On-surface formation of metal–organic coordination networks with C⋯Ag⋯C and C=O⋯Ag interactions assisted by precursor self-assembly

Bottom-up assembly has become a viable means for the atomically precise fabrication of nanostructures.¹ Intermolecular forces can be carefully tuned to build larger superstructures. Nanostructures can be stabilized via van der Waals forces, coordination bonds,^2–4 hydrogen bonds,⁵ and covalent bonds;⁶ and more recently halogen–halogen bonds^7–11 have been used to form supramolecular structures and assemblies on surfaces. The substrate nature, base monomer structure,¹² and fabrication method determine the ability to form desirable products with useful functions.^13,14 Subsequently, the design of nanocarbon materials for energy storage, conversion, and catalysis requires a fundamental understanding of the forces, bonds, and reactions that drive their formation.

Low-dimensional nanocarbon materials with defined chemical structures containing catalytically active ketonic groups have been explored as models to examine the catalytic process at the molecular scale.^15–17 To date, the synthesis of these conjugated polymers primarily relies upon established methods to couple aromatic molecules in solution or post-fabrication functionalization. On-surface reactions of precursors with functional groups can similarly be used to develop two-dimensional nanoarchitectures, and surface-sensitive analyses provide a means to study the products with techniques that provide atomic-scale spatial resolution. Additionally, although the reaction becomes constrained to two-dimensions, the surface adds a critical parameter to control the mechanism of the reaction and provides a means to form coordinated organometallic nanostructures¹⁸ and one- or even two-dimensional covalent polymers.^19–25 In this manner, selecting a surface requires careful consideration and an understanding of the role of the surface in catalyzing the coupling reaction.

Although there exist many options for on-surface homo-coupling reactions,¹³ the Ullmann-like coupling reaction has become one of the most popular reactions in on-surface synthesis due to its robustness and tunability. The initial Ullmann coupling reaction performed in solution uses a copper catalyst to covalently couple aryl halides via a mechanism that relies on a dehalogenation process, which is speculated and commonly considered, to proceed through a mechanism that involves the formation of an intermediate copper coordinated compound.^26,27 Recent research in on-surface synthesis has found that Ullmann-like reactions can be used to build up carbon-based scaffolds on a variety of single metal crystals with atomic precision.^1,28 These substrates include low-index facets, specifically (111),^29–31 (100),²¹ and less commonly (110),^32,33 of coinage metals, such as Ag,^34,35 Au,^36–38 and Cu.^20,39–42 Significantly, even in cases where the precursor molecules are identical, different metal surfaces can result in vastly different on-surface structures.^33,43 Metal atoms from the surface can become incorporated into stable coordinated organometallic structures or covalent networks predominant depending on conditions.^34,44 Furthermore, when confined to a surface, the halogen atoms that serve as leaving groups can remain adsorbed on the surface. In some cases, these halogen atoms on the surface can stabilize larger organometallic structures or radical intermediates that enable the formation of otherwise unstable or inaccessible products.^21,45

Efforts to optimize the Ullmann-like coupling reaction for the fabrication of unique low-dimensional materials primarily rely upon manipulating the precursor molecule. Changes in the carbon skeleton or the positions of the halogen leaving groups enable the ability to direct the growth process.^46–48 More recently, in an effort to expand the toolset, the inclusion of functional groups in the organic precursor molecule has become another method to control the reaction process and reliably fabricate unique low-dimensional structures that contain functional groups.^{20,37,48–51} On its own, the addition of carbonyl groups to a molecular precursor presents the opportunity for the formation of metal–organic coordination networks on a surface via coordination chemistry.^52,53 When the base molecule includes both carbonyl groups and aryl halides, it becomes possible for two types of coordination bonds to occur in a competing or synergistic process during the course of the on-surface reaction.⁵⁴ Metal adatoms can be captured either by the dehalogenation process, through coordination with the carbonyl groups, or through a combination of the two. The competition between two interactions, such as these, can result in mixed-valence two-dimensional coordination networks,⁵⁵ which can show significantly improved catalytic efficiencies when compared to metal–organic networks with only one coordination environment.⁵⁶ Ultimately, a study of the complex on-surface interactions and reactions requires a spatially sensitive technique in order to characterize the nanostructure and develop an understanding of the underlying chemistry that drives its formation.

Ullmann-like coupling reactions have previously been found to depend on the identity of the substrate. Although the titular Ullmann coupling reaction involves a copper catalyst in solution, on-surface synthetic methods have found that various metal surfaces can be used to grow nanostructures through dehalogenation reactions with a focus on gold, silver, and copper.^42,57,58 The different metal surfaces have been found to result in different pathways and reaction products, where covalent or coordination bonded nanostructures become accessible.^20,57,58 In this work, the self-assembly and reaction products of 3,6-dibromo-9,10-phenanthrenequinone (DBPQ) were studied on Ag(100) and Ag(110). It was found that the relatively simple planar molecular structure (C_2V symmetry), shown in Fig. 1(a), that results from the phenanthrene skeleton with a diketone and two peripheral bromines, self-assemble on Ag(100) and can form complex organometallic structures on the silver surfaces following the dissociation of the C–Br bonds.

Experiments took place in an ultrahigh vacuum (UHV) variable temperature scanning tunneling microscope (STM) system (Unisoku Co., Ltd.) at a base pressure of 6.0 × 10⁻¹¹ Torr previously described in more detail elsewhere.⁵⁹ The silver single crystals, Ag(100) and Ag(110), were prepared in a preparation chamber with a base pressure of 1.0 × 10⁻¹⁰ Torr and then transferred through a gate valve into the STM chamber for observation. The substrates were cleaned by standard cycles of argon ion sputtering followed by indirect thermal annealing to 800 K. The DBPQ molecules were deposited onto the silver substrates, which were held at room temperature via a K-cell style molecular evaporator. The molecular evaporator was heated to 135 °C during deposition in order to obtain sub-monolayer surface coverage. In the case of experiments requiring a thermal anneal, the anneal was carried out by indirect heating through a tungsten filament located behind the sample. STM experiments took place at liquid nitrogen temperatures (78 K). Electrochemically etched Ag tips were used for STM imaging. The tip fabrication method and methods to further process tips within the UHV chamber are explained elsewhere.⁶⁰ Biases were applied to the sample with respect to the grounded Ag tip with the STM scanning in the constant current mode. Gwyddion was used to process the STM images.⁶¹ 

As shown in Fig. 1(b), DBPQ forms self-assembled molecular islands on Ag(100) with clear long-range ordering of the molecules with a row-like motif. This behavior becomes more apparent in zoomed-in STM images, such as Fig. 2(a), where the high resolution enables the ability to identify individual molecules within the self-assembly and develop an understanding of the driving intermolecular interactions. The positions and orientations of the functional groups within a DBPQ molecule provide a means to identify the chemical species observed with STM and also guide an interpretation of the intermolecular interactions that drive the self-assembly of molecular islands. As shown in Fig. 1(a), the diketone occupies the 9 and 10 positions of the phenanthrene skeleton, with bromine atoms bonded to the carbons at the 3 and 6 positions. The inclusion of halogen atoms into the molecular structure enables the clear identification of the position and orientation of individual molecules within the self-assembly, as can be seen later in Figs. 2(a) and 3(a), since molecular halogen atoms have been previously found to appear brighter than molecular carbon atoms in STM images.^8,62,63 This unique feature of aryl halides combined with the identification of pristine bare Ag(100), with no adsorbed Br atoms, confirms that the C–Br bonds within DBPQ molecules remain intact following deposition onto the room temperature substrate.

On-surface coupling reactions require two molecules to come into close contact with each other in order to interact and form a new bond that links them. Figure 1(c) shows the possible intermediates or products of the Ullmann-like reaction of DBPQ on a Ag surface. This process depends upon the diffusion of the molecules across the surface. Through studying the self-assembly of the precursor molecules, it is possible to generate an understanding of the intermolecular forces and interactions that can play a role in the movement and stabilization of molecules on a surface. In fact, self-assembly strategies can be used to efficiently steer reaction pathways and dynamics.⁶⁴ Within this context, it is important to consider the nature of the long-range order of the self-assembled molecules observed on the Ag(100) substrate with finer details.

As a polycyclic aromatic hydrocarbon, the addition of two carbonyl groups to the molecular structure, as shown in Fig. 1(a), presents the opportunity for hydrogen bonding between molecules. Indeed, 9,10-phenanthrenequinone was previously investigated on a Au(111) surface and the C–H⋯O bonding between molecules was found to primarily result in well-ordered self-assemblies characterized by a row-like bonding motif.⁶⁵ As shown in Fig. 2(a), this row-like behavior is still observed on Ag(100), even with the addition of C–Br functional groups to the 9,10-phenanthrenequinone moiety.

Based upon STM imaging, the self-assembly of DBPQ on Ag(100) can be defined with two types of molecular rows that can be understood to be the result of hydrogen bond interactions between rows. Noodle-like rows and rows composed of dimer circles or rings, which will be referred to as circle rows, form an alternating pattern across the surface, Fig. 2(a). Due to the alternating pattern of these molecular rows, the two types were observed to occur in a 1:1 ratio. In the short range, from one circle row across a noodle-like row to the next circle row, the self-assembly can be represented by a simple pair of molecules interacting through hydrogen bonds between the diketonic oxygens of one molecule and the aromatic hydrogens of an adjacent molecule. The apparent distance (<3 Å) between molecules of different rows aligns with the expected distance for an on-surface C–H⋯O hydrogen bond, as visualized with STM.^66,67 Molecular models are overlaid on the zoomed-in STM image in Fig. 2(a), where a simple hydrogen bonded pair is outlined in blue.

As shown with line profiles extracted from the STM image [Fig. 2(a)], each DBPQ molecule has a brighter and a dimmer Br atom [Figs. 2(c) and 2(d)]. The bromine atoms closer to the edge of molecular rows and adjacent to hydrogen bond interactions show decreased heights, while those located more within the interior of a molecular row appear brighter. Figure 2(b) illustrates a model of the self-assembly of a few DBPQ molecules, where the hydrogen bond interactions are represented by green dashed lines. The brighter bromine atoms and aromatic hydrogen atoms that are not involved in hydrogen bonds are highlighted in yellow. This analysis reveals that the dimmer bromine atoms are proximal to the hydrogen bond interactions. This difference in contrast confirms a change in the relative electronic densities of the bromine atoms due to hydrogen bond interactions between molecules of adjacent rows. Significantly, this interaction breaks the electronic symmetry of a DBPQ molecule since only aromatic hydrogens at the edges of the molecular rows can form hydrogen bonds with the diketonic oxygens of a molecule in an adjacent row. Hydrogen bonding explains the short-range alternating assembly of noodle-like and circle rows and the row-like motif that was previously observed for 9,10-phenanthrenequinone.⁶⁵ However, in contrast to the previous work, where simple linear rows were observed, the inclusion of bromine atoms into the molecule’s structure results in chiral noodle-like rows and circle rows, necessitating further explanation.

The Ullmann-like coupling reaction requires the inclusion of halogen atoms to serve as leaving groups and allow coupling between molecules; however, prior to reaction, they can play an important role in mediating self-assembly. In the case of DBPQ, the C–Br bonds at the 3 and 6 positions introduce the possibility for halogen bonding, which can compete or cooperate with hydrogen bonding.⁶⁸ Due to their similar relative strengths, hydrogen bonds and halogen bonds have been found to compete in the self-assembly of crystals, both experimentally and theoretically.^69–71 The halogen bonds arise from interactions between the anisotropic distributions of electron density in the adjacent halogen atoms. An electron-depleted σ-hole at the pole of a C–X (X = Cl, Br, I) bond orients toward the electron-rich equatorial region of another X atom.^7,72–74 This interaction can result in chiral self-assemblies due to the ability for halogen bonds to exhibit a clockwise or counterclockwise (CCW) nature.^8–10,75 This chirality is apparent within the molecular rows of DBPQ. As illustrated in Fig. 3(b), the pairs that compose a circle row can be understood to be stabilized by halogen bonding within the molecular pair, where the halogen bond is shown with a red dashed line. Significantly, each of the noodle-like and circle rows has two enantiomer forms, i.e., circle rows consist of C¹ or C² enantiomers and noodle-like rows consist of N¹ or N² enantiomers. Figures 3(c) and 3(d) show the series of transformations necessary to convert between the enantiomer subunits and describe the various molecular rows. In both cases, the reflection across an in-plane axis is necessary due to the enantiomer rows that result from the halogen bonds between molecules. These axes of reflection are denoted with blue dashed lines in Fig. 3. Ultimately, the combination of carbonyl groups and halogen atoms in the structure of DBPQ results in a complex self-assembly characterized by a molecular row motif that is defined by both hydrogen bonds and halogen bonds.

Figure 4(a) shows the results of thermally annealing DBPQ on Ag(100) to 300 °C. The ordered substructures evident on the surface appear reminiscent of the row motif previously observed for the self-assembly of DBPQ following a room temperature deposition. This suggests that the self-assembly of precursor molecules on the surface prior to the reaction plays a significant role in the formation of the structure that results from thermal annealing.⁷⁶ By varying the applied bias, it is possible to characterize the network and species that are adsorbed on the surface. As shown in Fig. 4(b) and its inset, STM imaging performed with a certain applied bias enables the identification of silver adatoms due to their increased brightness compared to the surrounding bromine atoms or organic molecules. As a result, it becomes possible to define a semi-ordered metal–organic coordination network composed of ladder-like substructures. Significantly, this bias-dependent imaging also provides a means to identify the bromine atoms that remain adsorbed on the surface following the dissociation of C–Br bonds, which now appear dimmer compared to the organic molecules and metal adatoms. Ag adatoms link two DBPQ molecules to form organometallic dimers, as shown in the inset of Fig. 4(b) and more clearly with models in Fig. 4(c). On silver surfaces, the Ullmann-like coupling reaction can proceed through an organometallic intermediate before terminating in covalently coupled products.^34,44,77 With certain reaction conditions, the growth process can terminate with the formation of the organometallic species as it becomes stable.⁷⁷ In both STM images, the bromine atoms are visible, adsorbed on the surface as well as surrounding the metal–organic network, suggesting a stabilizing interaction. The bromine adsorbates have previously been found to stabilize metal–organic hybrid chains on a silver surface.⁷⁸ 

However, as shown in Fig. 4, rather than forming long organometallic polymeric chains, this process for DBPQ appears to be capped at dimers in many instances, resulting in ladder-like substructures. This early termination can be explained by interactions of a diketone with the terminal Ag adatoms of the dimer. The carbonyl functional groups coordinate to the otherwise reactive Ag adatom preventing further Ullmann-like coupling reactions in favor of the formation of a metal–organic coordination network in an orientation perpendicular to the potential chain growth. This competing process between two types of coordination bonds, C⋯Ag and C=O⋯Ag, results in the ladder-like substructure shown in Fig. 4(c), where the coordination bonds are shown with blue dashed lines. These coordinated Ag adatoms exhibit a threefold symmetry despite the fourfold symmetry of the underlying Ag(100) lattice. Coordination bonds between organic ligands and surface metal adatoms have previously been found to exhibit an unusual threefold symmetry on various substrates,⁷⁹ and silver atoms are known to be capable of coordination with three ligands.⁸⁰ The structure observed in this case is likely a result of the complicated nature of the interactions between the diketone and the Ag adatom that becomes incorporated into the organometallic species formed by the Ullmann-like coupling reaction. Additionally, based on the structure apparent in STM images, the Ag adatoms incorporated into the ladder-like substructure are expected to have different coordination numbers, suggesting the formation of a mixed-valence two-dimensional coordination network. Through the simultaneous combination of two methods of bottom-up assembly, the Ullmann-like coupling reaction and metal carbonyl coordination chemistry, new and unique materials become accessible.

In order to identify facet effects on the self-assembly or Ullmann-like coupling reaction of DBPQ on silver surfaces, DBPQ was deposited onto Ag(110) at room temperature. Although both of the substrates are silver, the STM images of DBPQ on Ag(110) present significant differences compared to the long-range ordered assemblies observed on Ag(100). Figure 5(a) shows the presence of disordered structures. Additionally, the step edges of the Ag(110) surface show significant etching, suggesting the abstraction of silver atoms by the DBPQ molecules. The zoomed-in STM images provide a means to develop an understanding of the observed disordered networks [Figs. 5(b) and 5(c)]. Through using the same method of bias-dependent imaging, as was used to identify Ag adatoms within the metal–organic coordination structure on Ag(100), it is possible to identify the presence of Ag adatoms and dissociated Br atoms in Fig. 5(c). With a negative applied bias, the Ag adatoms appear significantly brighter compared to organic substituents, while slightly dimmer atoms correspond to Br atoms, which appear surrounding and interspersed within the structure. Although the location of DBPQ molecules cannot be precisely defined due to the disorder, the organic components of the metal–organic coordination network appear to adopt a preferred orientation that aligns with the corrugation of the Ag(110) surface. Overall, the Ag(110) surface was found to exhibit substantially increased reactivity toward inducing the dissociation of C–Br bonds.

Although both of the substrates used are silver, the marked difference in the behavior of DBPQ on these surfaces suggests distinct surface coordination chemistry. The room temperature dissociation of the C–Br bonds on Ag(110) suggests a strong molecule–substrate interaction on Ag(110) compared to that on Ag(100) where the self-assembly of unreacted molecules is mediated by intermolecular interactions. The surface silver atoms that compose the Ag(110) substrate are less coordinated than the silver atoms of the Ag(100) surface, resulting in the increased reactivity of this surface.⁸¹ Previous literature has found that the Ag(110) surface can catalyze the dissociation of C–Br bonds at room temperature.^33,34,82 However, the corrugation of the (110) surface can suppress thermally activated surface diffusion or result in the anisotropic movement of molecules on the surface, subsequently preventing the formation of an ordered two-dimensional structure.³³ The strong molecule–substrate interactions and anisotropic molecular diffusion result in the formation of the disordered metal–organic structures, composed of organic molecules with preferred orientations, observed on the surface.

Figure 6 serves to summarize the interplay of intermolecular and molecule–substrate interactions that result in the self-assemblies and metal–organic coordination networks formed by DBPQ molecules on the Ag(100) and Ag(110) substrates. The observed self-assembly of DBPQ on Ag(100), mediated by hydrogen and halogen bonds, results in the subsequent formation of a semi-ordered metal–organic coordination network following thermal annealing. However, the increased reactivity and corrugation of Ag(110) result in the immediate formation of a disordered metal–organic coordination network at room temperature.

In conclusion, the self-assembly and reaction products of DBPQ on Ag(100) and Ag(110) have been characterized with STM in order to understand the competition between intermolecular and molecule–substrate interactions and reactions relevant to bottom-up assembly. STM imaging shows that DBPQ self-assembles on Ag(100) following room temperature deposition. This self-assembly consists of chiral molecular rows that can be understood by the cooperation and competition of hydrogen bonding across rows and halogen bonding within rows. In comparison, the more reactive Ag(110) surface catalyzes the dissociation of the C–Br bonds in DBPQ molecules but also constrains on-surface diffusion, resulting in the formation of disordered metal–organic species on the surface. On Ag(100), the molecular row motif visible in the self-assembly of precursor molecules was found to carry over through the thermally induced reaction process to result in ladder-like substructures within the larger metal–organic coordination network. The ladder-like substructures were found to be the result of two different types of coordination bonds, C⋯Ag⋯C and C=O⋯Ag. Through the inclusion of multiple functional groups within a precursor molecule, it becomes possible to introduce competing interaction or reaction mechanisms, as shown in Fig. 6. Although this method complicates bottom-up assembly, necessitating a characterization technique with atomic-scale spatial resolution to develop a fundamental understanding, it provides a means to fabricate new low-dimensional materials with highly unique chemical, physical, and electronic properties.

See the supplementary material for STM images showing the reproducible functionalization of the STM tip with a Br atom and the change in image resolution and contrast that results.

J.F.S. and N.J. acknowledge support from the National Science Foundation (Grant No. CHE-1944796). B.Y. acknowledges the support of the National Natural Science Foundation of China (Grant No. 21872145) and the Foundation of Dalian Institute of Chemical Physics (Grant No. DICP I201943).

The data that support the findings of this study are available from the corresponding author upon reasonable request.