STM/TERS observation of (M)-type diphenyl[7]thiaheterohelicene on Ag(111)

The chiral recognition of a self-assembled structure of enantiopure (M)-type 2,13-diphenyl[7]thiaheterohelicene ((M)-Ph-[7]TH) was investigated on a Ag(111) substrate by scanning tunnelling microscopy (STM) and tip-enhanced Raman spectroscopy (TERS). In contrast to previous research of thiaheterohelicene and its derivatives showing zigzag row formation on the Ag(111) substrate, the hexagonal ordered structure was observed by STM. The obtained TERS spectra of (M)-Ph-[7]TH were consistent with the Raman spectra calculated on the basis of density functional theory (DFT), which suggests that (M)-Ph-[7]TH was adsorbed on the substrate without decomposition. The sample bias voltage dependence of STM images combined with the calculated molecular orbitals of (M)-Ph-[7]TH indicates that a phenyl ring was observed as a protrusion at +3.0 V, whereas the helicene backbone was observed at +0.5 V. From these results, a possible model of the hexagonal structure was proposed. Owing to the phenyl ring, the van der Waals interaction between (M)-Ph-[7]TH and the substrate becomes strong. This leads to the formation of the hexagonal structure with the same symmetry as the substrate.

Dual-Responsive Supramolecular Chiral Assemblies from Amphiphilic Dendronized Tetraphenylethylenes

Supramolecular assembly of amphiphilic molecules in aqueous solutions to form stimuli-responsive entities is attractive for developing intelligent supramolecular materials for bioapplications. Here we report on the supramolecular chiral assembly of amphiphilic dendronized tetraphenylethylenes (TPEs) in aqueous solutions. Hydrophobic TPE moieties were connected to the hydrophilic three-fold dendritic oligoethylene glycols (OEGs) through a tripeptide proline-hydroxyproline-glycol (POG) to afford the characteristic topological structural effects of dendritic OEGs and the peptide linker. Both ethoxyl- and methoxyl-terminated dendritic OEGs were used to modulate the overall hydrophilicity of the dendronized TPEs. Their supramolecular aggregates exhibited thermoresponsive behavior that originated from the dehydration and collapse of the dendritic OEGs, and their cloud point temperatures (Tcps) were tailored by solution pH conditions. Furthermore, aggregation-induced fluorescent emission (AIE) from TPE moieties was used as an indicator to follow the assembly, which was reversibly tuned by temperature variation at different pH conditions. Supramolecular assemblies from these dendronized amphiphiles exhibited enhanced supramolecular chirality, which was dominated mainly by the interaction balance between TPE with dendritic OEG and TPE with POG moieties and was modulated through different solvation by changing solution temperature or pH conditions. More interestingly, ethoxyl-terminated dendritic OEG provided a much stronger shielding effect than its methoxyl-terminated counterpart to prevent amino groups within the peptide from protonation, even in strong acidic conditions, resulting in different responsive behavior to the solution temperature and pH conditions for these supramolecular aggregates.

Toward Two-Dimensional Tessellation through Halogen Bonding between Molecules and On-Surface-Synthesized Covalent Multimers

The ability to engineer sophisticated two-dimensional tessellation organic nanoarchitectures based on triangular molecules and on-surface-synthesized covalent multimers is investigated using scanning tunneling microscopy. 1,3,5-Tris(3,5-dibromophenyl)benzene molecules are deposited on high-temperature Au(111) surfaces to trigger Ullmann coupling. The self-assembly into a semi-regular rhombitrihexagonal tiling superstructure not only depends on the synthesis of the required covalent building blocks but also depends on their ratio. The organic tessellation nanoarchitecture is achieved when the molecules are deposited on a Au(111) surface at 145 °C. This halogen-bonded structure is composed of triangular domains of intact molecules separated by rectangular rows of covalent dimers. The nearly hexagonal vertices are composed of covalent multimers. The experimental observations reveal that the perfect semi-regular rhombitrihexagonal tiling cannot be engineered because it requires, in addition to the dimers and intact molecules, the synthesis of covalent hexagons. This building block is only observed above 165 °C and does not coexist with the other required organic buildings blocks.

Single-molecule visualization determines conformational substate ensembles in β-sheet-rich peptide fibrils

An understanding of protein conformational ensembles is essential for revealing the underlying mechanisms of interpeptide recognition and association. However, experimentally resolving multiple simultaneously existing conformational substates remains challenging. Here, we report the use of scanning tunneling microscopy (STM) to analyze the conformational substate ensembles of β sheet peptides with a submolecular resolution (in-plane <2.6 Å). We observed ensembles of more than 10 conformational substates (with free energy fluctuations between several k_BTs) in peptide homoassemblies of keratin (KRT) and amyloidal peptides (-5Aβ42 and TDP-43 341-357). Furthermore, STM reveals a change in the conformational ensemble of peptide mutants, which is correlated with the macroscopic properties of peptide assemblies. Our results demonstrate that the STM-based single-molecule imaging can capture a thorough picture of the conformational substates with which to build an energetic landscape of interconformational interactions and can rapidly screen conformational ensembles, which can complement conventional characterization techniques.

Minor adjustments in the chemical structures of pyridine derivatives induced different co-assemblies by O-H⋯N hydrogen bonds

The co-adsorption behaviours of aromatic carboxylic acids with various pyridine derivatives were investigated with scanning tunneling microscopy and density functional theory. Surprisingly, minor adjustments in the chemical structures of the pyridine derivatives, such as the relative position of the nitrogen atom or the lengths of the side chains on the backbone would evidently affect the intermolecular O-H⋯N hydrogen bonds and further form various co-adsorption structures.

Rotational dynamics and transition mechanisms of surface-adsorbed proteins

The exquisite organization exhibited by hybrid biomolecular–inorganic materials in nature has inspired the development of synthetic analogues for numerous applications. Nevertheless, a mechanistic picture of the energetic controls and response dynamics leading to organization is lacking. Here, we pair high-speed atomic force microscopy with machine learning and Monte Carlo simulations to analyze the rotational dynamics of rod-like proteins on a crystal lattice, simultaneously quantifying the orientational energy landscape and transition probabilities between energetically favorable orientations. Although rotations largely follow Brownian diffusion, proteins often make large jumps in orientation, thus rapidly overcoming barriers that usually inhibit rotation. Moreover, the rotational dynamics can be tuned via protein size and solution chemistry, providing tools for controlling biomolecular assembly at inorganic interfaces.

Assembly of biomolecules at solid–water interfaces requires molecules to traverse complex orientation-dependent energy landscapes through processes that are poorly understood, largely due to the dearth of in situ single-molecule measurements and statistical analyses of the rotational dynamics that define directional selection. Emerging capabilities in high-speed atomic force microscopy and machine learning have allowed us to directly determine the orientational energy landscape and observe and quantify the rotational dynamics for protein nanorods on the surface of muscovite mica under a variety of conditions. Comparisons with kinetic Monte Carlo simulations show that the transition rates between adjacent orientation-specific energetic minima can largely be understood through traditional models of in-plane Brownian rotation across a biased energy landscape, with resulting transition rates that are exponential in the energy barriers between states. However, transitions between more distant angular states are decoupled from barrier height, with jump-size distributions showing a power law decay that is characteristic of a nonclassical Levy-flight random walk, indicating that large jumps are enabled by alternative modes of motion via activated states. The findings provide insights into the dynamics of biomolecules at solid–liquid interfaces that lead to self-assembly, epitaxial matching, and other orientationally anisotropic outcomes and define a general procedure for exploring such dynamics with implications for hybrid biomolecular–inorganic materials design.

Coronene and Phthalocyanine Trapping Efficiency of a Two-Dimensional Kagomé Host-Nanoarchitecture

The trapping of coronene and zinc phthalocyanine (ZnPc) molecules at low concentration by a two-dimensional self-assembled nanoarchitecture of a push–pull dye is investigated using scanning tunneling microscopy (STM) at the liquid–solid interface. The push–pull molecules adopt an L-shaped conformation and self-assemble on a graphite surface into a hydrogen-bonded Kagomé network with porous hexagonal cavities. This porous host-structure is used to trap coronene and ZnPc guest molecules. STM images reveal that only 11% of the Kagomé network cavities are filled with coronene molecules. In addition, these guest molecules are not locked in the host-network and are desorbing from the surface. In contrast, STM results reveal that the occupancy of the Kagomé cavities by ZnPc evolves linearly with time until 95% are occupied and that the host structure cavities are all occupied after few hours.

Diverse Self-assembly Structures of a Macrocycle Revealed with STM by Adjusting the Solution Concentration

The macrocyclic molecule [3]C₁₂ TT-TPA was synthesized by a Stille coupling reaction through alternately connecting 4,7-bisthienyl-2,1,3-thienothiazole and triphenylamine units. The concentration-dependent self-assembly structures of [3]C₁₂ TT-TPA were explored in liquid/solid interface by scanning tunneling microscopy and density functional theory. After increasing the solution concentration, five different nanostructures were constructed and the molecular packing densities were gradually enhanced. Those structural transformations from loose structures to compact structures are thermodynamically favourable because those transformations are accompanied by the adsorption of more [3]C₁₂ TT-TPA molecules from liquid phase, which increases the interactions between molecules and the interactions between molecules and substrate considerably. This study of fundamental exploration is important to understand the basic formation mechanisms and the stability of two-dimensional functional materials.

Two-Dimensional Molecular Network Built from Hierarchy Self-Assembly of Perylene Bisimide Derivatives

The structures of two-dimensional (2D) self-assembled molecular networks formed by a series of perylene bisimide (PBI) derivatives were investigated by scanning tunneling microscopy (STM). By introducing different functional groups to the PBI rings, we successfully built a different self-assembled molecular network on the liquid-solid interface. When the substituent is propanol, PBI is aligned in lines. When we introduced either an ester group or an amide group to the PBI compounds, they tended to form dimers and trimers. Especially, the PBI with the amide groups can form a 2D porous molecular network by hierarchy self-assembly. The 2D porous molecular network has a great potential to be the host molecule for the accommodation of a guest molecule, coronene (COR), and the structure of the 2D porous molecular network can be tuned by varying the concentration. The density functional theory calculations were also performed to disclose the mechanisms involved.

Photochemical [2 + 2] polymerization of metal-organic gels of a rigid and angular diene with silver-salts of diverse anions: selective dye-sorption and luminescence by xerogels

Two similar types of dienes, one rigid and the other flexible, were explored for their gel formation abilities with Ag(i) salts. The rigid and angular dienes have shown an exceptional ability for gel formation with silver salts of nitrate, triflate, tetrafluoro borate and hexafluorophosphate. These metal-organic gels (MOGs) and their xerogels are found to have an excellent ability to undergo the photochemical [2 + 2] polymerization reaction upon irradiation. The reactions were monitored, and the products were characterized via1H NMR and MALDI-TOF analyses. Further, the solid-state luminescence behaviour and the selective dye-sorption of the gels have been explored before and after the photo-polymerization reaction.

Hierarchical two-dimensional molecular assembly through dynamic combination of conformational states at the liquid/solid interface

Self-sorting of multiple building blocks for correctly positioning molecules through orthogonal recognition is a promising strategy for construction of a hierarchical self-assembled molecular network (SAMN) on a surface. Herein we report that a trigonal molecule, dehydrobenzo[12]annulene (DBA) derivative having three tetradecyloxy chains and three hydroxy groups in an alternating manner, forms hierarchical triangular clusters of different sizes ranging from 2.4 to 16.4 nm, consisting of 3 to 78 molecules, respectively, at the liquid/graphite interface. The key is the dynamic combination of three different conformational states, which is solvent and concentration dependent. The present knowledge extends design strategies for production of sophisticated hierarchical SAMNs using a single component at the liquid/solid interface.

Self-sorting of multiple building blocks for correctly positioning molecules through orthogonal recognition is a promising strategy for construction of a hierarchical self-assembled molecular network (SAMN) on a surface.

Solvent-Dependent Core-Modified Rubyrin Self-Assembly at Liquid/Solid Interfaces

Scanning tunneling microscopy (STM) was utilized to disclose four novel core-modified rubyrin self-assembly behaviors on the highly-oriented pyrolytic graphite (HOPG) surface, of which N₂S₄-OR(1)/N₂Se₄-OR(2) had no phenanthrene pyrrole ring and N₂S₄-OR(3)/N₂Se₄-OR(4) had phenanthrene-fused pyrrole rings and meso-aryl substituents. It was discovered that the core-modified rubyrin could self-assemble into either face-on or edge-on monolayer structures selectively at the liquid/HOPG interface in different solvents. There was an obvious solvent-dependent self-assembly for N₂S₄-OR(3)/N₂Se₄-OR(4), which adopted an edge-on and face-on structure in 1-phenyloctane and 1-heptanoic acid solvents, respectively, whereas N₂S₄-OR(1)/N₂Se₄-OR(2) showed no obvious difference in the assembly structure, which both adopted a face-on structure in the two solvents. Density functional theory (DFT) calculations were also utilized to reveal the relevant self-assembly mechanisms. This study shows a typical solvent effect regulating core-modified rubyrin self-assembly, which is essential for porphyrin-based functional devices' design and manufacture.

Solid or gel? Which one works better for [2 + 2] photochemical polymerization in pyridine appended flexible phenylene 1, 4-bis-olefins by Ag(i) templation?

Two diene molecules were shown to undergo photopolymerization reactions in their metal-organic gels and xerogels, while their respective crystalline CPs are photostable. These reactions reveal the advantages of the gels and xerogels compared to their crystalline counterparts and also the utility of AgAg interactions in the gels to promote topochemical polymerizations.

Electrostatically Driven Guest Binding in Self-Assembled Molecular Network of Hexagonal Pyridine Macrocycle at the Liquid/Solid Interface: Symmetry Breaking Induced by Coadsorbed Solvent Molecules

We present here the construction of a self-assembled two-dimensional network at the liquid/solid interface using a hexagonal pyridine macrocycle which binds an organic cation in its intrinsic porous space by electrostatic interactions. For this purpose, a hexagonal pyridinylene-butadiynylene macrocycle (PyBM) having six octyloxymethyl groups, PyBM-C8, was synthesized. As guests, tropylium (Tr) tetrafluoroborate and trioxatriangulenium (TOTA) hexafluorophosphate were used. In this study, we focused on (i) the network patterns of PyBM-C8 which change in response to its concentration and (ii) the position of the guest immobilized in the porous space of the macrocycle. Scanning tunneling microscopy (STM) observations at the interface of 1,2,4-trichlorobenzene (TCB) and highly oriented pyrolytic graphite (HOPG) revealed that PyBM-C8 formed four different polymorphs, oblique, loose hexagonal, linear, and rectangular, depending on the solute concentration and annealing treatment. Solvent TCB molecules are likely coadsorbed to not only the intrinsically porous space of PyBM-C8 (internal TCB) but also the space outside of the macrocycle between its alkyl chains (external TCB) in most of the cases. Upon adding the guest cation, whereas small Tr was not visualized in the pore due to size mismatching, larger TOTA was clearly observed in each pore. In addition, based on high-resolution STM images of the rhombus packing pattern of PyBM-C8, we revealed experimentally that TOTA was placed at an off-center position of the deformed hexagonal macrocyclic core in the rhombus pattern. On the basis of the molecular mechanics calculations, we hypothesize that the off-center location of TOTA is due to deformation of the hexagonal macrocycle through interaction with two external TCB molecules located at opposite edges of the macrocyclic core. Symmetry breaking of the macrocyclic host framework induced by coadsorbed surrounding solvent molecules thus plays a significant role in host-guest complexation at the liquid/solid interface.

Sequence-Defined Macrocycles for Understanding and Controlling the Build-up of Hierarchical Order in Self-Assembled 2D Arrays

Anfinsen's dogma that sequence dictates structure is fundamental to understanding the activity and assembly of proteins. This idea has been applied to all manner of oligomers but not to the behavior of cyclic oligomers, aka macrocycles. We do this here by providing the first proofs that sequence controls the hierarchical assembly of nonbiological macrocycles, in this case, at graphite surfaces. To design macrocycles with one (AAA), two (AAB), or three (ABC) different carbazole units, we needed to subvert the synthetic preferences for one-pot macrocyclizations. We developed a new stepwise synthesis with sequence-defined targets made in 11, 17, and 22 steps with 25, 10, and 5% yields, respectively. The linear build up of primary sequence (1°) also enabled a thermal Huisgen cycloaddition to proceed regioselectively for the first time using geometric control. The resulting macrocycles are planar (2° structure) and form H-bonded dimers (3°) at surfaces. Primary sequences encoded into the suite of tricarb macrocycles were shown by scanning-tunneling microscopy (STM) to impact the next levels of supramolecular ordering (4°) and 2D crystalline polymorphs (5°) at solution-graphite interfaces. STM imaging of an AAB macrocycle revealed the formation of a new gap phase that was inaccessible using only C3-symmetric macrocycles. STM imaging of two additional sequence-controlled macrocycles (AAD, ABE) allowed us to identify the factors driving the formation of this new polymorph. This demonstration of how sequence controls the hierarchical patterning of macrocycles raises the importance of stepwise syntheses relative to one-pot macrocyclizations to offer new approaches for greater understanding and control of hierarchical assembly.

Chlorine-assisted fabrication of hybrid supramolecular structures via electrostatic interactions

Supramolecular self-assembly is a spontaneous process relying on non-covalent intermolecular interactions. Among them, electrostatic interactions generated by organic molecules interacting with alkali metals and/or halogens play an important role in structural formation. Herein, we choose cytosine and NaCl as a model system and, from the interplay of STM imaging and DFT calculations, a hybrid network composed of both metal-organic and pure organic motifs interlinked by Cl ions via electrostatic interactions is observed on the Au(111) surface. Moreover, the occasionally missing Cl ions in connections are accompanied by the absence of adjacent organic motifs resulting in defects of the network. This study successfully demonstrates the generality of salt providing both cations and anions simultaneously in the modulation of the structure and provides fundamental knowledge on the formation of hybrid structures as well as the function of halogens in affecting the self-assembly process.

Progress in self-assembly of TTF derivatives at HOPG interface

Self-assembled structures of TTF derivatives can be observed according to different substituents.

Peptide Self-Assembly and Its Modulation: Imaging on the Nanoscale

This chapter intends to review the progress in obtaining site-specific structural information for peptide assemblies using scanning tunneling microscopy. The effects on assembly propensity due to mutations and modifications in peptide sequences, small organic molecules and conformational transitions of peptides are identified. The obtained structural insights into the sequence-dependent assembly propensity could inspire rational design of peptide architectures at the molecular level.

Self-Assembly of Supramolecular Fractals from Generation 1 to 5

In the seeking of molecular expression of fractal geometry, chemists have endeavored in the construction of molecules and supramolecules during the past few years, while only a few examples were reported, especially for the discrete architectures. We herein designed and constructed five generations of supramolecular fractals (G1-G5) based on the coordination-driven self-assembly of terpyridine ligands. All the ligands were synthesized from triphenylamine motif, which played a central role in geometry control. Different approaches based on direct Sonogashira coupling and/or ⟨tpy-Ru(II)-tpy⟩ connectivity were employed to prepare complex Ru(II)-organic building blocks. Fractals G1-G5 were obtained in high yields by precise coordination of organic or Ru(II)-organic building blocks with Zn(II) ions. Characterization of those architectures were accomplished by 1D and 2D NMR spectroscopy, electrospray ionization mass spectrometry (ESI-MS), traveling-wave ion mobility mass spectrometry (TWIM-MS), and transmission electron microscopy (TEM). Furthermore, the two largest fractals also hierarchically self-assemble into ordered supramolecular nanostructures either at solid/liquid interface or in solution on the basis of their well-defined scaffolds.

Two-dimensional self-assembled nanostructures of nucleobases and their related derivatives on Au(111)

The construction of two-dimensional (2D) self-assembled nanostructures has been one of the considerably interesting areas of on-surface chemistry in the past few decades, and has benefited from the rapid development and improvement of scanning probe microscopy techniques. In this research field, many attempts have been made in the controllable fabrication of well-ordered and multifunctional surface nanostructures, which attracted interest because of the prospect for artificial design of functional molecular nanodevices. DNA and RNA are considered to be programmable self-assembly systems and it is possible to use their base sequences to encode instructions for assembly in a predetermined fashion at the nanometer scale. As important constituents of nucleic acids, nucleobases, with intrinsic functional groups for hydrogen bonding, coordination bonding, and electrostatic interactions, can be employed as a potential system for the versatile construction of various biomolecular nanostructures, which may be used to structure the self-assembly of DNA-based artificial molecular constructions and play an important role in novel biosensors based on surface functionalization. In this article, we will review the recent progress of on-surface self-assembly of nucleobases and their derivatives together with different reactants (e.g., metals, halogens, salts and water), and as a result, various 2D surface nanostructures are summarized.

Single-molecule insights into surface-mediated homochirality in hierarchical peptide assembly

Homochirality is very important in the formation of advanced biological structures, but the origin and evolution mechanisms of homochiral biological structures in complex hierarchical process is not clear at the single-molecule level. Here we demonstrate the single-molecule investigation of biological homochirality in the hierarchical peptide assembly, regarding symmetry break, chirality amplification, and chirality transmission. We find that homochirality can be triggered by the chirality unbalance of two adsorption configuration monomers. Co-assembly between these two adsorption configuration monomers is very critical for the formation of homochiral assemblies. The site-specific recognition is responsible for the subsequent homochirality amplification and transmission in their hierarchical assembly. These single-molecule insights open up inspired thoughts for understanding biological homochirality and have general implications for designing and fabricating artificial biomimetic hierarchical chiral materials.

Most chiral molecules and structures in living organisms exist as single enantiomers, but why? Here, the authors investigated surface-mediated homochirality on the single-molecule level and show that it can be triggered by the chirality unbalance of two adsorption configuration monomers.

Electrostatically Driven Guest Binding in a Self-Assembled Porous Network at the Liquid/Solid Interface

We present here the construction of a self-assembled two-dimensional (2D) porous monolayer bearing a highly polar 2D space to study guest co-adsorption through electrostatic interactions at the liquid/solid interface. For this purpose, a dehydrobenzo[12]annulene (DBA) derivative, DBA-TeEG, having tetraethylene glycol (TeEG) groups at the end of the three alternating alkoxy chains connected by p-phenylene linkers was synthesized. As a reference host molecule, DBA-C10, having nonpolar C₁₀ alkyl chains at three alternating terminals, was employed. As guest molecules, hexagonal phenylene-ethynylene macrocycles (PEMs) attached by triethylene glycol (TEG) ester and hexyl ester groups, PEM-TEG and PEM-C6, respectively, at each vertex of the macrocyclic periphery were used. Scanning tunneling microscopy observations at the 1,2,4-trichlorobenzene/highly oriented pyrolytic graphite interface revealed that PEM-TEG was immobilized in the pores formed by DBA-TeEG at higher probability because of electrostatic interactions such as dipole-dipole and hydrogen bonding interactions between oligoether units of the host and guest, in comparison to PEM-C6 with nonpolar groups. These observations are discussed based on molecular mechanics simulations to investigate the role of the polar functional groups. When a nonpolar host matrix formed by DBA-C10 was used, however, only phase separation and preferential adsorption were observed; virtually no host-guest complexation was discernible. This is ascribed to the strong affinity between the guest molecules which form by themselves densely packed van der Waals networks on the surface.

Imaging on-surface hierarchical assembly of chiral supramolecular networks

The bottom-up assembly of chiral structures usually relies on a cascade of molecular recognition interactions. A thorough description of these complex stereochemical mechanisms requires the capability of imaging multilevel coordination in real-time. Here we report the first direct observation of hierarchical expression of supramolecular chirality at work, for 10,10'-dibromo-9,9'-bianthryl (DBBA) on Cu(111). Molecular recognition first steers the growth of chiral organometallic chains and then leads to the formation of enantiopure islands. The structure of the networks was determined by noncontact atomic force microscopy (nc-AFM), while high-speed scanning tunnelling microscopy (STM) revealed details of the assembly mechanisms at the ms time-scale. The direct observation of the chirality transfer pathways allowed us to evaluate the enantioselectivity of the interchain coupling.

Hierarchical formation of Fe-9eG supramolecular networks via flexible coordination bonds

From the interplay between high-resolution scanning tunneling microscopy imaging/manipulations and density functional theory calculations, we display the hierarchical formation of supramolecular networks by codeposition of 9eG molecules and Fe atoms on Au(111) based on the flexible coordination bonds (the adaptability and versatility in the coordination modes). In the first step, homochiral islands composed of homochiral G₄Fe₂ motifs are formed; and then in the second step, thermal treatment results in the transformation into the porous networks composed of heterochiral G₄Fe₂ motifs with the ratio of the components being constant. In situ STM manipulations and the coexistence of some other heterochiral G₄Fe₂ motifs and clusters also show the flexibility of the coordination bonds involved. These studies may provide a fundamental understanding of the regulations of multilevel supramolecular structures and shed light on the formation of designed supramolecular nanostructures.

Host-guest chemistry in two-dimensional supramolecular networks

Nanoporous supramolecular networks physisorbed on solid surfaces have been extensively used to immobilize a variety of guest molecules. Host-guest chemistry in such two-dimensional (2D) porous networks is a rapidly expanding field due to potential applications in separation technology, catalysis and nanoscale patterning. Diverse structural topologies with high crystallinity have been obtained to capture molecular guests of different sizes and shapes. A range of non-covalent forces such as hydrogen bonds, van der Waals interactions, coordinate bonds have been employed to assemble the host networks. Recent years have witnessed a surge in the activity in this field with the implementation of rational design strategies for realizing controlled and selective guest capture. In this feature article, we review the development in the field of surface-supported host-guest chemistry as studied by scanning tunneling microscopy (STM). Typical host-guest architectures studied on solid surfaces, both under ambient conditions at the solution-solid interface as well as those formed at the ultrahigh vacuum (UHV)-solid interface, are described. We focus on isoreticular host networks, hosts functionalized pores and dynamic host-guest systems that respond to external stimuli.

Self-assemblies of TTF derivatives programmed by alkyl chains and functional groups

Tetrathiafulvalenes (TTFs) are a class of important functional materials whose intermolecular interaction, which will contribute to constructing a supramolecular structure, still needs further understanding.

Tubular and lamellar hydrogen-bonding molecular assemblies of isophthalic acid derivatives bearing a –CONHCnH2n+1 chain

Isophthalic acid derivatives (CnIP), bearing alkylamide chains at the 5-position that can participate in hydrogen bonding, were prepared and evaluated for their hydrogen-bonding molecular assembly structures for organogelation and liquid crystal formation.

The leading role of the steric hindrance effect and dipole–dipole interaction in superlattice nanostructures formed via the assembly of discotic liquid crystals

The effect of steric hindrance and dipole–dipole interactions are a prerequisite for the formation of ordered plastic phases.

Hexagonal Molecular Tiling by Hexagonal Macrocycles at the Liquid/Solid Interface: Structural Effects on Packing Geometry

We present here hexagonal tiling using hexagonal phenylene-ethynylene and phenylene-butadiynylene macrocycles attached by alkyl ester groups, PEM-C6 and PBM-C8, respectively, or triethylene glycol ester groups, PEM-TEG and PBM-TEG, respectively, at each vertex of the macrocyclic periphery at the liquid/solid interface. In this study, we focused on the effects of macrocyclic core size and the chemical properties of side chains attached to macrocyclic cores as well as solute concentrations on the hexagonal geometry of self-assembled monolayers. STM observations at the 1,2,4-trichrolobenzene/graphite interface revealed that PEM-C6 formed a honeycomb structure by van der Waals interactions between the interdigitated alkyl chains. However, upon increasing solute concentration, it changed to more dense hexagonal structure (tentatively called loose hexagonal structure I). In contrast, PBM-C8 formed loose hexagonal structure II of a slightly different packing mode at low concentration, while at high concentration it formed a high-density hexagonal structure in which alkyl chains are not adsorbed on the surface (dense hexagonal structure). In the dense hexagonal structure, macrocyclic cores are linked by hydrogen bonds between the ester carbonyl oxygen and the aromatic hydrogen atoms of the neighboring macrocycles. The packing geometries of loose hexagonal structures of PEM-C6 and PBM-C8 are different due to the different distance between the attachment of the alkyl ester groups which are located in confined space. On the other hand, PEM-TEG and PBM-TEG formed dense hexagonal structures, similar to PBM-C8 at high concentration, with their TEG units not adsorbed on the surface.

Structural diversity of metal-organic self-assembly assisted by chlorine

From the combination of STM imaging and DFT calculations, we show that both alkali metal and halogens interact with different sites of the target molecules resulting in structural formation in a synergistic way. The elementary metal-organic motifs are connected by Cl in a variety of fashions demonstrating structural diversity.

13-cis-Retinoic acid on coinage metals: hierarchical self-assembly and spin generation

Hierarchical self-assembly of 13-cis-retinoic acid on Au(111) and Ag(111) was investigated using low-temperature scanning tunnelling microscopy. On both surfaces, molecules form dimers by hydrogen bonds and the dimers arrange into ordered two-dimensional arrays through van der Waals forces. Three packing modes are observed on Au(111) and only one on Ag(111). We tentatively attribute the different patterns on the two surfaces to a stronger molecule-substrate interaction on Ag(111) and site-dependent molecular adsorption on different atomic lattices. In addition, 13-cis-ReA on Au(111) can be made to carry a localized spin.

Peptide-Functionalized Nanomaterials for the Efficient Isolation of HER2-Positive Circulating Tumor Cells

The detection of circulating tumor cells (CTCs) with a specific antigen expression is necessary in therapeutic response monitoring and targeted therapy guidance. The existence of human epidermal growth factor receptor 2 (HER2) and the concentration of HER2-positive CTCs are strong indicators for patient diagnosis, prognosis, and therapeutic monitoring. Herein we report the direct isolation of HER2-positive CTCs by peptide-functionalized nanomaterials. We designed and screened out a peptide as an HER2 antibody alternative demonstrating high HER2 affinity and selectivity. This HER2 recognition peptide bound efficiently with HER2 at the ligand-binding domain. Efficient HER2-positive CTC capture and detection were demonstrated using magnetic nanoparticles functionalized with the HER2 recognition peptide.

Host-Guest Chemistry in Integrated Porous Space Formed by Molecular Self-Assembly at Liquid-Solid Interfaces

Host-guest chemistry in two-dimensional (2D) space, that is, physisorbed monolayers of a single atom or a single molecular thickness on surfaces, has become a subject of intense current interest because of perspectives for various applications in molecular-scale electronics, selective sensors, and tailored catalysis. Scanning tunneling microscopy has been used as a powerful tool for the visualization of molecules in real space on a conducting substrate surface. For more than a decade, we have been investigating the self-assembly of a series of triangle-shaped phenylene-ethynylene macrocycles called dehydrobenzo[12]annulenes (DBAs). These molecules are substituted with six alkyl chains and are capable of forming hexagonal porous 2D molecular networks via van der Waals interactions between interdigitated alkyl chains at the interface of organic solvents and graphite. The dimension of the nanoporous space or nanowell formed by the self-assembly of DBAs can be controlled from 1.6 to 4.7 nm by simply changing the alkyl chain length from C₆ to C₂₀. Single molecules as well as homoclusters and heteroclusters are capable of coadsorbing within the host matrix using shape- and size-complementarity principles. Moreover, on the basis of the versatility of the DBA molecules that allows chemical modification of the alkyl chain terminals, we were able to decorate the interior space of the nanoporous networks with functional groups such as azobenzenedicarboxylic acid for photoresponsive guest adsorption/desorption or fluoroalkanes and tetraethylene glycol groups for selective guest binding by electrostatic interactions and zinc-porphyrin units for complexation with a guest by charge-transfer interactions. In this Feature Article, we describe the general aspects of molecular self-assembly at liquid/solid interfaces, followed by the formation of programmed porous molecular networks using rationally designed molecular building blocks. We focus on our own work involving host-guest chemistry in integrated nanoporous space that is modified for specific purposes.

An STM/STS study of site-selective adsorption of C70 molecules onto arc-shaped BODIPY molecular-networks

In this article, a donor-acceptor H-T-BO/C70 system was studied by a STM/STS method on the molecular level. STM results revealed that H-T-BO, a BODIPY-based derivative, can form a semi-closed molecular network at the 1-phenyloctane/HOPG interface. After introducing C70 fullerene molecules into the network, two kinds of self-assembled nanoarrays were observed by STM. Density functional theory has been utilized to reveal the formation mechanism of the molecular nanoarrays. Scanning Tunneling Spectroscopy (STS) measurements were performed to investigate the electronic properties of H-T-BO/C70 systems. I-V spectra combined with theoretical analyses showed that the introduction of C70 into the H-T-BO system induced a great drop of the band gap, which should be a result of electrons transferring from the donor H-T-BO to the acceptor C70 molecules.

Kinetically controlled hierarchical self-assemblies of all-trans-retinoic acid on Au(111)

Kinetically controlled hierarchical self-assemblies of all-trans-retinoic acid on Au(111) were investigated via low-temperature scanning tunneling microscopy in ultra-high vacuum. The dominant molecular hierarchical superstructure could be selectively controlled to dimer, tetramer, or pentamer patterns, which were stabilized by hydrogen bonds and van der Waals interactions.

Self-Assembly and External Modulation of a Flexible Porphyrin Derivative on Highly Oriented Pyrolytic Graphite

With the aid of scanning tunneling microscopy, we have examined the two-dimensional hydrogen-bonded networks of carboxyl-functionalized porphyrin derivative H₂TCPp molecules at the heptanoic acid/HOPG interface. Moreover, we have successfully modulated the self-assembly structure of H₂TCPp by introducing 1,2-di(4-pyridyl)ethylene molecules into the assembled system. By performing density functional theory calculations, we also revealed the formation mechanisms of the different assemblies and the modulation process. Comparing the self-assembly structures at the liquid/solid interface with those in bulk crystals, we have obtained deep insight into the differences in H₂TCPp assemblies between 2D and 3D networks. Furthermore, this research is expected to deepen our understanding of on-surface phenomena and to provide a feasible process toward 2D assembly regulation.

Metal–organic gels of silver salts with an α,β-unsaturated ketone: the influence of anions and solvents on gelation

A bis-pyridyl substituted α,β-unsaturated ketone was shown to form MOGs with silver salts having anions BF₄, ClO₄, CF₃SO₃ and SF₆ in various organic solvents. They have shown selectivity towards adsorbing an anionic dye from a mixture of cationic and anionic dyes.

Complexity of two-dimensional self-assembled arrays at surfaces

The developing field of complexity in self-assembled systems on surfaces is discussed.

Two-dimensional (2D) self-assembly of oligo(phenylene-ethynylene) molecules and their triangular platinum(ii) diimine complexes studied using STM

The self-assembly of a series of cyclic oligo(phenylene-ethynylene) (OPE) molecules and their triangular Pt(ii) diimine complexes were studied using scanning tunneling microscope (STM).

The hierarchical construction of cross-junctions of molecular wires with covalent and noncovalent interactions at the liquid/solid interface

Hierarchical networks, constructed by non-covalent bond stabilized cross-junctions of covalent one-dimensional molecular wires, are synergistically formed at the liquid/solid interface through in situ on-surface condensation of aromatic amines and aldehydes. Our investigation demonstrates the significant impact of the concentration and structure of monomers on the hierarchical construction of these nanoarchitectures at the interface.

On-Surface Synthesis of Two-Dimensional Covalent Organic Structures versus Halogen-Bonded Self-Assembly: Competing Formation of Organic Nanoarchitectures

The competition between the on-surface synthesis of covalent nanoarchitectures and the self-assembly of star-shaped 1,3,5-Tris(4-iodophenyl)benzene molecules on Au(111) in vacuum is investigated using scanning tunneling microscopy above room temperature. The molecules form covalent polygonal nanoachitectures at the gold surface step edges and at the elbows of the gold reconstruction at low coverage. With coverage increasing two-dimensional halogen-bonded structures appear and grow on the surface terraces. Two different halogen-bonded nanoarchitectures are coexisting on the surface and hybrid covalent-halogen bonded structures are locally observed. At high coverage covalent nanoarchitectures are squeezed at the domain boundary of the halogen-bonded structures. The competitive growth between the covalent and halogen-bonded nanoarchitectures leads to formation of a two-layer film above one monolayer deposition. For this coverage, the covalent nanoarchitectures are propelled on top of the halogen-bonded first layer. These observations open up new opportunities for decoupling covalent nanoarchitectures from catalytically active and metal surfaces in vacuum.