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

Assessment of scanning tunneling spectroscopy modes inspecting electron confinement in surface-confined supramolecular networks

Scanning tunneling spectroscopy (STS) enables the local, energy-resolved investigation of a samples surface density of states (DOS) by measuring the differential conductance (dI/dV) being approximately proportional to the DOS. It is popular to examine the electronic structure of elementary samples by acquiring dI/dV maps under constant current conditions. Here we demonstrate the intricacy of STS mapping of samples exhibiting a strong corrugation originating from electronic density and local work function changes. The confinement of the Ag(111) surface state by a porous organic network is studied with maps obtained under constant-current (CC) as well as open-feedback-loop (OFL) conditions. We show how the CC maps deviate markedly from the physically more meaningful OFL maps. By applying a renormalization procedure to the OFL data we can mimic the spurious effects of the CC mode and thereby rationalize the physical effects evoking the artefacts in the CC maps.

Defects and domain boundaries in self-assembled terephthalic acid (TPA) monolayers on CVD-grown graphene on Pt(111)

Self-assembly of terephthalic acid (TPA), vacuum deposited on Pt(111) supported graphene, has been investigated by scanning tunneling microscopy (STM). TPA organizes in an ordered 3 × 4 superstructure with respect to the graphene lattice. This structure is a consequence of hydrogen-bonded TPA chains that arrange in a commensurate overlayer on graphene. Due to the polycrystalline nature of graphene on Pt(111), the TPA layer exhibits various grain boundaries and dislocations. Molecular resolved STM imaging has been used to characterize these defect structures in the TPA monolayer.

Five-vertex Archimedean surface tessellation by lanthanide-directed molecular self-assembly

The tessellation of the Euclidean plane by regular polygons has been contemplated since ancient times and presents intriguing aspects embracing mathematics, art, and crystallography. Significant efforts were devoted to engineer specific 2D interfacial tessellations at the molecular level, but periodic patterns with distinct five-vertex motifs remained elusive. Here, we report a direct scanning tunneling microscopy investigation on the cerium-directed assembly of linear polyphenyl molecular linkers with terminal carbonitrile groups on a smooth Ag(111) noble-metal surface. We demonstrate the spontaneous formation of fivefold Ce-ligand coordination motifs, which are planar and flexible, such that vertices connecting simultaneously trigonal and square polygons can be expressed. By tuning the concentration and the stoichiometric ratio of rare-earth metal centers to ligands, a hierarchic assembly with dodecameric units and a surface-confined metal-organic coordination network yielding the semiregular Archimedean snub square tiling could be fabricated.

Growth anomalies in supramolecular networks: 4,4'-biphenyldicarboxylic acid on cu(001)

We have used low energy electron microscopy to demonstrate how the interaction of 4,4'-biphenyldicarboxylic acid (BDA) molecules with (steps on) the Cu(001) surface determines the structure of supramolecular BDA networks on a mesoscopic length scale. Our in situ real time observations reveal that steps are permeable to individual molecules but that the change in crystal registry between different layers of the Cu substrate causes them to be completely impermeable to condensed BDA domains. The resulting growth instabilities determine the evolution of the domain shape and include a novel Mullins-Sekerka-type growth instability that is characterized by high growth rates along, instead of perpendicular to, the Cu steps. This growth instability is responsible for the majority of residual defects in the BDA networks.

Adsorption of self-assembled rigid rods on two-dimensional lattices

Monte Carlo (MC) simulations have been carried out to study the adsorption on square and triangular lattices of particles with two bonding sites that, by decreasing temperature or increasing density, polymerize reversibly into chains with a discrete number of allowed directions and, at the same time, undergo a continuous isotropic-nematic (IN) transition. The process has been monitored by following the behavior of the adsorption isotherms (chemical potential μ as a function of the surface coverage θ) for different values of lateral interaction energy/temperature. The numerical data were compared with mean-field analytical predictions and exact functions for noninteracting and 1D systems. The obtained results revealed the existence of three adsorption regimes in temperature. (1) At high temperatures, above the critical one characterizing the IN transition at full coverage T(c)(θ = 1), the particles are distributed at random on the surface and the adlayer behaves as a noninteracting 2D system. (2) At very low temperatures, the asymmetric monomers adsorb, forming chains over almost the entire range of coverage, and the adsorption process behaves as a 1D problem. (3) In the intermediate regime, the system exhibits a mixed regime and the filling of the lattice proceeds according to two different processes. In the first stage, the monomers adsorb isotropically on the lattice until the IN transition occurs in the system and, from this point, particles adsorb, forming chains so that the adlayer behaves as a 1D fluid. The two adsorption processes are present in the adsorption isotherms, and a marked singularity can be observed that separates both regimes. Thus, the adsorption isotherms appear as sensitive quantities with respect to the IN phase transition, allowing us (i) to reproduce the phase diagram of the system for square lattices and (ii) to obtain an accurate determination of the phase diagram for triangular lattices.

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.

Effect of head-group chemistry on surface-mediated molecular self-assembly

Surface molecular self-assembly is a fast advancing field with broad applications in sensing, patterning, device assembly, and biochemical applications. A vast number of practical systems utilize alkane thiols supported on gold surfaces. Whereas a strong Au-S bond facilitates robust self-assembly, the interaction is so strong that the surface is reconstructed, leaving etch pits that render the monolayers susceptible to degradation. By using different head group elements to adcust the molecule-surface interaction, a vast array of new systems with novel properties may be formed. In this paper we use a carefully chosen set of molecules to make a direct comparison of the self-assembly of thioether, selenoether, and phosphine species on Au(111). Using the herringbone reconstruction of gold as a sensitive readout of molecule-surface interaction strength, we correlate head-group chemistry with monolayer (ML) properties. It is demonstrated that the hard/soft rules of inorganic chemistry can be used to rationalize the observed trend of molecular interaction strengths with the soft gold surface, that is, P>Se>S. We find that the structure of the monolayers can be explained by the geometry of the molecules in terms of dipolar, quadrupolar, or van der Waals interactions between neighboring species driving the assembly of distinct ordered arrays. As this study directly compares one element with another in simple systems, it may serve as a guide for the design of self-assembled monolayers with novel structures and properties.

Varying molecular interactions by coverage in supramolecular surface chemistry

The possibility of modifying the intermolecular interactions of absorbed benzene-carboxylic acids from coordination to hydrogen bonding by changing their surface coverage is demonstrated through a combination of scanning tunnelling microscopy, X-ray photoemission spectroscopy and density functional theory calculations.

Agent-based modeling for the 2D molecular self-organization of realistic molecules

We extend our previously developed agent-based (AB) algorithm to the study of the self-assembly of a fully atomistic model of experimental interest. We study the 2D self-assembly of a rigid organic molecule (1,4-benzene-dicarboxylic acid or TPA), comparing the AB results with Monte Carlo (MC) and MC simulated annealing, a technique traditionally used to solve the global minimization problem. The AB algorithm gives a lower energy configuration in the same simulation time than both of the MC simulation techniques. We also show how the AB algorithm can be used as a part of the protocol to calculate the phase diagram with less computational effort than standard techniques.

Rotational and constitutional dynamics of caged supramolecules

The confinement of molecular species in nanoscale environments leads to intriguing dynamic phenomena. Notably, the organization and rotational motions of individual molecules were controlled by carefully designed, fully supramolecular host architectures. Here we use an open 2D coordination network on a smooth metal surface to steer the self-assembly of discrete trimeric guest units, identified as noncovalently bound dynamers. Each caged chiral supramolecule performs concerted, chirality-preserving rotary motions within the template honeycomb pore, which are visualized and quantitatively analyzed using temperature-controlled scanning tunneling microscopy. Furthermore, with higher thermal energies, a constitutional system dynamics appears, which is revealed by monitoring repetitive switching events of the confined supramolecules' chirality signature, reflecting decay and reassembly of the caged units.

Adsorption and bonding of first layer and bilayer terephthalic acid on the Cu(100) surface by high-resolution electron energy loss spectroscopy

The self-assembled and highly ordered first layer of terephthalic acid on Cu(100) as well as its bilayer on the same surface are studied here using high-resolution electron energy loss spectroscopy (HREELS), Auger electron spectroscopy, and low energy electron diffraction. These experiments show completion of the first layer before growth of the second layer. HREELS measurements show that the first layer of the acid deprotonates, which is seen in the absence of the OH stretching mode for the acid groups. However, this mode is present in the bilayer structure, confirming that the deprotonation is due to a reaction with the Cu surface and suggesting that there is little mixing of the layers. It has been suggested previously that the TPA monolayer structure is stabilized by an intermolecular hydrogen bonding interaction, but we are not able to resolve any distortion of the CH stretching mode for such an interaction, but instead see evidence for direct bonding to the Cu surface.

Metal-free phthalocyanine (H2Pc) molecule adsorbed on the Au(111) surface: formation of a wide domain along a single lattice direction

Using low-temperature scanning tunneling microscopy (STM), we observed the bonding configuration of the metal-free phthalocyanine (H2Pc) molecule adsorbed on the Au(111) surface. A local lattice formation started from a quasi-square lattice aligned to the close-packed directions of the Au(111) surface. Although we expected the lattice alignment to be equally distributed along the three crystallographically equivalent directions, the domain aligned normal to the ridge of the herringbone structure was missing in the STM images. We attribute this effect to the uniaxial contraction of the reconstructed Au(111) surface that can account for the formation of a large lattice domain along a single crystallographical direction.

Surface-mediated two-dimensional growth of the pharmaceutical carbamazepine

Scanning tunneling microscopy (STM) has become a staple surface microscopy technique for a number of research fields ranging from semiconductor research to heterogeneous catalysis. Pharmaceutical compounds, however, remain largely unstudied. Here we report the first STM study of carbamazepine (CBZ), an anti-epileptic drug, on Au(111) and Cu(111) surfaces. The analysis reveals that CBZ adopts unusual chiral molecular architectures on both metals. These previously unreported structures, which are strikingly different from CBZ packing arrangements observed in 3D crystal structures, indicate that the main molecular architecture is driven by a combination of CBZ intermolecular hydrogen bonding and metal-CBZ interactions. Comparison of the 2D molecular structures reveals large differences in local geometry and packing density that are dependent on the nature of the metal surface. These results have implications for the potential role of metal surfaces as heteronuclei or templating agents for controlling polymorph formation, which continues to be a problem for many compounds in the pharmaceutical industry including CBZ.

Self-assembly of enantiopure domains: the case of indigo on Cu(111)

The adsorption of indigo molecules on Cu(111) was investigated by low temperature (5 K) scanning tunneling microscopy from the isolated single molecule regime to one monolayer. Structural optimization and image calculations demonstrate that the molecules are in a physisorbed state. Because of the reduced symmetry at the surface, single molecules acquire a chiral character upon adsorption leading to a two-dimensional (2D) chirality. They adopt two adsorption configurations, related by a mirror symmetry of the substrate, each with a distinct molecular orientation. Consequently, the 2D chirality is expressed by the orientation of the molecule. For higher coverage, molecules self-assemble by hydrogen bonding in nearly homochiral molecular chains, whose orientation is determined by the orientation taken by the isolated molecules. When the coverage approaches one monolayer, these chains pack into domains. Finally, the completion of the monolayer induces the expulsion of the molecules of the wrong chirality that are still in these domains, leading to perfect resolution in enantiopure domains.

Experimental and theoretical investigations on the epitaxial growth of 4,4(') stilbenedicarboxylic acid molecules on Au(111)

We report on scanning tunneling microscope observations of the epitaxial growth of 4,4(') stilbenedicarboxylic acid (SDA) molecules on Au(111), with the coverage ranges from submonolayer to one monolayer. The surface assembly evolves from one-dimensional molecular chains to striped islands and finally monolayer films. For two-dimensional assembly, the head-to-tail hydrogen bonding is found to dominate the molecule-molecule interactions. Each linking region of the SDA molecular chains consists of two hydrogen bonds. This is confirmed by our first-principles calculations where the hydrogen bond length, hydrogen bond energy, and SDA-Au interaction energy are deduced theoretically. Moreover, the configurations with interchain hydrogen bonds are energetically unstable. The roles of the herringbone reconstruction of Au(111) and the compression effect of a complete film on the formation of molecular ribbons are discussed.

Carboxylic acids: versatile building blocks and mediators for two-dimensional supramolecular self-assembly

Two-dimensional (2D) supramolecular self-assembly of various organic molecules at the liquid-solid interface is presented and discussed with a focus on compounds that are primarily functionalized by carboxylic groups. The main analytical tool utilized is scanning tunneling microscopy (STM), a high-resolution real-space technique capable of readily providing full crystallographic information (i.e., not only lattice parameters but also number, type, and orientation of molecules within the unit cell). Carboxylic groups are of particular interest because their combined donor and acceptor character with regard to hydrogen bonds provides reliable intermolecular cross-linking, thereby facilitating the self-assembly of well-ordered, stable monolayers. By means of various homomeric (monomolecular) and heteromeric (here, bimolecular) examples, this feature article illustrates the influence of both molecular structure and external conditions (type of solvent, concentration, etc.) on monolayer self-assembly at the liquid-solid interface. A very intriguing aspect of interfacial self-assembly is that many systems are thermodynamically controlled (i.e., adsorbed molecules at the surface are in equilibrium with molecules dissolved in the supernatant liquid phase). This offers the unique possibility not only to steer the system reliably by intensive thermodynamic parameters such as temperature and concentration but also to gain fundamental knowledge about decisive processes and steps in supramolecular self-assembly.

Dichotomous array of chiral quantum corrals by a self-assembled nanoporous kagomé network

The confinement of surface-state electrons by a complex supramolecular network is studied with low-temperature scanning tunneling microscopy and rationalized by electronic structure calculations using a boundary element method. We focus on the self-assembly of dicarbonitrile-sexiphenyl molecules on Ag(111) creating an open kagomé topology tessellating the surface into pores with different size and symmetry. This superlattice imposes a distinct surface electronic structure modulation, as observed by tunneling spectroscopy and thus acts as a dichotomous array of quantum corrals. The inhomogenous lateral electronic density distribution in the chiral cavities is reproduced by an effective pseudopotential model. Our results demonstrate the engineering of ensembles of elaborate quantum resonance states by molecular self-assembly at surfaces.

High-quality 2D metal-organic coordination network providing giant cavities within mesoscale domains

A surface-supported open metal-organic nanomesh featuring a 24 nm(2) cavity size and extending to mum domains was fabricated by Co-directed assembly of para-hexaphenyl-dicarbonitrile linker molecules in two dimensions. The metallosupramolecular lattice is thermally robust and resides fully commensurate on the employed Ag(111) substrate as directly verified by high-resolution scanning tunneling microscopy observations.

An STM study on nonionic fluorosurfactant zonyl FSN self-assembly on Au(111): large domains, few defects, and good stability

Nonionic Fluorosurfactant Zonyl FSN self-assembly on Au(111) is investigated with scanning tunneling microscopy under ambient conditions. STM reveals that the FSN forms SAMs on Au(l11) with very large domain size and almost no defects. A (mean square root of 3 x mean square root of 3)R3 degree arrangement of the FSN SAM on Au(111) is observed. The SAMs show excellent chemical stability and last for at least a month in atmospheric conditions. The structure and stability of the FSN SAMs are compared with those of alkanethiols SAMs. It is expected that FSN may serve as a new kind of molecule to form SAMs for surface modification, which would benefit wider applications for various purposes.

Chiral kagomé lattice from simple ditopic molecular bricks

Self-assembly techniques allow for the fabrication of highly organized architectures with atomic-level precision. Here, we report on molecular-level scanning tunneling microscopy observations demonstrating the supramolecular engineering of complex, regular, and long-range ordered periodic networks on a surface atomic lattice using simple linear molecular bricks. The length variation of the employed de novo synthesized linear dicarbonitrile polyphenyl molecules translates to distinct changes of the bonding motifs that lead to hierarchic order phenomena and unexpected changes of the surface tessellations. The achieved 2D organic networks range from a close-packed chevron pattern via a rhombic network to a hitherto unobserved supramolecular chiral kagomé lattice.

Role of interaction anisotropy in the formation and stability of molecular templates

Surface templating via self-assembly of hydrogen-bonded molecular networks is a rapidly developing bottom-up approach in nanotechnology. Using the melamine-PTCDI molecular system as an example we show theoretically that the network stability in the parameter space of temperature versus molecular coupling anisotropy is highly restricted. Our kinetic Monte Carlo simulations predict a structural stability diagram that contains domains of stability of an open honeycomb network, a compact phase, and a high-temperature disordered phase. The results are in agreement with recent experiments, and reveal a relationship between the molecular size and the network stability, which may be used to predict an upper limit on pore-cavity sizes.

Extended one-dimensional supramolecular assembly on a stepped surface

2,6-naphthalene-dicarboxylic acid was adsorbed on a Ag110 surface with an average terrace width of only some tens of a nm. Scanning tunneling microscopy shows that the adsorbates self-assemble into one-dimensional mesoscale length chains. These extend over several hundred nanometers and thus the structure exhibits an unprecedented tolerance to monatomic surface steps. Density functional theory and x-ray photoelectron spectroscopy explain the behavior by a strong intermolecular hydrogen bond plus a distinct template-mediated directionality and a high degree of molecular backbone flexibility.

Metal-organic honeycomb nanomeshes with tunable cavity size

We present a systematic study of metal-organic honeycomb lattices assembled from simple ditopic molecular bricks and Co atoms on Ag(111). This approach enables us to fabricate size- and shape-controlled open nanomeshes with pore dimensions up to 5.7 nm. The networks are thermally robust while extending over microm2 large areas as single domains. They are shape resistant in the presence of further deposited materials and represent templates to organize guest species and realize molecular rotary systems.

Ensuring homology between 2D and 3D molecular crystals

Integrated studies using scanning tunneling microscopy and X-ray crystallography have established that 4,5,9,10-tetrahydropyrene-2,7-dicarboxylic acid and pyrene-2,7-dicarboxylic acid crystallize in 2D and 3D with striking homology. Different behavior is shown by related biphenyls that lack the planarizing conformational constraints of the pyrenyl core and the directing effects of intermolecular hydrogen bonding. The results of these studies show that molecules specifically designed to engage in multiple strong directional interadsorbate interactions are promising tools for imposing particular nanopatterns on surfaces and for revealing subtle aspects of crystallization.

Molecular architectonic on metal surfaces

The engineering of highly organized systems from instructed molecular building blocks opens up new vistas for the control of matter and the exploration of nanodevice concepts. Recent investigations demonstrate that well-defined surfaces provide versatile platforms for steering and monitoring the assembly of molecular nanoarchitectures in exquisite detail. This review delineates the principles of noncovalent synthesis on metal substrates under ultrahigh vacuum conditions and briefly assesses the pertaining terminology-self-assembly, self-organization, and self-organized growth. It presents exemplary scanning-tunneling-microscopy observations, providing atomistic insight into the self-assembly of organic clusters, chains, and superlattices, and the metal-directed assembly of low-dimensional coordination architectures. This review also describes hierarchic-assembly protocols leading to intricate multilevel order. Molecular architectonic on metal surfaces represents a versatile rationale to realize structurally complex nanosystems with specific shape, composition, and functional properties, which bear promise for technological applications.

Nitrate Adsorption and Reduction on Cu(100) in Acidic Solution

Nitrate adsorption and reduction on Cu(100) in acidic solution is studied by electrochemical methods, in situ electrochemical scanning tunneling microscopy (EC-STM), surface enhanced Raman spectroscopy (SERS), and density functional theory (DFT) calculations. Electrochemical results show that reduction of nitrate starts at -0.3 V vs Ag/AgCl and reaches maximum value at -0.58 V. Over the entire potential region interrogated adlayers composed of nitrate, nitrite, or other intermediates are observed by using in situ STM. From the open-circuit potential (OCP) to -0.22 V vs Ag|AgCl, the nitrate ion is dominant and forms a (2 x 2) adlattice on the Cu(100) surface while nitrate forms a dominantly c(2 x 2) structure from -0.25 to -0.36 V. The interconversion between the nitrate and nitrite adlattices is observed. DFT calculations indicate that both nitrate and nitrite are twofold coordinated to the Cu(100) surface.

Monitoring two-dimensional coordination reactions: directed assembly of co-terephthalate nanosystems on Au(111)

We report scanning tunneling microscopy observations on the formation of 2D Co-based coordination compounds on the reconstructed Au(111) surface. Preorganized arrays of Co bilayer islands are shown to be local reaction sites, which are consumed in the formation of Co-terephthalate aggregates and regular nanoporous grids. The latter exhibit a planar geometry stabilized by the smooth substrate. The nanogrids are based on a rectangular motif, which is understood as an intrinsic feature of a 2D cobaltous terephthalate sheet and dominates over the templating influence of the quasihexagonal substrate atomic lattice. The dynamics of the Co island dissolution and metallosupramolecular self-assembly could be monitored in situ. Complementary first-principles calculations were performed to analyze the underlying driving forces and to examine general trends in 2D metal-carboxylate formation. The findings indicate the wide applicability of coordination chemistry concepts at surfaces, which moreover can be spatially confined by using templated substrates, and its potential to synthesize arrangements unavailable in bulk materials.

Zwitterionic self-assembly of L-methionine nanogratings on the Ag(111) surface

The engineering of complex architectures from functional molecules on surfaces provides new pathways to control matter at the nanoscale. In this article, we present a combined study addressing the self-assembly of the amino acid L-methionine on Ag(111). Scanning tunneling microscopy data reveal spontaneous ordering in extended molecular chains oriented along high-symmetry substrate directions. At intermediate coverages, regular biomolecular gratings evolve whose periodicity can be tuned at the nanometer scale by varying the methionine surface concentration. Their characteristics and stability were confirmed by helium atomic scattering. X-ray photoemission spectroscopy and high-resolution scanning tunneling microscopy data reveal that the L-methionine chaining is mediated by zwitterionic coupling, accounting for both lateral links and molecular dimerization. This methionine molecular recognition scheme is reminiscent of sheet structures in amino acid crystals and was corroborated by molecular mechanics calculations. Our findings suggest that zwitterionic assembly of amino acids represents a general construction motif to achieve biomolecular nanoarchitectures on surfaces.