Polymorphic porous supramolecular networks mediated by halogen bonds on Ag(111)

Surface-confined alternating copolymerization with molecular precision by stoichiometric control

Keen desires for artificial mimicry of biological polymers and property improvement of synthesized ones have triggered intensive explorations for sequence-controlled copolymerization. However, conventional synthesis faces great challenges to achieve this goal due to the strict requirements on reaction kinetics of comonomer pairs and tedious synthetic processes. Here, sequence-controlled alternating copolymerization with molecular precision is realized on surface. The stoichiometric control serves as a thermodynamic strategy to steer the polymerization selectivity, which enables the selective alternating organometallic copolymerization via intermolecular metalation of 4,4"-dibromo-p-terphenyl (P-Br) and 2,5-diethynyl-1,4-bis(phenylethynyl)benzene (A-H) with Ag adatoms on Ag(111) at P-Br: A-H = 2, as verified by scanning tunneling microscopy and density functional theory studies. In contrast, homopolymerization yield increases as the stoichiometric ratio deviates from 2. The microscopic characterizations rationalize the mechanism, providing a delicate explanation of the stoichiometry-dependent polymerization. These findings pave a way to actualizing an efficient sequence control of copolymerization by surface chemistry.

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.

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.

Multiple Molecular Interactions between Alkyl Groups and Dissociated Bromine Atoms on Ag(111)

Multiple intermolecular interactions offer a high-degree of controllability of on-surface molecular assemblies. Here, two kinds of molecular networks were formed by depositing 11,11,12,12-tetrabromo-1,4,5,8-tetraaza-9,10-anthraquinodimethane derivatives with two different alkyl groups in...

Light assisted synthesis of poly-para-phenylene on Ag(001)

A detailed study of poly-para-phenylene (PPP) obtained by light-assisted on-surface-synthesis (OSS) on Ag(100) was carried out by scanning tunneling microscopy and spectroscopy together with density functional theory calculations. The use of light in combination with heat allows to lower by 50 K annealing temperature the each stage of the Ullmann coupling. Debromination of the 4,4″ dibromo-p-terphenyl precursors was thus realized at 300 K, the formation of the first oligomers from the organometallic intermediate by silver bridging atom release at 423 K and PPP by complete elimination of the silver at 473 K. This approach to lower the reaction temperature permits to enhance the Ag(100) surface reactivity to become comparable to that of Cu(111). The underlying mechanism of light effect was proposed to occur via surface mediated excitation, with the creation of photoexcited electrons known as hot electrons correlated with surface plasmon excitation. This original pathway combining both light and heat provides an additional parameter to control OSS by separating the precursor activation stage from the diffusion.

Near Fermi Superatom State Stabilized by Surface State Resonances in a Multiporous Molecular Network

Two-dimensional honeycomb molecular networks confine a substrate's surface electrons within their pores, providing an ideal playground to investigate the quantum electron scattering phenomena. Besides surface state confinement, laterally protruding organic states can collectively hybridize at the smallest pores into superatom molecular orbitals. Although both types of pore states could be simultaneously hosted within nanocavities, their coexistence and possible interaction are unexplored. Here, we show that these two types of pore states do coexist within the smallest nanocavities of a two-dimensional halogen-bonding multiporous network grown on Ag(111) studied using a combination of scanning tunneling microscopy and spectroscopy, density functional theory calculations, and electron plane wave expansion simulations. We find that superatom molecular orbitals undergo an important stabilization when hybridizing with the confined surface state, following the significant lowering of its free-standing energy. These findings provide further control over the surface electronic structure exerted by two-dimensional nanoporous systems.

Surface self-assembly involving the interaction between S and N atoms

Regulation of the self-assembly nanostructures by recruiting the electrostatic interaction between S and N atoms.

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.

Organometallic polymers synthesized from prochiral molecules by a surface-assisted synthesis on Ag(111)

Organometallic polymers can be successfully synthesized on a Ag(111) surface via a surface-assisted synthesis by choosing prochiral 4,4'-dibromo-2,2'-bis(2-phenylethynyl)-1,1'-biphenyl (DBPB) molecules as the designed precursor. High-resolution scanning tunneling microscopy investigation reveals that prochiral molecules show chirality on a surface and can evolve into organometallic chains on the Ag(111) surface based on Ullmann coupling. Due to the special structural features of DBPB molecules, chiral selectivity will be lost in the organometallic polymers. This result may provide an important basis for selecting suitable precursors to fabricate chiral covalent nanostructures on a surface.

Dissymmetric On-Surface Dehalogenation Reaction Steered by Preformed Self-Assembled Structure

Ullmann coupling of 4,4″-dibromo-p-terphenyl (DBTP) thermally catalyzed on a Ag(111) surface was studied by scanning tunneling microscopy. Detailed experimental measurement shows that the Ullmann coupling reaction pathways of DBTP molecules can be controlled by pre-self-assembly, and the dissymmetric dehalogenation reaction is realized. Moreover, self-assembly of the reactants in a rectangular network undergoes a dissymmetric debromination transfer to a newly observed rhombic network formed by organometallic dimers prior to the formation of longer symmetric organometallic intermediates on a Ag(111) surface, while the ladder assembled phase is more likely to induce the symmetric debromination reaction and converts into the symmetric organometallic intermediate. These findings help us to understand the essentials of the dissymmetric dehalogenation reaction that originated from a symmetric compound and pave new avenues for advancing the emerging field of on-surface synthesis.

Halogen Bonding in Two-Dimensional Crystal Engineering

Halogen bonds, which provide an intermolecular interaction with moderate strength and high directionality, have emerged as a promising tool in the repertoire of non-covalent interactions. In this review, we provide a survey of the literature where halogen bonding was used for the fabrication of supramolecular networks on solid surfaces. The definitions of, and the distinction between halogen bonding and halogen-halogen interactions are provided. Self-assembled networks formed at the solution/solid interface and at the vacuum-solid interface, stabilized in part by halogen bonding, are discussed. Besides the broad classification based on the interface at which the systems are studied, the systems are categorized further as those sustained by halogen-halogen and halogen-heteroatom contacts.

Synthesis and photophysics of new pyridyl end-capped 3D-dithia[3.3]paracyclophane-based Janus tectons: surface-confined self-assembly of their model pedestal on HOPG

Once synthesized, these new tectons demonstrated both ionic and coordination bonding. Surprisingly, P forms a quasi-square self-assembly independently of the underlying HOPG lattice.

Supramolecular Assemblies on Surfaces: Nanopatterning, Functionality, and Reactivity

Understanding how molecules interact to form large-scale hierarchical structures on surfaces holds promise for building designer nanoscale constructs with defined chemical and physical properties. Here, we describe early advances in this field and highlight upcoming opportunities and challenges. Both direct intermolecular interactions and those that are mediated by coordinated metal centers or substrates are discussed. These interactions can be additive, but they can also interfere with each other, leading to new assemblies in which electrical potentials vary at distances much larger than those of typical chemical interactions. Earlier spectroscopic and surface measurements have provided partial information on such interfacial effects. In the interim, scanning probe microscopies have assumed defining roles in the field of molecular organization on surfaces, delivering deeper understanding of interactions, structures, and local potentials. Self-assembly is a key strategy to form extended structures on surfaces, advancing nanolithography into the chemical dimension and providing simultaneous control at multiple scales. In parallel, the emergence of graphene and the resulting impetus to explore 2D materials have broadened the field, as surface-confined reactions of molecular building blocks provide access to such materials as 2D polymers and graphene nanoribbons. In this Review, we describe recent advances and point out promising directions that will lead to even greater and more robust capabilities to exploit designer surfaces.

Deprotonation-Induced Phase Evolutions in Co-Assembled Molecular Structures

In this work, we systematically studied the co-assembly behavior of 1,3,5-tris(4-carboxyphenyl)benzene (TCPB) and 4,4″-diamino- p-terphenyl (DATP) on a silver surface. Due to the thermal instability of carboxylic acids, the co-assembled structure exhibits temperature-dependent evolutions on Ag(111). The level of the deprotonation reactions of TCPB are clarified by the characteristic self-assembled footprints. Aided by these footprints, we are able to identify the structures of the complex co-assembly of TCPB and DATP entities at each stage. Finally, the conclusions are further evidenced by density functional theory calculations.

On-Surface Synthesis of Adenine Oligomers via Ullmann Reaction

Despite the fact that DNA bases have been well-studied on surface, the on-surface synthesis of one-dimensional DNA analogs through in situ reactions is still an interesting topic to be investigated. Herein, from the interplay of high-resolution scanning tunneling microscopy (STM) imaging and density functional theory (DFT) calculations, we have delicately designed a halogenated derivative of adenine as precursor to realize the combination of DNA bases and Ullmann reaction, and then successfully synthesized adenine oligomers on Au(111) via Ullmann coupling. This model system provides a possible bottom-up strategy of fabricating adenine oligomers on surface, which may further give access to man-made DNA strands with multiple bases.

Construction of Two-Dimensional Chiral Networks through Atomic Bromine on Surfaces

Using atomic bromine and 2,6-diphenylanthracene (DPA), we successfully constructed and characterized the large-area 2D chiral networks on Ag(111) and Cu(111) surfaces by combining molecular beam epitaxy with scanning tunneling microscopy. The Br atoms distribute themselves periodically in the network with the maximum number of -C-H···Br hydrogen bonds. Density functional theory calculations demonstrate that the hydrogen bonds contribute to the stability of the Br-organic networks. In addition, by controlling the ratio of bromine atoms to DPA molecules, different patterns of Br-organic networks were obtained on Ag(111) surfaces. Further experiments with 2,6-di(4-cyclohexylphenyl)anthracene on Ag(111) produced analogous atomic bromine guided 2D chiral networks.

The Halogen Bond

The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.

Effects of the position and number of bromine substituents on the concentration-mediated 2D self-assembly of phenanthrene derivatives

The effects of the position and number of bromine substituents on the self-assembled patterns of phenanthrene derivatives by changing multiple weak intermolecular interactions were investigated at the 1-octanoic acid/graphite interface at different concentrations by scanning tunneling microscopy. Two Br substituted DBHP molecules (2,7-DBHP, 3,6-DBHP) and BHP without a Br group formed a linear lamellar pattern by the van der Waals interactions between the alkoxyl chains in each lamella at high concentrations, which forces the phenanthrene derivatives to self-organize in a π-π stacked edge-on conformation. On decreasing the solution concentration, owing to the molecule-molecule van der Waals force and BrBr halogen bonds or the molecule-solvent cooperative BrO (C[double bond, length as m-dash]O) hydrogen and BrHO-hydrogen bonds, 2,7-DBHP molecules were found to form two kinds of network structures, whereas 3,6-DBHP molecules formed only a zigzag pattern due to the intermolecular BrBr van der Waals type interactions. One bromine substituted phenanthrene derivative (3-DBHP) formed a dislocated linear pattern by two C-HBr hydrogen bonds in each dimer. These observations revealed that an important modification of the position and number of halogen substituents might dramatically change the self-assembly behaviors by different intermolecular interactions including BrBr and BrO halogen bonding, BrBr van der Waals type interactions, and HBr hydrogen bonding. DFT calculations were explored to unravel how slightly tuning the molecular structure defines the geometry of a 2D self-assembled nanoarchitecture through the different elementary structural units having BrBr and BrH interactions.

Self-assembly of pyrene derivatives on Au(111): substituent effects on intermolecular interactions

The adsorption behaviour as well as the influence of bromine substituents on the formation of highly-ordered two-dimensional structures of pyrene derivatives on Au(111) are studied by a combination of scanning tunnelling microscopy (STM) and density functional theory (DFT) calculations.

Extended halogen bonding between fully fluorinated aromatic molecules

Halogen bonding is a noncovalent interaction where an electrophilic cap on a halogen atom, the so-called σ-hole, attracts a nucleophilic site on an adjacent molecule. The polarizability of halogens relates to the strength of the σ-hole, and accordingly the halogen-halogen distance becomes shorter in the order of Cl, Br, and I. Fully fluoro-substituted aromatic molecules, on the contrary, are generally believed not to form halogen bonds due to the absence of a σ-hole. Here, we study atomic-scale in-plane F-F contacts with high-resolution force microscopy. Our ab initio calculations show that the attractive dispersion forces can overcome the electrostatic repulsion between the fluorine atoms, while the anisotropic distribution of the negative electrostatic potential leads the directional bond and even changes the gap. The coexistence of these two competing forces results in the formation of a "windmill" structure, containing three C-F···F bonds among neighboring molecules. While the σ-hole is absent, the scheme of the C-F···F bonding has a high similarity to halogen bonding.

Halogen bonding in polymer science: from crystal engineering to functional supramolecular polymers and materials

The applications of halogen bonding in surface functionalization, soft, luminescent and magnetic materials, interpenetrated networks, synthetic methods, and separation and inclusion techniques are reviewed.

Thermodynamics of halogen bonded monolayer self-assembly at the liquid–solid interface

The overall enthalpy change associated with hexabromotriphenylene monolayer self-assembly at the heptanoic acid–graphite interface was assessed by an adapted Born–Haber cycle.

Supramolecular Cl⋅⋅⋅H and O⋅⋅⋅H interactions in self-assembled 1,5-dichloroanthraquinone layers on Au(111)

The role of halogen bonds in self-assembled networks for systems with Br and I ligands has recently been studied with scanning tunneling microscopy (STM), which provides physical insight at the atomic scale. Here, we study the supramolecular interactions of 1,5-dichloroanthraquinone molecules on Au(111), including Cl ligands, by using STM. Two different molecular structures of chevron and square networks are observed, and their molecular models are proposed. Both molecular structures are stabilized by intermolecular Cl⋅⋅⋅H and O⋅⋅⋅H hydrogen bonds with marginal contributions from Cl-related halogen bonds, as revealed by density functional theory calculations. Our study shows that, in contrast to Br- and I-related halogen bonds, Cl-related halogen bonds weakly contribute to the molecular structure due to a modest positive potential (σ hole) of the Cl ligands.

Halogen bonds in 2D supramolecular self-assembly of organic semiconductors

Weak interactions between bromine, sulphur, and hydrogen are shown to stabilize 2D supramolecular monolayers at the liquid-solid interface. Three different thiophene-based semiconducting organic molecules assemble into close-packed ultrathin ordered layers. A combination of scanning tunneling microscopy (STM) and density functional theory (DFT) elucidates the interactions within the monolayer. Electrostatic interactions are identified as the driving force for intermolecular Br···Br and Br···H bonding. We find that the SS interactions of the 2D supramolecular layers correlate with the hole mobilities of thin film transistors of the same materials.