Molecular and Supramolecular Networks on Surfaces: From Two-Dimensional Crystal Engineering to Reactivity

Functionalized surface-confined pores: guest binding directed by lateral noncovalent interactions at the solid-liquid interface

We present here the construction of self-assembled two-dimensional (2D) molecular networks that contain pores equipped with functional groups that promote guest-specific binding at the liquid/solid interface. For this purpose, a dehydrobenzo[12]annulene (DBA) derivative, DBA-F, having perfluoroalkyl groups at the end of the three alternating alkoxy chains connected by para-phenylene linkers was synthesized. For comparison DBA-H, having the same carbon backbone without fluorine substituents, was also prepared. STM observations revealed that these molecules formed porous 2D networks whose pores were decorated with either fluoroalkane or simple alkane perimeters. Hexakis(phenylethynyl)benzene, HPEB, and its octadecafluoro derivative, HPEB-F surrounded by 18 fluorine atoms, were employed as planar guest molecules of suitable size. The fluoroalkane-lined pores present in the network of DBA-F exhibited good binding ability toward both guest molecules via fluorophilicity and electrostatic interaction, respectively. In contrast the binding ability of the alkane-lined pore of the network of DBA-H for the fluorinated guest HPEB-F was poor as a result of weaker electrostatic interaction. Interestingly, with HPEB as a guest, this network underwent a periodical structural deformation through an induced-fit mechanism to form a superlattice structure consisting of free and occupied pores. These observations are discussed based on modeling experiments using molecular mechanics and quantum chemical methods to elucidate the roles of lateral noncovalent interactions and size matching between the pore and the guest molecules used for 2D guest binding.

Controlling two-phase self-assembly of an adenine derivative on HOPG via kinetic effects

Large-area self-assembled structures of a nucleobase adenine derivative were successfully realized through vacuum deposition. STM images reveal two types of structures, which could be regulated by substrate temperature and the evaporation rate, indicating the relevance of kinetic effects. The results are supported by computer simulations.

Surface-confined self-assembled Janus tectons: a versatile platform towards the noncovalent functionalization of graphene

A general strategy for simultaneously generating surface-based supramolecular architectures on flat sp(2) -hybridized carbon supports and independently exposing on demand off-plane functionality with controlled lateral order is highly desirable for the noncovalent functionalization of graphene. Here, we address this issue by providing a versatile molecular platform based on a library of new 3D Janus tectons that form surface-confined supramolecular adlayers in which it is possible to simultaneously steer the 2D self-assembly on flat C(sp(2))-based substrates and tailor the external interface above the substrate by exposure to a wide variety of small terminal chemical groups and functional moieties. This approach is validated throughout by scanning tunneling microscopy (STM) at the liquid-solid interface and molecular mechanics modeling studies. The successful self-assembly on graphene, together with the possibility to transfer the graphene monolayer onto various substrates, should considerably extend the application of our functionalization strategy.

Impact of heterocirculene molecular symmetry upon two-dimensional crystallization

Despite the development of crystal engineering, it remains a great challenge to predict the crystal structure even for the simplest molecules, and a clear link between molecular and crystal symmetry is missing in general. Here we demonstrate that the two-dimensional (2D) crystallization of heterocirculenes on a Au(111) surface is greatly affected by the molecular symmetry. By means of ultrahigh vacuum scanning tunneling microscopy, we observe a variety of 2D crystalline structures in the coverage range from submonolayer to monolayer for D_8h-symmetric sulflower (C₁₆S₈), whereas D_4h-symmetric selenosulflower (C₁₆S₄Se₄) forms square and rectangular lattices at submonolayer and monolayer coverages, respectively. No long-range ordered structure is observed for C_1h-symmetric selenosulflower (C₁₆S₅Se₃) self-assembling at submonolayer coverage. Such different self-assembly behaviors for the heterocirculenes with reduced molecular symmetries derive from the tendency toward close packing and the molecular symmetry retention in 2D crystallization due to van der Waals interactions.

Supramolecular self-assembly of metal-free naphthalocyanine on Au(111)

The self-assembly of metal-free naphthalocyanine (H2Nc) on the Au(111) surface is studied under ultrahigh vacuum conditions at room temperature using a combination of scanning tunnelling microscopy (STM), low-energy electron diffraction (LEED) and X-ray photoelectron spectroscopy (XPS). The STM measurements reveal that the molecules form a well-ordered, defect-free structure with a square-like unit cell at monolayer coverage with their molecular plane parallel to the substrate plane. The molecular lattice direction is aligned along one of the principal directions of the underlying Au(111) substrate while the molecular orientation remains unchanged for different domains. XPS measurements show that there is no significant difference in the electronic structure of H2Nc between monolayer and multilayer coverage. Combining the information obtained from STM, LEED and XPS measurements demonstrates that the self-assembled structure of H2Nc on Au(111) is mainly stabilized by intermolecular interactions while the molecule-substrate interactions are responsible for the rotational alignment of the molecules with respect to the principal Au directions.

Local electronic and chemical structure of oligo-acetylene derivatives formed through radical cyclizations at a surface

Semiconducting π-conjugated polymers have attracted significant interest for applications in light-emitting diodes, field-effect transistors, photovoltaics, and nonlinear optoelectronic devices. Central to the success of these functional organic materials is the facile tunability of their electrical, optical, and magnetic properties along with easy processability and the outstanding mechanical properties associated with polymeric structures. In this work we characterize the chemical and electronic structure of individual chains of oligo-(E)-1,1'-bi(indenylidene), a polyacetylene derivative that we have obtained through cooperative C1-C5 thermal enediyne cyclizations on Au(111) surfaces followed by a step-growth polymerization of the (E)-1,1'-bi(indenylidene) diradical intermediates. We have determined the combined structural and electronic properties of this class of oligomers by characterizing the atomically precise chemical structure of individual monomer building blocks and oligomer chains (via noncontact atomic force microscopy (nc-AFM)), as well as by imaging their localized and extended molecular orbitals (via scanning tunneling microscopy and spectroscopy (STM/STS)). Our combined structural and electronic measurements reveal that the energy associated with extended π-conjugated states in these oligomers is significantly lower than the energy of the corresponding localized monomer orbitals, consistent with theoretical predictions.

Redetermination of 2-methyl-4-nitropyridineN-oxide

An improved crystal structure of the title compound, C₆H₆N₂O₃, is reported. The structure, previously solved [Li et al. (1987 ▶). Jiegou Huaxue (Chin. J. Struct. Chem.), 6, 20–24] in the ortho­rhom­bic space group Pca2₁ and refined to R = 0.067, has been solved in the ortho­rhom­bic space group Pbcm with data of enhanced quality, giving an improved structure (R = 0.0485). The mol­ecule adopts a planar conformation with all atoms lying on a mirror plane. The crystal structure is composed of mol­ecular sheets extending parallel to the ab plane and connected via C—H⋯O contacts involving ring H atoms and O atoms of the N-oxide and nitro groups, while van der Waals forces consolidate the stacking of the layers.

Adaptive reorganization of 2D molecular nanoporous network induced by coadsorbed guest molecule

The ordered array of nanovoids in nanoporous networks, such as honeycomb, Kagome, and square, provides a molecular template for the accommodation of "guest molecules". Compared with the commonly studied guest molecules featuring high symmetry evenly incorporated into the template, guest molecules featuring lower symmetry are rare to report. Herein, we report the formation of a distinct patterned superlattice of guest molecules by selective trapping of guest molecules into the honeycomb network of trimesic acid (TMA). Two distinct surface patterns have been achieved by the guest inclusion induced adaptive reconstruction of a 2D molecular nanoporous network. The honeycomb networks can synergetically tune the arrangement upon inclusion of the guest molecules with different core size but similar peripherals groups, resulting in a trihexagonal Kagome or triangular patterns.

Controlled manipulation of gadolinium-coordinated supramolecules by low-temperature scanning tunneling microscopy

Coordination bonding between para-quarterphenyl-dicarbonitrile linkers and gadolinium on Ag(111) has been exploited to construct pentameric mononuclear supramolecules, consisting of a rare-earth center surrounded by five molecular linkers. By employing a scanning tunneling microscope tip, a manipulation protocol was developed to position individual pentamers on the surface. In addition, the tip was used to extract and replace individual linkers yielding tetrameric, pentameric, nonameric, and dodecameric metallosupramolecular arrangements. These results open new avenues toward advanced nanofabrication methods and rare-earth nanochemistry by combining the versatility of metal-ligand interactions and atomistic manipulation capabilities.

Interfacial growth of large-area single-layer metal-organic framework nanosheets

The air/liquid interface is an excellent platform to assemble two-dimensional (2D) sheets of materials by enhancing spontaneous organizational features of the building components and encouraging large length scale in-plane growth. We have grown 2D molecularly-thin crystalline metal-organic-framework (MOF) nanosheets composed of porphyrin building units and metal-ion joints (NAFS-13) under operationally simple ambient conditions at the air/liquid interface. In-situ synchrotron X-ray diffraction studies of the formation process performed directly at the interface were employed to optimize the NAFS-13 growth protocol leading to the development of a post-injection method –post-injection of the metal connectors into the water subphase on whose surface the molecular building blocks are pre-oriented– which allowed us to achieve the formation of large-surface area morphologically-uniform preferentially-oriented single-layer nanosheets. The growth of such large-size high-quality sheets is of interest for the understanding of the fundamental physical/chemical properties associated with ultra-thin sheet-shaped materials and the realization of their use in applications.

Polymorphism in porphyrin monolayers: the relation between adsorption configuration and molecular conformation

Self-assembled monolayers of meso-5,10,15,20-tetrakis(undecyl)porphyrin copper(II) on a graphite/1-octanoic acid interface have been studied by Scanning Tunnelling Microscopy. Four distinct polymorphs were observed, varying in their unit cell size. Arrays of unit cells of the various polymorphs seamlessly connect to each other via shared unit cell vectors. The monolayers are not commensurate, but coincident with the underlying graphite substrate. The seamless transition between the polymorphs is proposed to be the result of an adaptation of the molecular conformations in the polymorphs and at the boundaries, which is enabled by the conformational freedom of the alkyl tails of these molecules.

Templating fullerenes by domain boundaries of a nanoporous network

We present a new templating approach that combines the templating properties of nanoporous networks with the dynamic properties and the lattice mismatch of domain boundaries. This templating approach allows for the inclusion of guests with different sizes without the need for a strict molecular design to tailor the nanoporous network. With this approach, nonperiodic patterns of functional molecules can be formed and studied. We show that domain boundaries in a trimesic acid network are preferred over pores within the network as adsorption sites for fullerenes by a factor of 100-200. Pristine fullerenes of different sizes and functionalized fullerenes were templated in this way.

Self-Assembled Two-Dimensional Heteromolecular Nanoporous Molecular Arrays on Epitaxial Graphene

The development of graphene functionalization strategies that simultaneously achieve two-dimensional (2D) spatial periodicity and substrate registry is of critical importance for graphene-based nanoelectronics and related technologies. Here, we demonstrate the generation of a hydrogen-bonded molecularly thin organic heteromolecular nanoporous network on epitaxial graphene on SiC(0001) using room-temperature ultrahigh vacuum scanning tunneling microscopy. In particular, perylenetetracarboxylic diimide (PTCDI) and melamine are intermixed to form a spatially periodic 2D nanoporous network architecture with hexagonal symmetry and a lattice parameter of 3.45 ± 0.10 nm. The resulting adlayer is in registry with the underlying graphene substrate and possesses a characteristic domain size of 40-50 nm. This molecularly defined nanoporous network holds promise as a template for 2D ordered chemical modification of graphene at lengths scales relevant for graphene band structure engineering.

Control of a two-dimensional molecular structure by cooperative halogen and hydrogen bonds

The cooperative effect of hydrogen and halogen bonds on the two-dimensional (2D) molecular arrangement on highly oriented pyrolytic graphite (HOPG) was studied by scanning tunneling microscopy.

Synthesis of homochiral tris-indanyl molecular rods

By Ti-mediated alkyne trimerization and subsequent Sonogashira and Ohira–Bestman reactions, homochiral molecular rod molecules were prepared for surface self-assembly studies.

Molecular tectonics based nanopatterning of interfaces with 2D metal–organic frameworks (MOFs)

The nanostructuring of the graphite surface with 2DMOF, based on a combination of an acentric porphyrin tecton and a CoCl₂metallatecton, was achieved at the solid–liquid interface and characterized by scanning tunnelling microscopy.

Morphological self-assembly of enantiopure allenes for upstanding chiral architectures at interfaces

Upstanding chiral architectures (UCAs) were fabricated from chiroptically active allenes under surface-confined conditions with morphological complementarity being central to the self-assembly process.

Porous molecular networks formed by the self-assembly of positively-charged trigonal building blocks at the liquid/solid interfaces

Tris-(2-hydroxybenzylidene)triaminoguanidinium salts having six alkyl chains with proper spacing served as new molecular building blocks for the formation of porous honeycomb networks by van der Waals interaction between interdigitated alkyl chains at the liquid/graphite interfaces.

Efficient molecular recognition based on nonspecific van der Waals interaction at the solid/liquid interface

A surprising recognition phenomenon based on van der Waals interactions was observed, which proves that the design of the supramolecular assembly from its building blocks represents a highly promising and general strategy.

Bicomponent blend-directed amplification of the alkyl chain effect on the 2D structures

The 2D structures of bicomponent blends in isobutenyl compounds were observed by using scanning tunneling microscopy at the solid/liquid interface. Amplification of the alkyl chain effect was found on the 2D structures.

Competing thermodynamic and dynamic factors select molecular assemblies on a gold surface

Controlling the self-assembly of surface-adsorbed molecules into nanostructures requires understanding physical mechanisms that act across multiple length and time scales. By combining scanning tunneling microscopy with hierarchical ab initio and statistical mechanical modeling of 1,4-substituted benzenediamine (BDA) molecules adsorbed on a gold (111) surface, we demonstrate that apparently simple nanostructures are selected by a subtle competition of thermodynamics and dynamics. Of the collection of possible BDA nanostructures mechanically stabilized by hydrogen bonding, the interplay of intermolecular forces, surface modulation, and assembly dynamics select at low temperature a particular subset: low free energy oriented linear chains of monomers and high free energy branched chains.

Self-assembled air-stable supramolecular porous networks on graphene

Functionalization and modification of graphene at the nanometer scale is desirable for many applications. Supramolecular assembly offers an attractive approach in this regard, as many organic molecules form well-defined patterns on surfaces such as graphite via physisorption. Here we show that ordered porous supramolecular networks with different pore sizes can be readily fabricated on different graphene substrates via self-assembly of dehydrobenzo[12]annulene (DBA) derivatives at the interface between graphene and an organic liquid. Molecular resolution scanning tunneling microscopy (STM) and atomic force microscopy (AFM) investigations reveal that the extended honeycomb networks are highly flexible and that they follow the topological features of the graphene surface without any discontinuity, irrespective of the step-edges present in the substrate underneath. We also demonstrate the stability of these networks under liquid as well as ambient air conditions. The robust yet flexible DBA network adsorbed on graphene surface is a unique platform for further functionalization and modification of graphene. Identical network formation irrespective of the substrate supporting the graphene layer and the level of surface roughness illustrates the versatility of these building blocks.

Differentiating amino acid residues and side chain orientations in peptides using scanning tunneling microscopy

Single-molecule measurements of complex biological structures such as proteins are an attractive route for determining structures of the large number of important biomolecules that have proved refractory to analysis through standard techniques such as X-ray crystallography and nuclear magnetic resonance. We use a custom-built low-current scanning tunneling microscope to image peptide structures at the single-molecule scale in a model peptide that forms β sheets, a structural motif common in protein misfolding diseases. We successfully differentiate between histidine and alanine amino acid residues, and further differentiate side chain orientations in individual histidine residues, by correlating features in scanning tunneling microscope images with those in energy-optimized models. Beta sheets containing histidine residues are used as a model system due to the role histidine plays in transition metal binding associated with amyloid oligomerization in Alzheimer's and other diseases. Such measurements are a first step toward analyzing peptide and protein structures at the single-molecule level.

Cooperative assembly of magic number C60-Au complexes

We report the assembly of magic number (C60)m-(Au)n complexes on the Au(111) surface. These complexes have a unique structure consisting of a single atomic layer Au island wrapped by a self-selected number (seven, ten, or twelve) of C(60) molecules. The smallest structure consisting of 7 C60 molecules and 19 Au atoms, stable up to 400 K, has a preferred orientation on the surface. We propose a globalized metal-organic coordination mechanism for the stability of the (C(60))(m)-(Au)n complexes.

On-surface azide-alkyne cycloaddition on Au(111)

We present [3 + 2] cycloaddition reactions between azides and alkynes on a Au(111) surface at room temperature and under ultrahigh vacuum conditions. High-resolution scanning tunneling microscopy images reveal that these on-surface cycloadditions occur highly regioselectively to form the corresponding 1,4-triazoles. Density functional theory simulations confirm that the reactions can occur at room temperature, where the Au(111) surface does not participate as a catalytic agent in alkyne C-H activation but acts solely as a two-dimensional constraint for the positioning of the two reaction partners. The on-surface azide-alkyne cycloaddition offers great potential toward the development and fabrication of functional organic nanomaterials on surfaces.

Toward tunable doping in graphene FETs by molecular self-assembled monolayers

In this paper, we report the formation of self-assembled monolayers (SAMs) of oleylamine (OA) on highly oriented pyrolytic graphite (HOPG) and graphene surfaces and demonstrate the potential of using such organic SAMs to tailor the electronic properties of graphene. Molecular resolution Atomic Force Microscopy (AFM) and Scanning Tunneling Microscopy (STM) images reveal the detailed molecular ordering. The electrical measurements show that OA strongly interacts with graphene leading to n-doping effects in graphene devices. The doping levels are tunable by varying the OA deposition conditions. Importantly, neither hole nor electron mobilities are decreased by the OA modification. As a benefit from this noncovalent modification strategy, the pristine characteristics of the device are recoverable upon OA removal. From this study, one can envision the possibility to correlate the graphene-based device performance with the molecular structure and supramolecular ordering of the organic dopant.

Nano- and microstructuration of supramolecular materials driven by H-bonded uracil·2,6-diamidopyridine complexes

In the last few decades, multiple H-bonded arrays have been shown to be versatile tools to prepare functional supramolecular materials. Supramolecular complexes formed by uracil (Ur) and 2,6-diamidopyridine (DAP) developed by Lehn are the first examples of multiple H-bonded systems governing the formation of supramolecular polymers in solution. Although a large variety of complementary multiple H-bonded complexes has been prepared, the use of the heteromolecular Ur·DAP complex still remains very promising due to its ease of preparation and its intermediate association strength that ensures a dynamical character to the self-assembly and self-organisation processes. In this feature article, we report a detailed account on the results that our group has obtained in this field by designing and engineering a novel library of shape persistent molecular modules able to transfer their geometrical information to the final supramolecular architectures through the formation of Ur·DAP complexes both at the nanoscopic and microscopic levels.

Surface-confined crystalline two-dimensional covalent organic frameworks via on-surface Schiff-base coupling

We performed a co-condensation reaction between aromatic aldehyde and aromatic diamine monomers on a highly oriented pyrolytic graphite surface either at a solid/liquid interface at room temperature or in low vacuum with moderate heating. With this simple and moderate methodology, we have obtained surface-confined 2D covalent organic frameworks (COFs) with few defects and almost entire surface coverage. The single crystalline domain can extend to more than 1 μm(2). By varying the backbone length of aromatic diamines the pore size of 2D surface COFs is tunable from ∼1.7 to 3.5 nm. In addition, the nature of the surface COF can be modified by introducing functional groups into the aromatic amine precursor, which has been demonstrated by introducing methyl groups to the backbone of the diamine. Formation of small portions of bilayers was observed by both scanning tunneling microscopy (STM) and AFM, which clearly reveals an eclipsed stacking manner.

On-surface single molecule synthesis chemistry: a promising bottom-up approach towards functional surfaces

In this review, we introduce recent progress on surface synthesis and focus on supramolecular self-assembled structures driven by several typical chemical reactions at solid surfaces, with the aid of scanning tunneling microscopy (STM). We also emphasize the relationship between the non-covalent self-assembly and surface reactivity, by which we hope to find an effective way for further controllable nano-manufacture.

Born-Haber cycle for monolayer self-assembly at the liquid-solid interface: assessing the enthalpic driving force

The driving force for self-assembly is the associated gain in free energy with decisive contributions from both enthalpy and entropy differences between final and initial state. For monolayer self-assembly at the liquid-solid interface, solute molecules are initially dissolved in the liquid phase and then become incorporated into an adsorbed monolayer. In this work, we present an adapted Born-Haber cycle for obtaining precise enthalpy values for self-assembly at the liquid-solid interface, a key ingredient for a profound thermodynamic understanding of this process. By choosing terephthalic acid as a model system, it is demonstrated that all required enthalpy differences between well-defined reference states can be independently and consistently assessed by both experimental and theoretical methods, giving in the end a reliable value of the overall enthalpy gain for self-assembly of interfacial monolayers. A quantitative comparison of enthalpy gain and entropy cost reveals essential contributions from solvation and dewetting, which lower the entropic cost and render monolayer self-assembly a thermodynamically favored process.

Probing the electronic properties of trimesic acid nanoporous networks on Au(111)

Nowadays molecular nanoporous networks have numerous uses in surface nanopatterning applications and in studies of host-guest interactions. Trimesic acid (TMA), a benzene derivative with three carboxylic groups, is a marvelous building block for forming 2D H-bonded porous networks. Here, we report a low-temperature study of the nanoporous "chicken-wire" superstructure formed by TMA molecules adsorbed on a Au(111) surface. Distinct preferential orientations of the porous networks on Au(111) lead to the formation of peculiar TMA polymorphs that are stabilized only at the boundary between rotational molecular domains. Scanning tunneling microscopy (STM) and spectroscopy are used to investigate the electronic properties of both the molecular building blocks and the pores. Sub-molecular-resolution imaging and spatially resolved electronic spectroscopy reveal a remarkable change in the appearance of the molecules in the STM images at energies in the range of the lowest unoccupied molecular orbital, accompanied by highly extended molecular wave functions into the pores. The electronic structure of the pores reflects a weak confinement of surface electrons by the TMA network. Our experimental observations are corroborated by density-functional-theory-based calculations of the nanoporous structure adsorbed on Au(111).

Development of structural complexity by liquid-crystal self-assembly

Since the discovery of the liquid-crystalline state of matter 125 years ago, this field has developed into a scientific area with many facets. This Review presents recent developments in the molecular design and self-assembly of liquid crystals. The focus is on new exciting soft-matter structures distinct from the usually observed nematic, smectic, and columnar phases. These new structures have enhanced complexity, including multicompartment and cellular structures, periodic and quasiperiodic arrays of spheres, and new emergent properties, such as ferroelctricity and spontaneous achiral symmetry-breaking. Comparisons are made with developments in related fields, such as self-assembled monolayers, multiblock copolymers, and nanoparticle arrays. Measures of structural complexity used herein are the size of the lattice, the number of distinct compartments, the dimensionality, and the logic depth of the resulting supramolecular structures.

On-surface synthesis of single-layered two-dimensional covalent organic frameworks via solid-vapor interface reactions

Surface covalent organic frameworks (SCOFs), featured by atomic thick sheet with covalently bonded organic building units, are promised to possess unique properties associated with reduced dimensionality, well-defined in-plane structure, and tunable functionality. Although a great deal of effort has been made to obtain SCOFs with different linkages and building blocks via both "top-down" exfoliation and "bottom-up" surface synthesis approaches, the obtained SCOFs generally suffer a low crystallinity, which impedes the understanding of intrinsic properties of the materials. Herein, we demonstrate a self-limiting solid-vapor interface reaction strategy to fabricate highly ordered SCOFs. The coupling reaction is tailored to take place at the solid-vapor interface by introducing one precursor via vaporization to the surface preloaded with the other precursor. Following this strategy, highly ordered honeycomb SCOFs with imine linkage are obtained. The controlled formation of SCOFs in our study shows the possibility of a rational design and synthesis of SCOFs with desired functionality.