On the origin of cooperativity effects in the formation of self-assembled molecular networks at the liquid/solid interface

In this work we investigate the behaviour of molecules at the nanoscale using scanning tunnelling microscopy in order to explore the origin of the cooperativity in the formation of self-assembled molecular networks (SAMNs) at the liquid/solid interface. By studying concentration dependence of alkoxylated dimethylbenzene, a molecular analogue to 5-alkoxylated isophthalic derivatives, but without hydrogen bonding moieties, we show that the cooperativity effect can be experimentally evaluated even for low-interacting systems and that the cooperativity in SAMN formation is its fundamental trait. We conclude that cooperativity must be a local effect and use the nearest-neighbor Ising model to reproduce the coverage vs. concentration curves. The Ising model offers a direct link between statistical thermodynamics and experimental parameters, making it a valuable tool for assessing the thermodynamics of SAMN formation.

Halogen Bonds Fabricate 2D Molecular Self-Assembled Nanostructures by Scanning Tunneling Microscopy

Halogen bonds are currently new noncovalent interactions due to their moderate strength and high directionality, which are widely investigated in crystal engineering. The study about supramolecular two-dimensional architectures on solid surfaces fabricated by halogen bonding has been performed recently. Scanning tunneling microscopy (STM) has the advantages of realizing in situ, real-time, and atomic-level characterization. Our group has carried out molecular self-assembly induced by halogen bonds at the liquid–solid interface for about ten years. In this review, we mainly describe the concept and history of halogen bonding and the progress in the self-assembly of halogen-based organic molecules at the liquid/graphite interface in our laboratory. Our focus is mainly on (1) the effect of position, number, and type of halogen substituent on the formation of nanostructures; (2) the competition and cooperation of the halogen bond and the hydrogen bond; (3) solution concentration and solvent effects on the molecular assembly; and (4) a deep understanding of the self-assembled mechanism by density functional theory (DFT) calculations.

Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding

Scanning tunnelling microscopy (STM) is commonly used to identify on-surface molecular self-assembled structures. However, its limited ability to reveal only the overall shape of molecules and their relative positions is not always enough to fully solve a supramolecular structure. Here, we analyse the assembly of a brominated polycyclic aromatic molecule on Au(111) and demonstrate that standard STM measurements cannot conclusively establish the nature of the intermolecular interactions. By performing high-resolution STM with a CO-functionalised tip, we clearly identify the location of rings and halogen atoms, determining that halogen bonding governs the assemblies. This is supported by density functional theory calculations that predict a stronger interaction energy for halogen rather than hydrogen bonding and by an electron density topology analysis that identifies characteristic features of halogen bonding. A similar approach should be able to solve many complex 2D supramolecular structures, and we predict its increasing use in molecular nanoscience at 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.

Halogen bonding versus hydrogen bonding induced 2D self-assembled nanostructures at the liquid-solid interface revealed by STM

We design a bifunctional molecule (5-bromo-2-hexadecyloxy-benzoic acid, 5-BHBA) with a bromine atom and a carboxyl group and its two-dimensional self-assembly is experimentally and theoretically investigated by using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. The supramolecular self-organization of 5-BHBA in two different solvents (1-octanoic acid and n-hexadecane) at the liquid-solid interface at different solution concentrations is obviously different due to the cooperative and competitive intermolecular halogen and hydrogen bonds. Three kinds of nanoarchitectures composed of dimers, trimers and tetramers are formed at the 1-octanoic acid/graphite interface based on -COOHHOOC-, triangular C[double bond, length as m-dash]OBrH-C, -BrO(H), BrBr, and OH interactions. Furthermore, by using n-hexadecane as the solvent, two kinds of self-assembled linear patterns can be observed due to the coadsorption, in which the dimers are formed by intermolecular -COOHHOOC- hydrogen bonds. The molecule-solvent and solvent-solvent van der Waals force and intermolecular hydrogen bonds dominate the formation of coadsorbed patterns. We propose that the cooperative and competitive halogen and hydrogen bonds are related to the polarity of the solvent and the type of molecule-solvent interaction. The intermolecular binding energy of different dimers and their stability are supported by theoretical calculations. The result provides a new and innovative insight to induce the 2D self-assembled nanostructures by halogen and hydrogen bonds at the liquid-solid interface.

Construction of Two-Dimensional Chiral Networks through Atomic Bromine on Surfaces

Using atomic bromine and 2,6-diphenylanthracene (DPA), we successfully constructed and characterized the large-area 2D chiral networks on Ag(111) and Cu(111) surfaces by combining molecular beam epitaxy with scanning tunneling microscopy. The Br atoms distribute themselves periodically in the network with the maximum number of -C-H···Br hydrogen bonds. Density functional theory calculations demonstrate that the hydrogen bonds contribute to the stability of the Br-organic networks. In addition, by controlling the ratio of bromine atoms to DPA molecules, different patterns of Br-organic networks were obtained on Ag(111) surfaces. Further experiments with 2,6-di(4-cyclohexylphenyl)anthracene on Ag(111) produced analogous atomic bromine guided 2D chiral networks.

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.

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.

Effects of the position and number of bromine substituents on the concentration-mediated 2D self-assembly of phenanthrene derivatives

The effects of the position and number of bromine substituents on the self-assembled patterns of phenanthrene derivatives by changing multiple weak intermolecular interactions were investigated at the 1-octanoic acid/graphite interface at different concentrations by scanning tunneling microscopy. Two Br substituted DBHP molecules (2,7-DBHP, 3,6-DBHP) and BHP without a Br group formed a linear lamellar pattern by the van der Waals interactions between the alkoxyl chains in each lamella at high concentrations, which forces the phenanthrene derivatives to self-organize in a π-π stacked edge-on conformation. On decreasing the solution concentration, owing to the molecule-molecule van der Waals force and BrBr halogen bonds or the molecule-solvent cooperative BrO (C[double bond, length as m-dash]O) hydrogen and BrHO-hydrogen bonds, 2,7-DBHP molecules were found to form two kinds of network structures, whereas 3,6-DBHP molecules formed only a zigzag pattern due to the intermolecular BrBr van der Waals type interactions. One bromine substituted phenanthrene derivative (3-DBHP) formed a dislocated linear pattern by two C-HBr hydrogen bonds in each dimer. These observations revealed that an important modification of the position and number of halogen substituents might dramatically change the self-assembly behaviors by different intermolecular interactions including BrBr and BrO halogen bonding, BrBr van der Waals type interactions, and HBr hydrogen bonding. DFT calculations were explored to unravel how slightly tuning the molecular structure defines the geometry of a 2D self-assembled nanoarchitecture through the different elementary structural units having BrBr and BrH interactions.

One “Click” access to self-complementary molecular modules for halogen bonding

The application of “click chemistry” has proved its efficacy for the construction of novel molecular modules for halogen bonding driven self-assembly.

Engineering porous and compact two-dimensional nanoarchitectures on surfaces taking advantage of bisterpyridine-derivatives self-assembly

The self-assembly of bis-terpyridine molecules is investigated using STM. Images reveal that close-packed as well as porous two-dimensional nanoarchitectures can be engineered by changing the molecular backbone separating the terpyridine groups.