Control of intermolecular bonds by deposition rates at room temperature: hydrogen bonds versus metal coordination in trinitrile monolayers

Lying or Standing of Thiophene on a Surface Determines the Reaction Difference

Adsorption configurations of molecules on a surface play an important role in the on-surface reaction. In the on-surface synthesis reaction, most of the molecules prefer the lying adsorption configuration to maximize the interaction between the molecule and substrate. In this work, we report an on-surface study of 2,3,4,5-tetrabromothiophene by scanning tunneling microscopy, density functional theory, and X-ray photoelectron spectroscopy. Due to different interactions between thiophene and metal surfaces, lying or standing configurations of 2,3,4,5-tetrabromothiophene can be selected by the choice of metal substrates. Moreover, a catalytic role of the metal substrate in the molecular reaction with lying and standing adsorption configurations is demonstrated at the molecular level. This work broadens the understanding of thiophene's configurations in surface reactions and the product diversity driven by adsorption configurations. It also offers a guiding framework for synthesizing multifunctional materials by thiophene derivatives.

Mechanistic insights into on-surface reactions from isothermal temperature-programmed X-ray photoelectron spectroscopy

On-surface synthesis often proceeds under kinetic control due to the irreversibility of key reaction steps, rendering kinetic studies pivotal. The accurate quantification of reaction rates also bears potential for unveiling reaction mechanisms. Temperature-Programmed X-ray Photoelectron Spectroscopy (TP-XPS) has emerged as an analytical tool for kinetic studies with splendid chemical and sufficient temporal resolution. Here, we demonstrate that the common linear temperature ramps lead to fitting ambiguities. Moreover, pinpointing the reaction order remains intricate, although this key parameter entails information on atomistic mechanisms. Yet, TP-XPS experiments with a stepped temperature profile comprised of isothermal segments facilitate the direct quantification of rate constants from fitting time courses. Thereby, rate constants are obtained for a series of temperatures, which allows independent extraction of both activation energies and pre-exponentials from Arrhenius plots. By using two analogous doubly versus triply brominated aromatic model compounds, we found that their debromination on Ag(111) is best modeled by second-order kinetics and thus proceeds via the involvement of a second, non-obvious reactant. Accordingly, we propose that debromination is activated by surface supplied Ag adatoms. This hypothesis is supported by Density Functional Theory (DFT) calculations. We foresee auspicious prospects for this TP-XPS variant for further exploring the kinetics and mechanisms of on-surface reactions.

Discarding metal incorporation in pyrazole macrocycles and the role of the substrate on single-layer assemblies

Pyrazole derivatives are key in crystal engineering and liquid crystal fields and thrive in agriculture, pharmaceutical, or biomedicine industries. Such versatility relies in their supramolecular bond adaptability when forming hydrogen bonds or metal-pyrazole complexes. Interestingly, the precise structure of pyrazole-based macrocycles forming widespread porous structures is still unsolved. We bring insight into such fundamental question by studying the self-assembled structures of a bis-pyrazole derivative sublimed in ultra-high-vacuum conditions (without solvents) onto the three (111) noble metal surfaces. By means of high-resolution scanning tunneling microscopy that is validated by gas phase density functional theory calculations, we find a common hexagonal nanoporous network condensed by triple hydrogen bonds at the molecule-metal interface. Such assembly is disrupted and divergent after annealing: (i) on copper, the molecular integrity is compromised leading to structural chaos, (ii) on silver, an incommensurate new oblique structure requiring molecular deprotonation is found and, (iii) on gold, metal-organic complexes are promoted yielding irregular chain structures. Our findings confirm the critical role of these metals on the different pyrazole nanoporous structure formation, discarding their preference for metal incorporation into the connecting nodes whenever there is no solvent involved.

Supramolecular Tiling of a Conformationally Flexible Precursor

Supramolecular self-assembly offers a possible pathway for nanopatterning and functionality. In particular, molecular tiling such as trihexagonal tiling (also known as the Kagome lattice) has promising chemical and physical properties. Distorted Kagome lattices are not well understood due to their complexity, and studies of their controllable fabrication are few. Here, by employing a conformationally flexible precursor, 2,4,6-tris(3-bromophenyl)-1,3,5-triazine (mTBPT), we demonstrate two-dimensional distorted Kagome lattice p3, (333) by supramolecular self-assembly and achieve tuning of the metastable phases, including the homochiral porous network and distorted Kagome lattice p3, (333) by steering deposition rates on a cold Ag(111) substrate. By a combination of scanning tunneling microscopy and density functional theory calculations, the distorted Kagome lattice is energetically unfavorable but can be trapped at a high deposition rate, and the process mainly depends on surface kinetics. This work using conformationally flexible mTBPT molecules provides a pathway for the controllable growth of different phases, including metastable Kagome lattices.

Transformation of the coordination nanostructures of 4,4',4''-(1,3,5-triazine-2,4,6-triyl) tribenzoic acid molecules on HOPG triggered by the change in the concentration of metal ions

The modulation effects of Cu2+/Fe3+ ions on the hydrogen-bonded structure of 4,4',4''-(1,3,5-triazine-2,4,6-triyl) tribenzoic acid (TATB) on a HOPG surface have been investigated at the liquid-solid interface by scanning tunneling microscopy (STM). STM observations directly demonstrated that the self-assembled honeycomb network of TATB has been dramatically transformed after introducing CuCl2/FeCl3 with different concentrations. The metal-organic coordination structures are formed due to the incorporation of the Cu2+/Fe3+ ions. Interestingly, a Cu2+ ion remains coordinated to two COOH groups and only the number of COOH groups involved in coordination doubles when the concentration of Cu2+ ions doubled. A Fe3+ ion changes from coordination to three COOH groups to two COOH groups after increasing the concentration of Fe3+ ions in a mixed solution. Such results suggest that the self-assembled structures of TATB molecules formed by metal-ligand coordination bonds can be effectively adjusted by regulating the concentration of metal ions in a mixed solution, which has rarely been reported before. It explains that the regulatory effect of concentration leads to the diversity of molecular architectures dominated by coordination bonds.

Adatoms in the Surface-Confined Ullmann Coupling of Phenyl Groups

Despite the importance of the on-surface Ullmann coupling for synthesis of atomically precise carbon nanostructures, it is still unclear whether this reaction is catalyzed by surface atoms or adatoms. Here, the feasibility of the adatom creation and adatom-catalyzed Ullmann coupling of chloro-, bromo-, and iodobenzene on Cu(111), Ag(111), and Au(111) surfaces is examined using density functional theory modeling. The extraction of a metal atom is found to be greatly facilitated by the formation of strong phenyl-metal bonds, making the extraction energy barrier comparable to, and in the case of Ag(111) even lower than, that for the competing surface-catalyzed phenyl-phenyl bond formation. However, if the phenyl-adatom bonds are too strong, as on Cu(111) and Ag(111), they create an insurmountable barrier for the subsequent adatom-catalyzed C-C coupling. In contrast, Au adatoms do not bind phenyl groups strongly and can catalyze the C-C bond formation almost as efficiently as surface atoms.

Dysprosium-directed metallosupramolecular network on graphene/Ir(111)

On-surface design of dysprosium-directed metal-organic network on graphene/Ir(111).

Elucidating the intramolecular contrast in the STM images of 2,4,6-tris(4',4'',4'''-trimethylphenyl)-1,3,5-triazine molecules recorded at room-temperature and at the liquid-solid interface

Star-shaped 2,4,6-tris(4',4'',4'''-trimethylphenyl)-1,3,5-triazine molecules self-assemble at the solid-liquid interface into a compact hexagonal nanoarchitecture on graphite. High resolution scanning tunneling microscopy (STM) images of the molecules reveal intramolecular features. Comparison of the experimental data with calculated molecular charge density contours shows that the molecular features in the STM images correspond to molecular LUMO+2.

On-surface synthesis of gold–coronene molecular wires

Perchlorocoronene undergoes selective dehalogenation under the one-dimensional constraint by intermolecular interactions, resulting in the formation of gold–coronene wires on Au(111) surfaces.

Simultaneous Detection of Cu2+ and Hg2+ via Two Mutually Independent Sensing Pathways of Biimidazole Push-Pull Dye

An easy-to-synthesize, biimidazole push-pull dye has been designed, comprising two mutually independent analyte binding sites. It has been found that Hg²⁺ coordinates with the compound via thiophene residue and inhibits the charge-transfer (CT) process, which transforms the yellow-colored solution colorless. On the other hand, an unusually large bathochromic shift is observed in CT band upon addition of Cu²⁺, accompanied by a change in the color from yellow to red. A rather surprising observation is made from mechanistic studies, where it indicates that Cu²⁺ catalyzes the formation of 6-imino-5,6-dihydropyrrolo[3,4- d]imidazole-4(3 H)-one (IPIMO) derivative. This strongly affects the charge-transfer state of the compound as well as its polarizability. Most importantly, this is the first report where IPIMO formation reaction has been exploited for sensing of a metal ion. Further, the system was employed for screening of both of these metal ions in wastewater samples. Recovery values ranging from 93.3 to 105.0% confirm the suitability of the present method for estimating trace level of metal ions in complex matrices. In addition, inexpensive on-site detection systems were developed using paper strips.

Linear array of cesium atoms assisted by uracil molecules on Au(111)

A series of metal–organic U + Cs structures are achieved in which the Cs cations tend to form linear arrays.

Influence of Relativistic Effects on Assembled Structures of V-Shaped Bispyridine Molecules on M(111) Surfaces Where M = Cu, Ag, Au

The self-assembly behavior of a V-shaped bispyridine, 1,3-bi(4-pyridyl)benzene (BPyB), was studied by scanning tunneling microscopy on the (111) surfaces of Cu, Ag, and Au. BPyB molecules coordinately bonded with active Cu adatoms on Cu(111) in the form of complete polygonal rings at low coverages. On Ag(111), BPyB molecules aggregated into two-dimensional islands by relatively weak intermolecular hydrogen bonds. The coexistence of hydrogen bonds and coordination interaction was observed on the BPyB-covered Au(111) substrate. Density functional theory calculations of the metal-molecule binding energy and Monte Carlo simulations were performed to help understand the forming mechanism of molecular superstructures on the surfaces. In particular, the comprehensive orbital composition analysis interprets the observed metal-organic complexes and reveals the importance of relativistic effects for the extraordinary activity of gold adatoms. The relativistic effects cause the energy stability of the Au 6s atomic orbital and decrease the energy separation between the Au 6s and 5d orbitals. The enhanced sd hybridization strengthens the N-Au-N bond in BPyB-Au-BPyB complexes.

Liquid/Liquid Interfacial Synthesis of a Click Nanosheet

A liquid/liquid interfacial synthesis is employed, for the first time, to synthesize a covalent two-dimensional polymer nanosheet. Copper-catalyzed azide-alkyne cycloaddition (CuAAC) between a three-way terminal alkyne and azide at a water/dichloromethane interface generates a 1,2,3-triazole-linked nanosheet. The resultant nanosheet, with a flat and smooth texture, has a maximum domain size of 20 μm and minimum thickness of 5.3 nm. The starting monomers in the organic phase and the copper catalyst in the aqueous phase can only meet at the liquid/liquid interface as a two-dimensional reaction space; this allows them to form the two-dimensional polymer. The robust triazole linkage generated by irreversible covalent-bond formation allows the nanosheet to resist hydrolysis under both acidic and alkaline conditions, and to endure pyrolysis up to more than 300 °C. The coordination ability of the triazolyl group enables the nanosheet to act as a reservoir for metal ions, with an affinity order of Pd²⁺ >Au³⁺ >Cu²⁺ .

Competition between Hydrogen Bonds and Coordination Bonds Steered by the Surface Molecular Coverage

In addition to the choices of metal atoms/molecular linkers and surfaces, several crucial parameters, including surface temperature, molecular stoichiometric ratio, electrical stimulation, concentration, and solvent effect for liquid/solid interfaces, have been demonstrated to play key roles in the formation of on-surface self-assembled supramolecular architectures. Moreover, self-assembled structural transformations frequently occur in response to a delicate control over those parameters, which, in most cases, involve either conversions from relatively weak interactions to stronger ones (e.g., hydrogen bonds to coordination bonds) or transformations between the comparable interactions (e.g., different coordination binding modes or hydrogen bonding configurations). However, intermolecular bond conversions from relatively strong coordination bonds to weak hydrogen bonds were rarely reported. Moreover, to our knowledge, a reversible conversion between hydrogen bonds and coordination bonds has not been demonstrated before. Herein, we have demonstrated a facile strategy for the regulation of stepwise intermolecular bond conversions from the metal-organic coordination bond (Cu-N) to the weak hydrogen bond (CH···N) by increasing the surface molecular coverage. From the DFT calculations we quantify that the loss in intermolecular interaction energy is compensated by the increased molecular adsorption energy at higher molecular coverage. Moreover, we achieved a reversible conversion from the weak hydrogen bond to the coordination bond by decreasing the surface molecular coverage.

Self-assembled nanostructures of a di-carbonitrile molecule on copper single-crystal surfaces

A di-carbonitrile molecule prefers to form nanostructures by hydrogen bonds rather than coordination bonds on Cu(110) and Cu(100) at RT.

Two-Dimensional Ketone-Driven Metal-Organic Coordination on Cu(111)

Two-dimensional metal-organic nanostructures based on the binding of ketone groups and metal atoms were fabricated by depositing pyrene-4,5,9,10-tetraone (PTO) molecules on a Cu(111) surface. The strongly electronegative ketone moieties bind to either copper adatoms from the substrate or codeposited iron atoms. In the former case, scanning tunnelling microscopy images reveal the development of an extended metal-organic supramolecular structure. Each copper adatom coordinates to two ketone ligands of two neighbouring PTO molecules, forming chains that are linked together into large islands through secondary van der Waals interactions. Deposition of iron atoms leads to a transformation of this assembly resulting from the substitution of the metal centres. Density functional theory calculations reveal that the driving force for the metal substitution is primarily determined by the strength of the ketone-metal bond, which is higher for Fe than for Cu. This second class of nanostructures displays a structural dependence on the rate of iron deposition.

Structure and role of metal clusters in a metal-organic coordination network determined by density functional theory

We present a comprehensive theoretical investigation of the structures formed by self-assembly of tetrahydroxybenzene (THB)-derivatives on Cu(111). The THB molecule is known to dehydrogenate completely during annealing, forming a reactive radical which assembles into a close-packed structure or a porous metal-coordinated network depending on the coverage of the system. Here, we present details on how the structures are determined by density functional theory calculations, using scanning tunneling microscopy-derived information on the periodicity. The porous network is based on adatom trimers. By analysing the charge distribution of the structure, it is found that this unusual coordination motif is preferred because it simultaneously provides a good coordination of all oxygen atoms and allows for the formation of a two-dimensional network on the surface.

Cyano-Functionalized Triarylamines on Coinage Metal Surfaces: Interplay of Intermolecular and Molecule-Substrate Interactions

The self-assembly of cyano-functionalized triarylamine derivatives on Cu(111), Ag(111) and Au(111) was studied by means of scanning tunnelling microscopy, low-energy electron diffraction, X-ray photoelectron spectroscopy and density functional theory calculations. Different bonding motifs, such as antiparallel dipolar coupling, hydrogen bonding and metal coordination, were observed. Whereas on Ag(111) only one hexagonally close-packed pattern stabilized by hydrogen bonding is observed, on Au(111) two different partially porous phases are present at submonolayer coverage, stabilized by dipolar coupling, hydrogen bonding and metal coordination. In contrast to the self-assembly on Ag(111) and Au(111), for which large islands are formed, on Cu(111), only small patches of hexagonally close-packed networks stabilized by metal coordination and areas of disordered molecules are found. The significant variety in the molecular self-assembly of the cyano-functionalized triarylamine derivatives on these coinage metal surfaces is explained by differences in molecular mobility and the subtle interplay between intermolecular and molecule-substrate interactions.

Tuning the formation of discrete coordination nanostructures

Novel surface coordination nanostructures based on cyanosexiphenyl molecules are assembled on a gold surface and investigated by scanning tunneling microscopy and density functional theory. Their formation can be tuned by varying the surface temperature during deposition. Diffusing gold adatoms act as coordination centers for the cyano groups present on one end of the nonsymmetrical molecules.

On-surface construction of a metal-organic Sierpiński triangle

Through a careful design of the molecular precursor we have successfully constructed the metal-organic Sierpiński triangles on Au(111) via on-surface coordination chemistry, which is demonstrated by the interplay of high-resolution STM imaging and DFT calculations. The coordination Sierpiński triangles show high stabilities as evidenced by room temperature STM imaging, and could withstand a thermal treatment up to 450 K.

A photofunctional bottom-up bis(dipyrrinato)zinc(II) complex nanosheet

Two-dimensional polymeric nanosheets have recently gained much attention, particularly top-down nanosheets such as graphene and metal chalcogenides originating from bulk-layered mother materials. Although molecule-based bottom-up nanosheets manufactured directly from molecular components can exhibit greater structural diversity than top-down nanosheets, the bottom-up nanosheets reported thus far lack useful functionalities. Here we show the design and synthesis of a bottom-up nanosheet featuring a photoactive bis(dipyrrinato)zinc(II) complex motif. A liquid/liquid interfacial synthesis between a three-way dipyrrin ligand and zinc(II) ions results in a multi-layer nanosheet, whereas an air/liquid interfacial reaction produces a single-layer or few-layer nanosheet with domain sizes of >10 μm on one side. The bis(dipyrrinato)zinc(II) metal complex nanosheet is easy to deposit on various substrates using the Langmuir-Schäfer process. The nanosheet deposited on a transparent SnO2 electrode functions as a photoanode in a photoelectric conversion system, and is thus the first photofunctional bottom-up nanosheet.

Solvent-dependent stabilization of metastable monolayer polymorphs at the liquid-solid interface

Self-assembly of 1,3,5-tris(4'-biphenyl-4"-carbonitrile)benzene monolayers was studied at the liquid-solid interface by scanning tunneling microscopy. Application of different fatty acid homologues as solvents revealed a solvent-induced polymorphism. Yet, tempering triggered irreversible phase transitions of the initially self-assembled monolayers, thereby indicating their metastability. Interestingly, in either case, the same thermodynamically more stable and more densely packed monolayer polymorph was obtained after thermal treatment, irrespective of the initial structure. Again, the same densely packed structure was obtained in complementary solvent-free experiments conducted under ultrahigh vacuum conditions. Thus, self-assembly of metastable polymorphs at room temperature is explained by adsorption of partially solvated species under kinetic control. The irreversible phase transitions are induced by thermal desolvation, that is, desorption of coadsorbed solvent molecules.