Atomically Precise Prediction of 2D Self‐Assembly of Weakly Bonded Nanostructures: STM Insight into Concentration‐Dependent Architectures

A joint experimental and computational study is reported on the concentration‐dependant self‐assembly of a flat C₃‐symmetric molecule on a graphite surface. As a model system a tripodal molecule, 1,3,5‐tris(pyridin‐3‐ylethynyl)benzene, has been chosen, which can adopt either C_3h or C_s symmetry when planar, as a result of pyridyl rotation along the alkynyl spacers. Density functional theory (DFT) simulations of 2D nanopatterns with different surface coverage reveal that the molecule can generate different types of self‐assembled motifs. The stability of fourteen 2D patterns and the influence of concentration are analyzed. It is found that ordered, densely packed monolayers and 2D porous networks are obtained at high and low concentrations, respectively. A concentration‐dependent scanning tunneling microscopy (STM) investigation of this molecular self‐assembly system at a solution/graphite interface reveals four supramolecular motifs, which are in perfect agreement with those predicted by simulations. Therefore, this DFT method represents a key step forward toward the atomically precise prediction of molecular self‐assembly on surfaces and at interfaces.     

Tunable Two‐Dimensional Binary Molecular Networks

A novel approach to constructing tunable and robust 2D binary molecular nanostructures on an inert graphite surface is presented. The guest molecules are embedded into a host molecular matrix and constrained via the formation of multiple intermolecular hydrogen bonds. By varying the binary molecular ratio and the molecular geometry, various molecular arrays with tunable intermolecular distances are fabricated. The results suggest a promising route for the fabrication of ordered and stable molecular nanostructure arrays for molecular sensors, molecular spintronic devices, and molecular p–n nanojunctions.     

Molecular Self‐Assembly on Graphene

The formation of ordered arrays of molecules via self‐assembly is a rapid, scalable route towards the realization of nanoscale architectures with tailored properties. In recent years, graphene has emerged as an appealing substrate for molecular self‐assembly in two dimensions. Here, the first five years of progress in supramolecular organization on graphene are reviewed. The self‐assembly process can vary depending on the type of graphene employed: epitaxial graphene, grown in situ on a metal surface, and non‐epitaxial graphene, transferred onto an arbitrary substrate, can have different effects on the final structure. On epitaxial graphene, the process is sensitive to the interaction between the graphene and the substrate on which it is grown. In the case of graphene that strongly interacts with its substrate, such as graphene/Ru(0001), the inhomogeneous adsorption landscape of the graphene moiré superlattice provides a unique opportunity for guiding molecular organization, since molecules experience spatially constrained diffusion and adsorption. On weaker‐interacting epitaxial graphene films, and on non‐epitaxial graphene transferred onto a host substrate, self‐assembly leads to films similar to those obtained on graphite surfaces. The efficacy of a graphene layer for facilitating planar adsorption of aromatic molecules has been repeatedly demonstrated, indicating that it can be used to direct molecular adsorption, and therefore carrier transport, in a certain orientation, and suggesting that the use of transferred graphene may allow for predictible molecular self‐assembly on a wide range of surfaces.     

Molecular Design and Control Over the Morphology of Self‐Assembled Films on Ionic Substrates

Achieving control over formation of molecular films on insulating substrates is important for designing novel 2D functional materials and devices. To study the main factors governing successful control, organic molecules with interchangeable polar functional groups, a variable length aromatic body, and flexible hydrocarbon chains are designed, synthesized and then deposited on the (001) surfaces of bulk sodium chloride, potassium chloride, and rubidium chloride. The deposited structures are imaged using noncontact atomic force microscopy and modeled using density functional theory. The results show that it is possible to form large‐scale, highly ordered, 2D, porous molecular domains (>10⁴ pores), which are stable at room temperature, and to control the size of the 2D pores. Alternatively, it is possible to form line structures or droplets (through molecular dewetting) by altering the molecular structure or changing the substrate lattice constant. Theoretical calculations explain the balance of the molecule–molecule and molecule–surface interactions and the structure and thermodynamic stability of the grown films.     

Substrate Templating upon Self‐Assembly of Hydrogen‐Bonded Molecular Networks on an Insulating Surface

Molecular self‐assembly on insulating surfaces, despite being highly relvant to many applications, generally suffers from the weak molecule–surface interactions present on dielectric surfaces, especially when benchmarked against metallic substrates. Therefore, to fully exploit the potential of molecular self‐assembly, increasing the influence of the substrate constitutes an essential prerequisite. Upon deposition of terephthalic acid and trimesic acid onto the natural cleavage plane of calcite, extended hydrogen‐bonded networks are formed, which wet the substrate. The observed structural complexity matches the variety realized on metal surfaces. A detailed analysis of the molecular structures observed on calcite reveals a significant influence of the underlying substrate, clearly indicating a substantial templating effect of the surface on the resulting molecular networks. This work demonstrates that choosing suitable molecule/substrate systems allows for tuning the balance between intermolecular and molecule–surface interactions even in the case of typically weakly interacting insulating surfaces. This study, thus, provides a strategy for deliberately exploiting substrate templating to increase the structural variety in molecular self‐assembly on a bulk insulator at room temperature.     

Self‐Assembly: I‐Motif Nanospheres: Unusual Self‐Assembly of Long Cytosine Strands (Small 8/2011)

The synthesis and characterization of novel DNA structures based on tetraplex cytosine (C) arrangements, known as i‐motifs or i‐tetraplexes, is reported. Atomic force microscopy (AFM) investigation shows that long C‐strands in mild acidic conditions form compact spherically shaped nanostructures. The DNA nanospheres are characterized by a typical uniform shape and narrow height distribution. Electrostatic force microscopy (EFM) measurements performed on the i‐motif spheres clearly show their electrical polarizability. Further investigations by scanning tunneling microscopy (STM) at ultrahigh vacuum reveals that the structures exhibit an average voltage gap of 1.9 eV, which is narrower than the voltage gap previously measured for poly(dG)–poly(dC) molecules in similar conditions.     

Tuning Molecular Self‐Assembly on Bulk Insulator Surfaces by Anchoring of the Organic Building Blocks

Molecular self‐assembly constitutes a versatile strategy for creating functional structures on surfaces. Tuning the subtle balance between intermolecular and molecule‐surface interactions allows structure formation to be tailored at the single‐molecule level. While metal surfaces usually exhibit interaction strengths in an energy range that favors molecular self‐assembly, dielectric surfaces having low surface energies often lack sufficient interactions with adsorbed molecules. As a consequence, application‐relevant, bulk insulating materials pose significant challenges when considering them as supporting substrates for molecular self‐assembly. Here, the current status of molecular self‐assembly on surfaces of wide‐bandgap dielectric crystals, investigated under ultrahigh vacuum conditions at room temperature, is reviewed. To address the major issues currently limiting the applicability of molecular self‐assembly principles in the case of dielectric surfaces, a systematic discussion of general strategies is provided for anchoring organic molecules to bulk insulating materials.     

Lattice Deformation and Domain Distortion in the Self‐Assembly of Block Copolymer Thin Films on Chemical Patterns

The self‐assembly of cylinder‐forming block copolymer (BCP) microdomains confined within chemical stripe patterns of widths incommensurate with the natural period of the copolymers, L₀, is studied. It is shown that this incommensurability causes changes in both the shapes of the microdomains and their spatial period. Specifically, a transition from n to n + 1 rows of microdomains is observed when the stripe width is about n ± 1/2 L₀. When the stripe's width is comparable to L₀, ellipticity of microdomains can be induced with an aspect ratio up to 2.2. Free energy models are applied to describe the energetic origin of such behavior. Although our observations qualitatively resemble results in sphere‐forming BCPs confined in topographical trenches, the quantitative difference is noteworthy and technologically important for the design of nanostructures with programmable shapes.     

Organometallic Bonding in an Ullmann‐Type On‐Surface Chemical Reaction Studied by High‐Resolution Atomic Force Microscopy

The on‐surface Ullmann‐type chemical reaction synthesizes polymers by linking carbons of adjacent molecules on solid surfaces. Although an organometallic compound is recently identified as the reaction intermediate, little is known about the detailed structure of the bonded organometallic species and its influence on the molecule and the reaction. Herein atomic force microscopy at low temperature is used to study the reaction with 3,9‐diiododinaphtho[2,3‐b:2′,3′‐d]thiophene (I‐DNT‐VW), which is polymerized on Ag(111) in vacuum. Thermally sublimated I‐DNT‐VW picks up a Ag surface atom, forming a C? Ag bond at one end after removing an iodine. The C? Ag bond is usually short‐lived, and a C? Ag? C organometallic bond immediately forms with an adjacent molecule. The existence of the bonded Ag atoms strongly affects the bending angle and adsorption height of the molecular unit. Density functional theory calculations reveal the bending mechanism, which reveals that charge from the terminus of the molecule is transferred via the Ag atom into the organometallic bond and strengths the local adsorption to the substrate. Such deformations vanish when the Ag atoms are removed by annealing and C? C bonds are established.     

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.     

Guided Molecular Assembly on a Locally Reactive 2D Material

Atomically precise engineering of the position of molecular adsorbates on surfaces of 2D materials is key to their development in applications ranging from catalysis to single‐molecule spintronics. Here, stable room‐temperature templating of individual molecules with localized electronic states on the surface of a locally reactive 2D material, silicene grown on ZrB₂, is demonstrated. Using a combination of scanning tunneling microscopy and density functional theory, it is shown that the binding of iron phthalocyanine (FePc) molecules is mediated via the strong chemisorption of the central Fe atom to the sp³‐like dangling bond of Si atoms in the linear silicene domain boundaries. Since the planar Pc ligand couples to the Fe atom mostly through the in‐plane d orbitals, localized electronic states resembling those of the free molecule can be resolved. Furthermore, rotation of the molecule is restrained because of charge rearrangement induced by the bonding. These results highlight how nanoscale changes can induce reactivity in 2D materials, which can provide unique surface interactions for enabling novel forms of guided molecular assembly.     

Local Electronic Structure of Molecular Heterojunctions in a Single‐Layer 2D Covalent Organic Framework

The synthesis of a single‐layer covalent organic framework (COF) with spatially modulated internal potentials provides new opportunities for manipulating the electronic structure of molecularly defined materials. Here, the fabrication and electronic characterization of COF‐420: a single‐layer porphyrin‐based square‐lattice COF containing a periodic array of oriented, type II electronic heterojunctions is reported. In contrast to previous donor–acceptor COFs, COF‐420 is constructed from building blocks that yield identical cores upon reticulation, but that are bridged by electrically asymmetric linkers supporting oriented electronic dipoles. Scanning tunneling spectroscopy reveals staggered gap (type II) band alignment between adjacent molecular cores in COF‐420, in agreement with first‐principles calculations. Hirshfeld charge analysis indicates that dipole fields from oriented imine linkages within COF‐420 are the main cause of the staggered electronic structure in this square grid of atomically–precise heterojunctions.     

Light‐Induced Contraction/Expansion of 1D Photoswitchable Metallopolymer Monitored at the Solid–Liquid Interface

The use of a bottom‐up approach to the fabrication of nanopatterned functional surfaces, which are capable to respond to external stimuli, is of great current interest. Herein, the preparation of light‐responsive, linear supramolecular metallopolymers constituted by the ideally infinite repetition of a ditopic ligand bearing an azoaryl moiety and Co(II) coordination nodes is described. The supramolecular polymerization process is followed by optical spectroscopy in dimethylformamide solution. Noteworthy, a submolecularly resolved scanning tunneling microscopy (STM) study of the in situ reversible trans‐to‐cis photoisomerization of a photoswitchable metallopolymer that self‐assembles into 2D crystalline patterns onto a highly oriented pyrolytic graphite surface is achieved for the first time. The STM analysis of the nanopatterned surfaces is corroborated by modeling the physisorbed species onto a graphene slab before and after irradiation by means of density functional theory calculation. Significantly, switching of the monolayers consisting of supramolecular Co(II) metallopolymer bearing trans‐azoaryl units to a novel pattern based on cis isomers can be triggered by UV light and reversed back to the trans conformer by using visible light, thereby restoring the trans‐based supramolecular 2D packing. These findings represent a step forward toward the design and preparation of photoresponsive “smart” surfaces organized with an atomic precision.