Molecular and Supramolecular Networks on Surfaces: From Two-Dimensional Crystal Engineering to Reactivity

Patterned monolayer self-assembly programmed by side chain shape: four-component gratings

A molecular recognition strategy based on alkadiyne side chain shape is used to self-assemble a four-component, 1D-patterned monolayer at the solution-HOPG interface. The designed monolayer unit cell contains six molecules and spans 23 nm × 1 nm. The unit cell's internal structure and packing are driven by complementary shapes and lengths of six different alkadiyne side chains. A solution of the four compounds on HOPG self-assembles monolayers (i) comprised, almost entirely, of the intended unit cell, (ii) exhibiting patterned domains spanning 10(4) nm(2), and (iii) which are sufficiently robust that patterned domains survive solvent rinsing and drying. The patterned monolayer affords 1D-feature spacings ranging from 3.3 to 23 nm. The results demonstrate the remarkable selectivity afforded by molecular recognition based on alkadiyne side chain shape and the ability to program highly complex 1D-patterns in self-assembled monolayers.

Two-dimensional polymer as a mask for surface nanopatterning

NaCl islands are used as a sacrificial layer to selectively deposit a boronic acid based two-dimensional polymer. The nanostructured polymer layer can be used as a negative mask to create Fe islands in a nanolithography mimicking process.

One building block, two different nanoporous self-assembled monolayers: a combined STM and Monte Carlo study

With the use of a single building block, two nanoporous patterns with nearly equal packing density can be formed upon self-assembly at a liquid-solid interface. Moreover, the formation of both of these porous networks can be selectively and homogenously induced by changing external parameters like solvent, concentration, and temperature. Finally, their porous properties are exploited to host up to three different guest molecules in a spatially resolved way.

Hierarchically organized bimolecular ladder network exhibiting guided one-dimensional diffusion

The assembly and dynamics of a hierarchical, bimolecular network of sexiphenyl dicarbonitrile and N,N'-diphenyl oxalic amide molecules on the Ag(111) surface are studied by scanning tunneling microscopy at controlled temperature. The network formation is governed by a two-step protocol involving hierarchic interactions, including a novel carbonitrile-oxalic amide bonding motif. For temperatures exceeding ~70 K, more weakly bound sexiphenyl dicarbonitrile molecules carry out one-dimensional diffusion guided by the more stable substructure of the network held together by the carbonitrile-oxalic amide bonding motif. A theoretical investigation at the ab initio level confirms the different binding energies of the two coupling motifs and rationalizes the network formation and the diffusion pathway.

Random and ordered phases of off-lattice rhombus tiles

We study the covering of the plane by nonoverlapping rhombus tiles, a problem well studied only in the limiting case of dimer coverings of regular lattices. We go beyond this limit by allowing tiles to take any position and orientation on the plane, to be of irregular shape, and to possess different types of attractive interactions. Using extensive numerical simulations, we show that at large tile densities there is a phase transition from a fluid of rhombus tiles to a solid packing with broken rotational symmetry. We observe self-assembly of broken-symmetry phases, even at low densities, in the presence of attractive tile-tile interactions. Depending on the tile shape and interactions, the solid phase can be random, possessing critical orientational fluctuations, or crystalline. Our results suggest strategies for controlling tiling order in experiments involving "molecular rhombi."

Template-assisted assembly: scanning tunneling microscopy study of solvent-dependent adlattices of alkyl-derivatized tetrathiafulvalene

The self-assembly of an adsorbate as a function of the strength of solvent-substrate adsorption is an important yet relatively unexplored subject. In this study, how the strength of solvent-substrate adsorption and solvent-solvent attraction affects the assembly of tetrakis(octadecylthio)tetrathiafulvalene (1) is scrutinized by scanning tunneling microscopy (STM). For solvents with strong intermolecular interactions and adsorption onto graphite, such as long n-alkanes (C(n)H(2n+2), n ≥ 13), STM reveals that the solvent molecules form lamellae which become a template to direct the assembly of 1 into one-dimensional arrays. The lengths of one of the unit cell vectors for the assemblies are increased and well correlated with the solvent sizes. In situ STM monitoring of 1 introduced onto graphite with preadsorbed n-tetradecane adlattices shows that the developed assemblies of 1 have striped features aligned parallel to the underlying template. In contrast, for solvents with weak adsorption, such as short n-alkanes (C(n)H(2n+2), n ≤ 12), toluene, and 1,2,4-trichlorobenzene, the adlattice structures of 1 are solvent-independent.

Synthesis of well-ordered COF monolayers: surface growth of nanocrystalline precursors versus direct on-surface polycondensation

Two different straightforward synthetic approaches are presented to fabricate long-range-ordered monolayers of a covalent organic framework (COF) on an inert, catalytically inactive graphite surface. Boronic acid condensation (dehydration) is employed as the polymerization reaction. In the first approach, the monomer is prepolymerized by a mere thermal treatment into nanocrystalline precursor COFs. The precursors are then deposited by drop-casting onto a graphite substrate and characterized by scanning tunneling microscopy (STM). While in the precursors monomers are already covalently interlinked into the final COF structure, the resulting domain size is still rather small. We show that a thermal treatment under reversible reaction conditions facilitates on-surface ripening associated with a striking increase of the domain size. Although this first approach allows studying different stages of the polymerization, the direct polymerization, that is, without the necessity of preceding reaction steps, is desirable. We demonstrate that even for a comparatively small diboronic acid monomer a direct thermally activated polymerization into extended COF monolayers is achievable.

Interfacial self-assembly of amino acids and peptides: scanning tunneling microscopy investigation

Proteins play important roles in human daily life. To take advantage of the lessons learned from nature, it is essential to investigate the self-assembly of subunits of proteins, i.e., amino acids and polypeptides. Due to its high resolution and versatility of working environment, scanning tunneling microscopy (STM) has become a powerful tool for studying interfacial molecular assembly structures. This review is intended to reflect the progress in studying interfacial self-assembly of amino acids and peptides by STM. In particular, we focus on environment-induced polymorphism, chiral recognition, and coadsorption behavior with molecular templates. These studies would be highly beneficial to research endeavors exploring the mechanism and nanoscale-controlling molecular assemblies of amino acids and polypeptides on surfaces, understanding the origin of life, unravelling the essence of disease at the molecular level and deeming what is necessary for the "bottom-up" nanofabrication of molecular devices and biosensors being constructed with useful properties and desired performance.

To mix or not to mix: 2D crystallization and mixing behavior of saturated and unsaturated aliphatic primary amides

Physisorbed monolayers based on relatively weak noncovalent interactions can serve as excellent model systems for understanding crystallization of materials in reduced dimensionality. Here we employ a powerful combination of scanning tunneling microscopy (STM), differential scanning calorimetry (DSC), and computational modeling to reveal two-dimensional (2D) crystallization and mixing behavior of saturated and unsaturated (cis as well as trans) aliphatic primary amides. The foundation of the present work is laid by DSC measurements, which reveal characteristic adsorption and mixing behavior of aliphatic amides. These results are further supported by STM visualization of the adlayers. STM reveals, at submolecular resolution, the adsorption as well as the two-component 2D phase behavior of these molecules at the liquid-solid interface. The saturated and trans-unsaturated amides exhibit random mixing in view of their size and shape complementarity. Binary mixtures of saturated and cis-unsaturated amides, on the other hand, display unprecedented mixing behavior. The linear saturated and bent cis-unsaturated amide molecules are found to mix surprisingly better at the liquid-solid interface than might have been expected on account of the dissimilarity in their shapes. Strong, directional intermolecular hydrogen-bonding interactions as well as the relative stabilization energies of the adlayers are responsible for such unusual mixing behavior. Computational modeling provides additional insight into all the possible interactions in 2D assemblies and their impact on stabilization energies of the supramolecular networks. This study provides a model for understanding the effect of nanoscale cocrystallization on the thin film structure at interfaces and demonstrates the importance of molecular geometry and hydrogen bonding in determining the coadsorption behavior.

Heat-to-connect: surface commensurability directs organometallic one-dimensional self-assembly

Recent experiments demonstrated the assembly of unfunctionalized porphyrin molecules into organometallic wires on the Cu(110) surface through the formation of stable C-Cu-C bonds involving Cu adatoms. The remarkable property of the observed structures is that they adopt a clear direction, despite the lack of functional ligands to direct the assembly. Here we use density functional theory calculations and scanning tunneling microscopy to clarify the mechanism for the highly one-dimensional assembly of the observed nanostructures. An energetic preference for the formation of C-Cu-C bonds is found in several lattice directions, but self-assembly critically relies on the commensurability of appropriate adsorption sites for the Cu atoms involved in the coupling. The experimentally observed structures arise from a geometric self-limitation of the assembly process, which proceeds in the energetically and geometrically most preferred direction. A further extension of the structure in the orthogonal dimension to form 2D assemblies is prevented by the lattice mismatch between the repeat lengths in the <linear span>001<linear span> and <linear span>110<linear span> directions of the underlying (110) lattice and the apparent rigidity of the molecules involved. However, the fusing of two parallel chains is geometrically allowed and leads to some of the energetically most favorable configurations. Finally, the role of van der Waals forces is investigated for the covalent couplings and chemisorbed interactions found in this system.

Broken symmetry and the variation of critical properties in the phase behaviour of supramolecular rhombus tilings

The tiling of surfaces has long attracted the attention of scientists, not only because it is intriguing intrinsically, but also as a way to control the properties of surfaces. However, although random tiling networks are studied increasingly, their degree of randomness (or partial order) has remained notoriously difficult to control, in common with other supramolecular systems. Here we show that the random organization of a two-dimensional supramolecular array of isophthalate tetracarboxylic acids varies with subtle chemical changes in the system. We quantify this variation using an order parameter and reveal a phase behaviour that is consistent with long-standing theoretical studies on random tiling. The balance between order and randomness is driven by small differences in intermolecular interaction energies, which can be related by numerical simulations to the experimentally measured order parameter. Significant variations occur with very small energy differences, which highlights the delicate balance between entropic and energetic effects in complex self-assembly processes.

Molecular patterning at a liquid/solid interface: the foldamer approach

Molecular patterning has received a lot of attention in the past decade; however, the functionalization of these surface-confined 2D patterns on the nanoscale level remains a challenge. Assembling 2D patterns from oligomeric foldamers turns out to be an interesting approach to accomplishing the controlled positioning of functional elements. We designed a family of peptidomimetic foldamers bearing a 2D turn element folding at the liquid/solid interface. The turning element was developed while studying derivatives with one turning unit. Furthermore, folding was found to be induced by the confinement of the surface. This achievement paves the way for the design of foldamers with multiple turns, providing a higher versatility in the functionalization of nanopatterns.

Anhydrous thallium hydrogen L-glutamate: polymer networks formed by sandwich layers of oxygen-coordinated thallium ions cores shielded by hydrogen L-glutamate counterions

Anhydrous thallium hydrogen L-glutamate [Tl(L-GluH)] crystallizes from water (space group P2(1)) with a layer structure in which the thallium ions are penta- and hexacoordinated exclusively by the oxygen atoms of the γ-carboxylate group of the hydrogen L-glutamate anions to form a two-dimensional coordination polymer. The thallium-oxygen layer is composed of Tl(2)O(2) and TlCO(2) quadrangles and is only 3 Å high. Only one hemisphere of the thallium ions participates in coordination, indicative of the presence of the 6s(2) lone pair of electrons. The thallium-oxygen assemblies are shielded by the hydrogen l-glutamate anions. Only the carbon atom of the α-carboxylate group deviates from the plane spanned by the thallium ions, the γ-carboxylate groups and the proton bearing carbon atoms, which are in trans conformation. Given the abundance of L-glutamic and L-aspartic acid in biological systems on the one hand and the high toxicity of thallium on the other hand, it is worth mentioning that the dominant structural motifs in the crystal structure of [Tl(L-GluH)] strongly resemble their corresponding analogues in the crystalline phase of [K(L-AspH)(H(2)O)(2)].

Coalescence of 3-phenyl-propynenitrile on Cu(111) into interlocking pinwheel chains

3-phenyl-propynenitrile (PPN) adsorbs on Cu(111) in a hexagonal network of molecular trimers formed through intermolecular interaction of the cyano group of one molecule with the aromatic ring of its neighbor. Heptamers of trimers coalesce into interlocking pinwheel-shaped structures that, by percolating across islands of the original trimer coverage, create the appearance of gear chains. Density functional theory aids in identifying substrate stress associated with the chemisorption of PPN's acetylene group as the cause of this transition.

Self-assembled monolayer of Cr7Ni molecular nanomagnets by sublimation

We show, by complementary spectroscopic and STM analysis, that Cr(7)Ni derivatives are suitable to be sublimed in UHV conditions. Cr(7)Ni-bu weakly bonds to gold surface and can diffuse relatively freely on it, forming monolayers with hexagonal 2D packing. Conversely, by adding a functional thiol group to the central dibutylamine, a covalent bond between the molecule and surface gold adatoms is promoted, leading to a strong molecular grafting and the formation of a disordered monolayer. These two examples demonstrate the possibility to control the assembly of a large molecular complex, as rationalized by DFT calculations that establish different energy scales in the deposition processes. Moreover, low-temperature XMCD sprectra show that the magnetic features of Cr(7)Ni rings deposited in UHV on gold remain unchanged with respect to those of the corresponding bulk sample.

Polymorphic porous supramolecular networks mediated by halogen bonds on Ag(111)

Intermolecular structures of porous two-dimensional supramolecular networks are studied using scanning tunnelling microscopy combined with density functional theory calculations. The local configurations of halogen bonds in polymorphic porous supramolecular networks are directly visualized in support of previous bulk crystal studies.

Peculiar adsorbed phase behaviour of binary mixtures of oligopyridines and extension to a ternary mixture in a host-guest system

Binary mixtures of bis(terpyridine)s show a U shape behaviour in concentration dependent surface coverage at constant molar ratio. The phase separation can be exploited to create ternary mixtures with exclusive adsorption of the third component in one phase.

Heterogeneous bilayer molecular structure at a liquid-solid interface

Hexaphenylbenzene (HPB) derivatives, HPB-6a and HPB-6pa, can form a supramolecular network which is stabilized by the intermolecular hydrogen bonding between carboxyl group at an octanoic acid/graphite interface. The observation of the heterogeneous bilayer structure formed exclusively by coronene and HPB-6pa at the octanoic acid/graphite interface is reported. Pronounced selectivity of coronene for the supramolecular networks with different sizes is reflected through the formation of bilayer structure for HPB-6pa network with the introduction of coronene as the guest species, indicating stronger interactions between HPB-6pa and coronene.

Locking the free-rotation of a prochiral star-shaped guest molecule inside a two-dimensional nanoporous network by introduction of chlorine atoms

Two star-shaped triazatrinaphthylene (TrisK) derivatives form highly-organized nanoporous honeycomb networks when adsorbed at the n-tetradecane/HOPG interface. STM reveals that replacing three H-atoms by three Cl-atoms in the chemical structure of the TrisK skeleton results in locking the free-rotation of the guest molecules inside the pore of the host network as a result of symmetry breaking.

Little exchange at the liquid/solid interface: defect-mediated equilibration of physisorbed porphyrin monolayers

The transition from low to high density 2D surface structures of copper porphyrins at a liquid/solid interface requires specific defects at which nearly all exchange of physisorbed molecules with those dissolved in the supernatant occurs.

Steric blocking as a tool to control molecular film geometry at a metal surface

The application of steric blocking in surface science is exemplified by the control of surface patterns through the selective methylation of pentacenetetrone. Pentacenetetrones interact (with one another) on Cu(111) via intermolecular hydrogen bonding involving the carbonyl oxygen and the adjacent hydrogen atoms. Steric blocking of the intermolecular interaction by the successive insertion of inert methyl groups at terminal locations transforms a dense molecular pattern first into isolated double rows and eventually into single rows in a highly predictable fashion. Density functional theory modeling reveals the underlying energetics.

Combined SPM investigation on the interfacial structure of a phthalocyanine/conjugated polymer composite film

The morphology of the composite film of organic semiconductors determines the properties and performances of devices to a large extent. In this work, we present a combined AFM and STM study on the interfacial structures of CuPcOC8 and CuPcOC8/PmPV composite films on graphite surface. For CuPcOC8 thin films, the face-on epitaxial growth of CuPcOC8 could persist within 3 to 5 monolayers and the formation of π-π stacked columns will occur with edge-on configuration when the film thickness further increases. For the CuPcOC8/PmPV composite film with 1:1 weight ratio, STM results reveal a preferential adsorption of PmPV on graphite surface, while AFM results indicate the phase segregation in the upper layer. STM also reveals in the molecular scale good compatibility of CuPcOC8 with PmPV.

Control of self-assembled 2D nanostructures by methylation of guanine

Methylation of DNA nucleobases is an important control mechanism in biology applied, for example, in the regulation of gene expression. The effect of methylation on the intermolecular interactions between guanine molecules is studied through an interplay between scanning tunneling microscopy (STM) and density functional theory with empirical dispersion correction (DFT-D). The present STM and DFT-D results show that methylation of guanine can have subtle effects on the hydrogen-bond strength with a strong dependence on the position of methylation. It is demonstrated that the methylation of DNA nucleobases is a precise means to tune intermolecular interactions and consequently enables very specific recognition of DNA methylation by enzymes. This scheme is used to generate four different types of artificial 2D nanostructures from methylated guanine. For instance, a 2D guanine windmill motif that is stabilized by cooperative hydrogen bonding is revealed. It forms by self-assembly on a graphite surface under ambient conditions at the liquid-solid interface when the hydrogen-bonding donor at the N1 site of guanine is blocked by a methyl group.