Competition between Hexagonal and Tetragonal Hexabromobenzene Packing on Au(111)

Evolution of Br⋯Br contacts in enantioselective molecular recognition during chiral 2D crystallization

Halogen-mediated interactions play an important role in molecular recognition and crystallization in many chemical and biological systems, whereas their effect on homochiral versus heterochiral recognition and crystallization has rarely been explored. Here we demonstrate the evolution of Br⋯Br contacts in chiral recognition during 2D crystallization. On Ag(100), type I contacts prevail at low coverage and lead to homochiral recognition and the formation of 2D conglomerates; whereas type II contacts mediating heterochiral recognition are suppressed at medium coverage and appear in the racemates induced by structural transitions at high coverage. On Ag(111), type I contacts dominate the 2D crystallization and generate 2D conglomerates exclusively. DFT calculations suggest that the energy difference between type I and type II contacts is reversed upon adsorption due to the substrate induced mismatch energy penalty. This result provides fundamental understanding of halogen-mediated interactions in molecular recognition and crystallization on surface.

Halogen-mediated interactions control molecular recognition in many chemical and biological systems. Here, the authors demonstrate two types of Br⋯Br contacts and their importance in chiral on-surface crystallization.

Substrate-Selective Intermolecular Interaction and the Molecular Self-Assemblies: 1,3,5-Tris(4-bromophenyl)benzene Molecules on the Ag(111) and Si(111) (√3 × √3)-Ag Surfaces

We report the formation processes of the self-assembled layer of 1,3,5-tris(4-bromophenyl)benzene (TBB) molecules on the Ag(111) and Si(111) (√3 × √3)-Ag surfaces by STM measurements and density functional theory (DFT) calculations. The self-assembled layers on the surfaces show characteristic structures controlled by the interplay between the intermolecular interaction and the molecule-substrate interaction. Through the cooperative interplay between the molecule-substrate interaction and the intermolecular halogen bond (XB), the periodic arrangement of TBB molecules appears on the Ag(111) surface. On the other hand, the two types of TBB arrangement appear on the Si(111) (√3 × √3)-Ag surface (phases 1 and 2). Phase 1 is the periodic arrangement of the TBB molecules and is derived from the cooperative interplay between the molecule-substrate interaction and the intermolecular van der Waals (vdW) interaction and the hydrogen bond (HB), and phase 2 is a random arrangement and is derived from the competitive interplay between the molecule-substrate interaction and the intermolecular XB and HB. Our present study specifies the role of the substrate in the molecular self-assembly of the substrate. Although the structure of the molecular self-assembly is controlled by the choice of the substrate, the cooperative interplay between the molecule-substrate interaction and the intermolecular interaction is necessary to realize the ideal periodic arrangement.

On-Surface Debromination of C6Br6: C6 Ring versus C6 Chain

Carbon allotropes comprising sp-hybridized carbon atoms have been investigated for decades for their molecular structure. One of the unsolved mysteries is whether they should take a linear or cyclic configuration in condensed phases due to the lack of atomistic characterizations. Herein, we designed a molecule with a C₆ skeleton as a model system to address this issue, which was achieved by eliminating Br atoms from hexabromobenzene (C₆Br₆) molecule on the Ag(111) substrate via thermal treatment. It is found that the C₆ ring intermediate resulting from complete debromination is energetically unstable at room temperature based on theoretical calculations. It subsequently transforms into the C₆ polyynic chain via a ring-opening process and ultimately polymerizes into the organometallic polyyne, whose triyne structural unit is revealed by bond-resolved noncontact atomic force microscopy. Theoretical calculations demonstrated an energetically favorable pathway in which the ring-opening process occurs after complete debromination of C₆Br₆. Our study provides a platform for the synthesis of elusive carbon-rich materials.

Fast dopamine detection based on evanescent wave detection platform

A compact evanescent wave detection platform (EWDP) is developed for the detection of fluorescence gold nanoclusters. The EWDP employs a simple optical system and a Si-based photodetector SOP-1000 assembly to improve the optical efficiency and detection sensitivity. A microfluidic sample cell is also used to decrease the amount of analyte to 200 μL (The volume of sample cell is really about 30 μL). On this basis, we design a strategy for detecting dopamine (DA) based on the photoinduced electron transfer (PET) quenching mechanism. By introduction of tyrosinase (TYR) during the detection, the testing time is shortened to 1 min. The fluorescence emission signal decreased dramatically and the quenching ratio (F₀-F)/F₀ is linearly related to the concentration of DA in the range of 0.03-60 μM with a detection limit of 0.03 μM. Additionally, this detection platform has potential applications for DA fast detection in the microsamples.

2D constraint modifies packing behaviour: a halobenzene monolayer with X3 halogen-bonding motif

Using a combination of X-ray diffraction and simulation techniques, we are able to identify a crystalline monolayer of 1,3,5-triiodotrifluorobenzene formed on graphite. The monolayer is found to exhibit an incommensurate hexagonal unit cell with a lattice parameter of 9.28(7) Å, exhibiting a trigonal arrangement of iodine atoms not found in the bulk structure. DFT simulations have been performed exhibiting close agreement with the experimental structure. Importantly these simulations can be used to compare the strength of the intermolecular interactions both with and without Van der Waals corrections. Thus it is possible to estimate that halogen bonding consists of approximately half the total interaction energy. This demonstrates that despite the presence of strong directional non-covalent bonding, dispersion interactions account for a very significant proportion of the total energy.

Real-space imaging of anisotropic charge of σ-hole by means of Kelvin probe force microscopy

[Figure: see text].

Surface-controlled reversal of the selectivity of halogen bonds

Intermolecular halogen bonds are ideally suited for designing new molecular assemblies because of their strong directionality and the possibility of tuning the interactions by using different types of halogens or molecular moieties. Due to these unique properties of the halogen bonds, numerous areas of application have recently been identified and are still emerging. Here, we present an approach for controlling the 2D self-assembly process of organic molecules by adsorption to reactive vs. inert metal surfaces. Therewith, the order of halogen bond strengths that is known from gas phase or liquids can be reversed. Our approach relies on adjusting the molecular charge distribution, i.e., the σ-hole, by molecule-substrate interactions. The polarizability of the halogen and the reactiveness of the metal substrate are serving as control parameters. Our results establish the surface as a control knob for tuning molecular assemblies by reversing the selectivity of bonding sites, which is interesting for future applications.

Structural Characterization of a Novel Two-Dimensional Material: Cobalt Sulfide Sheets on Au(111)

Transition metal dichalcogenides (TMDCs) are a type of two-dimensional (2D) material that has been widely investigated by both experimentalists and theoreticians because of their unique properties. In the case of cobalt sulfide, density functional theory (DFT) calculations on free-standing S-Co-S sheets suggest there are no stable 2D cobalt sulfide polymorphs, whereas experimental observations clearly show TMDC-like structures on Au(111). In this study, we resolve this disagreement by using a combination of experimental techniques and DFT calculations, considering the substrate explicitly. We find a 2D CoS(0001)-like sheet on Au(111) that delivers excellent agreement between theory and experiment. Uniquely this sheet exhibits a metallic character, contrary to most TMDCs, and exists due to the stabilizing interactions with the Au(111) substrate.

Structural Phase Transitions of Molecular Self-Assembly Driven by Nonbonded Metal Adatoms

The involvement of metal atoms in molecular assemblies has enriched the structural and functional diversity of two-dimensional supramolecular networks, where metal atoms are incorporated into the architecture via coordination or ionic bonding. Here we present a temperature-variable study of the self-assembly of the 1,3,5-tribromobenzene (TriBB) molecule on Cu(111) that reveals the involvement of nonbonded adatoms in the molecular matrix. By means of scanning tunneling microscopy and noncontact atomic force microscopy, we demonstrate the molecular-level details of a phase transition of TriBB assembly from the close-packed to porous honeycomb structures at 78 K. This is an unexpected transformation because the close-packed phase is thermodynamically favored in view of its higher molecular density and more intermolecular bonds as compared to the honeycomb lattice. A comprehensive density functional theory calculation suggests that Cu adatoms should be involved in the formation of the honeycomb network, where the Cu adatoms help stabilize the molecular assembly via enhanced van der Waals interactions between TriBB molecules and the underlying substrate. Both calculation and experimental results suggest no chemical bonding or direct charge transfer between the adatoms and the molecules, thus the electronic characteristics of the Cu adatoms trapped in the molecular confinement are close to the intrinsic ones on a clean metal surface and different from those in the traditional coordination-bonded framework. The nonbonded metal adatoms embedded self-assemblies may complement the metal-organic coordination system and can be used to tailor the chemical reactivity and electronic properties of supramolecular structures.

Interfacial Interaction of Absorbate Copper Phthalocyanine with PVDF Based Ferroelectric Polymer Substrates: A Spectroscopic Study

Studies of CuPc thin films on underlying ferroelectric copolymeric and terpolymeric substrates have been performed by ultraviolet photoelectron spectroscopy (UPS), X-ray photoelectron spectroscopy (XPS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Work function (WF) and highest occupied molecular orbital (HOMO) energy level shift observed from UPS spectroscopy for successive deposition of CuPc molecules on ferroelectric polymer surfaces confirm the formation of interface dipole at the CuPc-ferroelectric polymer interface owing to charge transfer from the tailing region of the CuPc HOMO density of states (DOS) to the ferroelectric polymer layer. According to our thickness dependent XPS data, CuPc molecules are coupled to the organic ferroelectric surfaces through the central metal atom of the CuPc molecules, i.e., copper atom, and the halogens of underlying ferroelectric polymer surfaces, and hence support the charge transfer phenomenon from CuPc molecules to the ferroelectric polymer substrate. Polarization dependent NEXAFS results reveal that CuPc molecules retain their tilted geometrical configuration even at submonolayer thickness of the molecular films on both ferroelectric surfaces and confirms the electronic structural disturbance associated with structural modification of CuPc molecules due to interfacial charge transfer. Therefore, the energy level alignment with increment in the thickness of CuPc films at both the organic semiconductor-ferroelectric polymer interface is controlled by the charge transfer phenomenon from deposited CuPc molecules to the organic ferroelectric substrates. Our results provide a clear understanding about chemical interactions, molecular configurations, energy level alignment, and their correlation at CuPc/polymeric ferroelectric interfaces that can be important for organic nonvolatile memory and synaptic based thin-film transistor devices.

Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding

Scanning tunnelling microscopy (STM) is commonly used to identify on-surface molecular self-assembled structures. However, its limited ability to reveal only the overall shape of molecules and their relative positions is not always enough to fully solve a supramolecular structure. Here, we analyse the assembly of a brominated polycyclic aromatic molecule on Au(111) and demonstrate that standard STM measurements cannot conclusively establish the nature of the intermolecular interactions. By performing high-resolution STM with a CO-functionalised tip, we clearly identify the location of rings and halogen atoms, determining that halogen bonding governs the assemblies. This is supported by density functional theory calculations that predict a stronger interaction energy for halogen rather than hydrogen bonding and by an electron density topology analysis that identifies characteristic features of halogen bonding. A similar approach should be able to solve many complex 2D supramolecular structures, and we predict its increasing use in molecular nanoscience at surfaces.

Construction of 2D extended cocrystals on the Au(111) surface via IOaldehyde halogen bonds

2D extended organic cocrystals were constructed using 1,4-diiodotetrafluorobenzene and aromatic aldehydes via IOaldehyde halogen bonds on an Au(111) surface. The competition and synergy of halogen bonds and hydrogen bonds in 2D co-crystallization were revealed by scanning tunneling microscopy.

Conformational Transitions of Phase-Separated Binary Molecules Assisted by Surface Dehalogenation

Molecular devices have become an emergent branch of nanoscience and technology beyond traditional silicon-based electronic devices. The properties of these devices are intimately related to the molecular conformation and packing. In this article, three different conformations of melamine molecules are observed on Au(111), and a transition from the lying-down to standing-up phase with long-range order is realized in melamine chains with the assistance of hexabromobenzene (HBB). We argue that it is the expanding of HBB domains from hexagonal to the dimer phase due to surface dehalogenation that facilitates the dehydrogenation of melamine to form a standing-up conformation. Similar transitions are also accomplished on the Ag(111) surface. Our results provide an effective way to achieve standing-up molecular arrays with long-range order on relatively less active metals. This may have significant implications in fabricating organic thin film transistors.

Three-dimensional hydrogen bonding between Landers and planar molecules facilitated by electrostatic interactions with Ni adatoms

Using a combination of UHV-STM and molecular mechanics calculations, we investigate the surface self-assembly of a complex multi-component metal-molecule system with synergistic non-covalent interactions. Hydrogen bonding between three-dimensional Lander-DAT molecules and planar PTCDI molecules, adsorbed closer to the surface, is found to be facilitated by electrostatic interactions between co-adsorbed Ni adatoms and the flexible molecular DAT groups.

Revealing Factors Influencing the Fluorine-Centered Non-Covalent Interactions in Some Fluorine-Substituted Molecular Complexes: Insights from First-Principles Studies

We examine the equilibrium structure and properties of six fully or partially fluorinated hydrocarbons and several of their binary complexes using computational methods. In the monomers, the electrostatic surface of the fluorine is predicted to be either entirely negative or weakly positive. However, its lateral sites are always negative. This enables the fluorine to display an anisotropic distribution of charge density on its electrostatic surface. While this is the electrostatic surface scenario of the fluorine atom, its negative sites in some of these monomers are shown to have the potential to engage in attractive engagements with the negative site(s) on the same atom in another molecule of the same type, or a molecule of a different type, to form bimolecular complexes. This is revealed by analyzing the results of current state-of-the-art computational approaches such as DFT, together with those obtained from the quantum theory of atoms in molecules, molecular electrostatic surface potential and symmetry adapted perturbation theories. We demonstrate that the intermolecular interaction energy arising in part from the universal London dispersion, which has been underappreciated for decades, is an essential factor in explaining the attraction between the negative sites, although energy arising from polarization strengthens the extent of the intermolecular interactions in these complexes.

Surface Adatom Mediated Structural Transformation in Bromoarene Monolayers: Precursor Phases in Surface Ullmann Reaction

Structural transformations of supramolecular systems triggered by external stimuli maintain great potential for application in the fabrication of molecular storage devices. Using combined ultrahigh vacuum scanning tunneling microscopy, X-ray photoemission spectroscopy, and density functional theory calculations, we observed the surface adatom mediated structural transformation from 4,4''-dibromo- m-terphenyl (DMTP)-based halogen-bonded networks to DMTP-Cu(Ag) coordination networks on Cu(111) and Ag(111) at low temperatures. The halogen-bonded networks, which were formed on Cu(111) at 97 K and on Ag(111) at 93 K, consist of intact DMTP molecules stabilized by triple Br···Br bonds. The DMTP-Cu(Ag) coordination networks form on Cu(111) at 113 K and on Ag(111) at 103 K. They contain alternatingly arranged intact DMTP molecules and Cu(Ag) adatoms stabilized by weak C-Br···Cu(Ag) coordination bonds. Annealing the DMTP-Ag structure to 333 K leads to the initiation of C-Br bond scission. This observation suggests that the DMTP-Ag coordination network represents the intermediate phase ready for dehalogenation, which is the first step of the surface Ullmann reaction.

Halogen-Adatom Mediated Phase Transition of Two-Dimensional Molecular Self-Assembly on a Metal Surface

Construction of tunable and robust two-dimensional (2D) molecular arrays with desirable lattices and functionalities over a macroscopic scale relies on spontaneous and reversible noncovalent interactions between suitable molecules as building blocks. Halogen bonding, with active tunability of direction, strength, and length, is ideal for tailoring supramolecular structures. Herein, by combining low-temperature scanning tunneling microscopy and systematic first-principles calculations, we demonstrate novel halogen bonding involving single halogen atoms and phase engineering in 2D molecular self-assembly. On the Au(111) surface, we observed catalyzed dehalogenation of hexabromobenzene (HBB) molecules, during which negatively charged bromine adatoms (Br^δ-) were generated and participated in assembly via unique C-Br^δ+···Br^δ- interaction, drastically different from HBB assembly on a chemically inert graphene substrate. We successfully mapped out different phases of the assembled superstructure, including densely packed hexagonal, tetragonal, dimer chain, and expanded hexagonal lattices at room temperature, 60 °C, 90 °C, and 110 °C, respectively, and the critical role of Br^δ- in regulating lattice characteristics was highlighted. Our results show promise for manipulating the interplay between noncovalent interactions and catalytic reactions for future development of molecular nanoelectronics and 2D crystal engineering.

Chiral Self-Assembly of Nonplanar 10,10'-Dibromo-9,9'-bianthryl Molecules on Ag(111)

We report on the low-temperature scanning tunneling microscopy (STM) measurements of the self-assembly of nonplanar 10,10'-dibromo-9,9'-bianthryl (DBBA) molecules on Ag(111) combined with density functional theory (DFT) calculations. DBBA molecules have two enantiomorphous adsorption configurations, from which more chiral structures can be formed. At a low coverage [0.4 monolayer (ML)], DBBA forms racemic netlike islands consisting of molecular chains along ⟨1 2 3̅⟩_Ag. Moreover, the gliding between the molecular chains gives rise to chiral windmill-like patterns in the islands. At 0.8 ML, DBBA forms a racemic row phase and a homochiral hexamer phase. The molecular appearance difference between the two coexisted phases and the DFT calculated molecular adsorption configuration reveal a decrease in the molecular dihedral angle of DBBA, which implies an enhancement in the intermolecular interactions via CH···π and halogen bonds. The transition from a racemic packing mode to a homochiral one suggests that the suitability of steric configurations is dominant in the close-packing mode under enhanced intermolecular interactions.