homocoupling of 6,6'-(1,4-buta-1,3-diynyl)bis(2-naphthoic acid) (BDNA) via bisacylperoxide formation on different Au substrates. By using this unprecedented dehydrogenative polymerization of a biscarboxylic acid, linear poly-BDNA with a chain length of over 100 nm was prepared. It is shown that the monomer BDNA can be prepared in situ at the surface via on-surface Glaser coupling of 6-ethynyl-2-naphthoic acid (ENA). Under the Glaser coupling conditions, BDNA directly undergoes polymerization to give the polymeric peroxide (poly-BDNA) representing a first example of an on-surface domino reaction. It is shown that the reaction outcome varies as a function of surface topography (Au(111) or Au(100)) and also of the surface coverage, to give branched polymers, linear polymers, or 2D metal-organic networks.

Generalized lattice-gas model for adsorption of functional organic molecules in terms of pair directional interactions

A generalized lattice-gas model that takes into account the directional character of pair interactions between the lattice sites is proposed. It is demonstrated that the proposed model can be successfully used to deeply understand the self-assembly process in adsorption monolayers of functional organic molecules driven by specified directional interactions between such molecules (e.g., hydrogen bonding). To illustrate the idea, representative cases of the general model with different numbers of identical functional groups in the chemical structure of the adsorbed molecule are investigated with Monte Carlo and the transfer-matrix methods. The model reveals that the phase behavior of the adsorption systems considered can be characterized as a hierarchical self-assembly process. It is predicted that in real adsorption systems of this type, the energy of hydrogen bonding sufficiently depends on the mutual orientation of the adsorbed molecules.

Surface-Supported Robust 2D Lanthanide-Carboxylate Coordination Networks

Lanthanide-based metal-organic compounds and architectures are promising systems for sensing, heterogeneous catalysis, photoluminescence, and magnetism. Herein, the fabrication of interfacial 2D lanthanide-carboxylate networks is introduced. This study combines low- and variable-temperature scanning tunneling microscopy (STM) and X-ray photoemission spectroscopy (XPS) experiments, and density functional theory (DFT) calculations addressing their design and electronic properties. The bonding of ditopic linear linkers to Gd centers on a Cu(111) surface gives rise to extended nanoporous grids, comprising mononuclear nodes featuring eightfold lateral coordination. XPS and DFT elucidate the nature of the bond, indicating ionic characteristics, which is also manifest in appreciable thermal stability. This study introduces a new generation of robust low-dimensional metallosupramolecular systems incorporating the functionalities of the f-block elements.

Trapping of Charged Gold Adatoms by Dimethyl Sulfoxide on a Gold Surface

We report the formation of dimethyl sulfoxide (DMSO) molecular complexes on Au(111) enabled by native gold adatoms unusually linking the molecules via a bonding of ionic nature, yielding a mutual stabilization between molecules and adatom(s). DMSO is a widely used polar, aprotic solvent whose interaction with metal surfaces is not fully understood. By combining X-ray photoelectron spectroscopy, low temperature scanning tunneling microscopy, and density functional theory (DFT) calculations, we show that DMSO molecules form complexes made by up to four molecules arranged with adjacent oxygen terminations. DFT calculations reveal that most of the observed structures are accurately reproduced if, and only if, the negatively charged oxygen terminations are linked by one or two positively charged Au adatoms. A similar behavior was previously observed only in nonstoichiometric organic salt layers, fabricated using linkage alkali atoms and strongly electronegative molecules. These findings suggest a motif for anchoring organic adlayers of polar molecules on metal substrates and also provide nanoscale insight into the interaction of DMSO with gold.

Nitrogen-Doping Induced Self-Assembly of Graphene Nanoribbon-Based Two-Dimensional and Three-Dimensional Metamaterials

Narrow graphene nanoribbons (GNRs) constructed by atomically precise bottom-up synthesis from molecular precursors have attracted significant interest as promising materials for nanoelectronics. But there has been little awareness of the potential of GNRs to serve as nanoscale building blocks of novel materials. Here we show that the substitutional doping with nitrogen atoms can trigger the hierarchical self-assembly of GNRs into ordered metamaterials. We use GNRs doped with eight N atoms per unit cell and their undoped analogues, synthesized using both surface-assisted and solution approaches, to study this self-assembly on a support and in an unrestricted three-dimensional (3D) solution environment. On a surface, N-doping mediates the formation of hydrogen-bonded GNR sheets. In solution, sheets of side-by-side coordinated GNRs can in turn assemble via van der Waals and π-stacking interactions into 3D stacks, a process that ultimately produces macroscopic crystalline structures. The optoelectronic properties of these semiconducting GNR crystals are determined entirely by those of the individual nanoscale constituents, which are tunable by varying their width, edge orientation, termination, and so forth. The atomically precise bottom-up synthesis of bulk quantities of basic nanoribbon units and their subsequent self-assembly into crystalline structures suggests that the rapidly developing toolset of organic and polymer chemistry can be harnessed to realize families of novel carbon-based materials with engineered properties.

Organic molecules deposited on graphene: a computational investigation of self-assembly and electronic structure

We use ab initio simulations to investigate the adsorption and the self-assembly processes of tetracyanoquinodimethane (TCNQ), tetrafluoro-tetracyanoquinodimethane (F4-TCNQ), and tetrasodium 1,3,6,8-pyrenetetrasulfonic acid (TPA) on the graphene surface. We find that there are no chemical bonds at the molecule-graphene interface, even at the presence of grain boundaries on the graphene surface. The molecules bond to graphene through van der Waals interactions. In addition to the molecule-graphene interaction, we performed a detailed study of the role played by the (lateral) molecule-molecule interaction in the formation of the, experimentally verified, self-assembled layers of TCNQ and TPA on graphene. Regarding the electronic properties, we calculate the electronic charge transfer from the graphene sheet to the TCNQ and F4-TCNQ molecules, leading to a p-doping of graphene. Meanwhile, such charge transfer is reduced by an order of magnitude for TPA molecules on graphene. In this case, it is not expected a significant doping process upon the formation of self-assembled layer of TPA molecules on the graphene sheet.

A competitive amino-carboxylic hydrogen bond on a gold surface

A novel amino-carboxylic hetero-synthon is described, which drives the formation of a complex 2D hetero-organic architecture.

Investigation of the non-covalent interactions of molecular self-assembly by scanning tunneling microscopy using the association of aromatic structures in pyrene-4,5,9,10-tetraone and phenanthrene-9,10-dione molecules

The self-assembled monolayers of aromatic molecules (pyrene-4,5,9,10-tetraone and phenanthrene-9,10-dione) were investigated at the liquid/solid (1-phenyloctane/graphite) interface using scanning tunneling microscopy, respectively.

Self-assembly of hydrogen-bonded two-dimensional quasicrystals

The process of molecular self-assembly on solid surfaces is essentially one of crystallization in two dimensions, and the structures that result depend on the interplay between intermolecular forces and the interaction between adsorbates and the underlying substrate. Because a single hydrogen bond typically has an energy between 15 and 35 kilojoules per mole, hydrogen bonding can be a strong driver of molecular assembly; this is apparent from the dominant role of hydrogen bonding in nucleic-acid base pairing, as well as in the secondary structure of proteins. Carboxylic acid functional groups, which provide two hydrogen bonds, are particularly promising and reliable in creating and maintaining surface order, and self-assembled monolayers of benzoic acids produce structure that depends on the number and relative placement of carboxylic acid groups. Here we use scanning tunnelling microscopy to study self-assembled monolayers of ferrocenecarboxylic acid (FcCOOH), and find that, rather than producing dimeric or linear structures typical of carboxylic acids, FcCOOH forms highly unusual cyclic hydrogen-bonded pentamers, which combine with simultaneously formed FcCOOH dimers to form two-dimensional quasicrystallites that exhibit local five-fold symmetry and maintain translational and rotational order (without periodicity) for distances of more than 400 ångströms.

Hydrogen-bonded clusters of ferrocenecarboxylic acid on Au(111)

A STM image of ferrocenecarboxylic acid clusters on Au(111), showing molecular clusters with both double-row and regular pentagonal geometries.

Born-Haber cycle for monolayer self-assembly at the liquid-solid interface: assessing the enthalpic driving force

The driving force for self-assembly is the associated gain in free energy with decisive contributions from both enthalpy and entropy differences between final and initial state. For monolayer self-assembly at the liquid-solid interface, solute molecules are initially dissolved in the liquid phase and then become incorporated into an adsorbed monolayer. In this work, we present an adapted Born-Haber cycle for obtaining precise enthalpy values for self-assembly at the liquid-solid interface, a key ingredient for a profound thermodynamic understanding of this process. By choosing terephthalic acid as a model system, it is demonstrated that all required enthalpy differences between well-defined reference states can be independently and consistently assessed by both experimental and theoretical methods, giving in the end a reliable value of the overall enthalpy gain for self-assembly of interfacial monolayers. A quantitative comparison of enthalpy gain and entropy cost reveals essential contributions from solvation and dewetting, which lower the entropic cost and render monolayer self-assembly a thermodynamically favored process.