Selective effect of guest molecule length and hydrogen bonding on the supramolecular host structure

A host supramolecular structure consisting of bis-(2,2':6',2' '-terpyridine)-4'-oxyhexadecane (BT-O-C16) is shown to respond to guest molecules in dramatic ways, as observed by using scanning tunneling microscopy (STM) on a highly oriented pyrolytic graphite surface under ambient conditions. It is observed that small linear molecules can be encapsulated within the host supramolecular lattice. The characteristics of the host structure were nearly unaffected by the encapsulated guest molecules of terphthalic acid (TPA) dimers, whereas appreciable changes in cavity dimension can be observed with azobenzene-4,4'-dicarboxylic acid. The STM study and density functional theory (DFT) analysis reveal that intermolecular hydrogen bonding interaction plays an essential role in forming the assembling structures. The difference in guest molecule length is considered the important cause for the different guest-host complexes.     

Self-organization of gold-containing hydrogen-bonded rosette assemblies on graphite surface

The self-organization of supramolecular structures, in particular gold-containing hydrogen-bonded rosettes, on highly oriented pyrolytic graphite (HOPG) surfaces was investigated by tapping-mode atomic force microscopy (TM-AFM) and scanning tunneling microscopy (STM). TM-AFM and high-resolution STM results show that these hydrogen-bonded assemblies self-organize to form highly ordered domains on HOPG surfaces. We find that a subtle change in one of the building blocks induces two different orientations of the assembly with respect to the surface. These results provide information on the control over the construction of supramolecular nanoarchitectures in 2D with the potential for the manufacturing of functional materials based on structural manipulation of molecular components.     

Self-assembly of [Et,Et]-bacteriochlorophyll cF on highly oriented pyrolytic graphite revealed by scanning tunneling microscopy

The chlorosomal light-harvesting antennae of green phototrophic bacteria consist of large supramolecular aggregates of bacteriochlorophyll c (BChl c). The supramolecular structure of (3(1)-R/S)-BChl c on highly oriented pyrolytic graphite (HOPG) and molybdenum disulfide (MoS2) has been investigated by scanning tunneling microscopy (STM). On MoS2, we observed single BChl c molecules, dimers or tetramers, depending on the polarity of the solvent. On HOPG, we observed extensive self-assembly of the dimers and tetramers. We propose C=O...H-O...Mg bonding networks for the observed dimer chains, in agreement with former ultraviolet-visible and infrared spectroscopic work. The BChl c moieties in the tetramers are probably linked by four C=O...H-O hydrogen bonds to form a circle and further stabilized by Mg...O-H bondings to underlying BChl c layers. The tetramers form highly ordered, distinct chains and extended two-dimensional networks. We investigated semisynthetic chlorins for comparison by STM but observed that only BChl c self-assembles to well-structured large aggregates on HOPG. The results on the synthetic chlorins support our structure proposition.     

Supramolecular structures and dynamics of organic adsorbate layers at the solid-liquid interface

We report on atomic force microscopy (AFM) and scanning tunnelling microscopy (STM) studies of the dynamic structure of adsorbate layers at the interface between highly oriented pyrolytic graphite and solutions of a fluorophore with two alkyl chains in phenyloctane. Layers grown above the saturation concentration showed a stable but highly corrugated surface. Below saturation an adsorbate film with a thickness of several molecular layers formed in equilibrium with the solution. The outer layers exhibit a dynamic supramolecular structure consisting of stripes with a spacing of 7 ± 1 nm. The cross-correlation analysis of several sequences of images revealed a characteristic reorganization time for the pattern of tens of seconds. By scanning at elevated forces (> 5 nN) the outer layers could be removed, thus revealing the structure of the first adsorbate layer, namely a stable stripe pattern. STM images of this first layer confirmed this stripe pattern and revealed details of the molecular arrangement at atomic resolution.     

Coadsorption-induced reconstruction of supramolecular assembly characteristics.

A host supramolecular structure consisting of bis-(2,2':6',2"-terpyridine)-4'-oxyhexadecane (BT-O-C16) is shown to respond to coadsorbed molecules in dramatic ways, as observed by scanning tunneling microscopy (STM) on a highly oriented pyrolytic graphite (HOPG) surface under ambient conditions. Interestingly, the lattice parameter of the triphenylene-filled complex differs significantly from that of the coronene-filled one, although the triphenylene and coronene molecules are nearly the same size. The STM study and density functional theory calculations reveal that intermolecular hydrogen-bond interactions play an essential role in forming the assembly structures. The different electronic properties of coronene and triphenylene molecules are responsible for the difference in lattice parameters and consequently for the difference in filling behaviors in the coronene/BT-O-C16 and triphenylene/BT-O-C16 binary systems.     

Nanopatterning of donor/acceptor hybrid supramolecular architectures on highly oriented pyrolytic graphite: a scanning tunneling microscopy study

Hybrid supramolecular architectures have been fabricated with acceptor 1,4-bis(4-pyridylethynyl)-2,3-bis-dodecyloxy-benzene (PBP) and donor 2,6-bis(3,4,5-tris-dodecyloxy-phenyl)dithieno[3,2-b:2',3'-d]thiophene (DTT) compounds on highly oriented pyrolytic graphite (HOPG) surfaces, and their structures and molecular conductance are characterized by scanning tunneling microscopy/spectroscopy (STM/STS). Stable, one-component adlayers of PBP and DTT are also investigated. The coadsorption of two-component mixtures of PBP and DTT results in a variety of hybrid nanopattern architectures that differ from those of their respective one-component surface assemblies. Adjusting the acceptor/donor molar ratio in mixed adlayer assemblies results in dramatic changes in the structure of the hybrid nanopatterns. STS measurements indicate that the HOMO and LUMO energy levels of PBP and DTT on an HOPG surface are relatively insensitive to changes in the hybrid supramolecular architectures. These results provide important insight into the design and fabrication of two-dimensional hybrid supramolecular architectures.     

Noncovalent control for bottom-up assembly of functional supramolecular wires

Noncovalent bonds have been used to assemble stacks of pi-electron-rich moieties at a surface, generating a pathway for charge transport. The system is comprised of a tetrathiafulvalene (TTF) derivative incorporating two amide groups which fasten the relative orientations of the electroactive moieties in the supramolecular polymer that is formed at the surface of graphite in octanoic acid. Scanning tunneling microscopy (STM) combined with molecular mechanics calculations has been used to prove the structure of the wires, and theory, corroborated with STS experiments, predicts that they are promising superstructures for charge transport.     

Expression of Chirality by Achiral Coadsorbed Molecules in Chiral Monolayers Observed by STM

The supramolecular packing mode of physisorbed monolayers built up by chiral isophthalic acid derivatives and coadsorbed achiral solvent molecules was imaged at the liquid/graphite interface with scanning tunneling microscopy (STM). The picture on the right shows the submolecularly resolved STM image of an enantiomorphous domain composed of the R enantiomer of the isophthalic acid derivative studied and 1-heptanol molecules; the latter express the chirality of the monolayer. Upon adsorption a racemic mixture is separated into enantiomorphous domains.     

Hydrogen bond partner reorganization in the coadsorption of a monodendron and pyridylethynyl derivatives

Hydrogen bonds with high selectivity and directionality are significant in harnessing molecules to form 2D supramolecular nanostructures. The competition and reorganization of hydrogen bond partners determine the ultimate molecular assembly and pattern in a 2D supramolecular system. In this study, multicomponent assemblies of a monodendron (5-benzyloxy-isophthalic acid derivative, BIC) and pyridylethynyl derivatives [1,4-bis(4-pyridylethynyl)-2,3-bis-dodecyloxy-benzene (PBPC12) and 1,4-bis(4-pyridylethynyl)-2,3-bis-octadecyloxy-benzene (PBPC18)] have been studied by scanning tunneling microscopy (STM) on a graphite surface. BIC molecules are able to associate with PBPC12 and PBPC18 molecules to induce the rearrangement of hydrogen bond partners and form coassembly structures. Interestingly, BIC acts as a template molecule in the coassembly process, and these multicomponent structures exhibit similar structural features to the assembly structures of BIC itself. The structural details of the coassembled structures are revealed by high-resolution STM images, and their relationship with the original BIC assemblies is discussed. These results provide important insights into the design and fabrication of hydrogen-bond-directed multicomponent molecular nanostructures on solid surfaces.     

Addressing metal centres in supramolecular assemblies

Supramolecular metal ion assemblies are deposited from their solutions onto highly orientated pyrolytic graphite (HOPG) substrates to be imaged by scanning tunnelling microscopy (STM). Since the structural and electronic information of STM measurements are strongly entangled, the spectroscopic interpretation and analysis of the images of such molecular assemblies has proven to be challenging. This tutorial review focuses on a general room temperature scanning tunnelling spectroscopy (STS) protocol, current induced tunnelling spectroscopy (CITS), applied to free-standing 1D and 2D arrangements of supramolecular metal ion assemblies rendering local tunnelling probabilities with submolecular resolution. The size of the investigated molecular assemblies was confirmed by comparison with X-ray crystallographic data, while the consistency of the spectroscopic investigations and of the determined positions of the metal ions within the assemblies was checked by DFT calculations. Due to the genuine level structure of coordinated metal centers, it was possible to map exclusively the position of the coordination bonds in supramolecular transition metal assemblies with submolecular spatial resolution using the CITS technique. CITS might thus constitute an important tool to achieve directed bottom-up construction and controlled manipulation of fully electronically functional, two-dimensional molecular designs.     

Effect of molecular mass on supramolecular organisation of poly(4,4'-dioctyl-2,2':5',2'-terthiophene)

The effect of the chain length on the type and extent of the 2D supramolecular organization in poly(4,4'-dioctyl-2,2':5',2'-terthiophene) (PDOTT) monomolecular layers deposited on highly oriented pyrolytic graphite (HOPG) is studied by scanning tunneling microscopy (STM) and analyzed in terms of molecular modeling. The strictly monodispersed fractions of increasing molecular mass used in this study were obtained by chromatographic fractionation of the crude product of 4,4'-dioctyl-2,2':5',2'-terthiophene oxidative polymerization. STM investigations of PDOTT layers, deposited on HOPG from poly- and monodispersed fractions, show that polydispersity can be considered as a key factor seriously limiting supramolecular ordering. This is a consequence of significant differences in the type of supramolecular order observed for molecules of different chain length. It has been demonstrated that shorter molecules (consisting of 6 and 9 thiophene units) form well-defined two-dimensional islands, while the interactions between longer molecules (consisting of 12 and 15 thiophene units) become anisotropic. Consequently, for higher molecular mass fractions, the supramolecular organization is one-dimensional and consists of more or less separated rows of ordered macromolecules. In this case an increase of the chain length leads to amplification of the intermolecular interactions proceeding via interdigitation of the alkyl substituents of adjacent molecules. Polydispersed fractions show much less ordered organization because of the incompatibility of the supramolecular structures of molecules of different molecular masses. This finding is of crucial importance for the application of polythiophene derivatives in organic and molecular electronics since ordered supramolecular organization constitutes the condition sine qua non of good electrical transport properties.     

Solvent induced polymorphism in supramolecular 1,3,5-benzenetribenzoic acid monolayers

This work presents a scanning tunneling microscopy (STM) based study of benzenetribenzoic acid (BTB) monolayer structures at the liquid-solid interface. On graphite(0001) the tailored molecules self-assemble into 2D supramolecular host systems, suitable for the incorporation of other nanoscopic objects. Two crystallographically different BTB structures were found-both hydrogen bonded networks. A specific structure was deliberately selected by solvent identity. One of the BTB polymorphs is a 6-fold chicken-wire structure with circular, approximately 2.8 nm wide cavities. The other structure exhibits an oblique unit cell and a different hydrogen bonding pattern. The large cavity size of the chicken-wire structure was made possible through comparatively strong 2-fold hydrogen bonds between carboxylic groups. In addition, the low conformational flexibility of BTB was supportive to combat the tendency for dense packing.     

The Unexpected Base-Pairing Behavior of Cyanuric Acid in RNA and Ribose versus Cyanuric Acid Induced Helicene Assembly of Nucleic Acids: Implications for the Pre-RNA Paradigm

The cyanuric acid (CA) heterocycle forms supramolecular structures with adenine nucleobases/nucleosides and oligonucleotides, leading to speculation that they can act as forerunners to RNA. Herein, the assembly behavior of RNA containing CA and CA–ribose nucleoside was studied. Contrary to previous reports, CA in RNA and the CA-ribonucleoside resulted in destabilization of supramolecular assemblies, which led to a reevaluation of the CA–adenine hexameric rosette structure. An unprecedented noncovalent supramolecular helicene structure is proposed to account for the striking difference in behavior, which has implications for novel paradigms for reorganizing the structures of nucleic acids, the synthesis of long helicenes, and pre-RNA world paradigms. The results caution against extrapolating the self-assembly behavior of individual heterocycles from the level of monomers to oligomers because the base-paring properties of (non-)canonical nucleobases are impacted by the type of oligomeric backbone to which they are attached.     

Visualization of various supramolecular assemblies of oligo(para-phenylenevinylene)-melamine and perylene bisimide

A melamine derivative has been covalently equipped with two oligo(para-phenylenevinylene) (OPV) chromophores. This procedure yields a bifunctional molecule with two hydrogen-bonding arrays available for complementary binding to perylene bisimide derivatives. Depending on the solvent, hydrogen-bonded trimers, tetramers, and dimers on a graphite surface are observed for pure OPV-melamine by using scanning tunneling microscopy (STM). Upon the addition of perylene bisimide, linear tapes of perylene bisimide, 12-membered rosettes that consist of alternating hydrogen-bonded OPV-melamine and perylene bisimide moieties are visualized. These results provide direct evidence for the possible modes of hydrogen bonding within a supramolecular co-assembly in solution. Subsequently, the optical properties of pure OPV-melamine and co-assemblies with a perylene bisimide derivative were characterized in solution. In an apolar solvent, OPV-melamine self-assembles into chiral superstructures. Disassembly into molecularly dissolved species is reversibly controlled by concentration and temperature. Complementary hydrogen bonding to a perylene bisimide derivative in an apolar solvent yields multicomponent, pi-stacked dye assemblies of enhanced stability that are characterized by fluorescence quenching of the constituent chromophores. Titration experiments reveal that a mixture of hydrogen-bonded oligomers is present in solution, rather than a single discrete assembly. The solution experiments are consistent with the STM results, which revealed various supramolecular assemblies. Our system is likely not to be optimally programmed to obtain a discrete co-assembled structure in quantitative yield.     

Single molecule visualization of coordination-assembled porphyrin macrocycles reinforced with covalent linkings

Coordination-assembled porphyrin macrocycles reinforced with covalent bondings were deposited on a metal surface by a pulse injection method, and their scanning tunneling microscopy (STM) images were recorded under ultrahigh vacuum conditions at liquid nitrogen temperature. The decamer ring consisting of 30 porphyrins gave clear circular STM images with hollow structure, whereas that without covalent linking did not give clear circular images, showing that covalent linking of the coordination pairs by ring-closing metathesis reaction was effective to reinforce the supramolecular structure on a metal surface. This strategy will be applicable to a variety of supramolecular assemblies.     

Assignment of the Absolute-Handedness Chirality of Single-Walled Carbon Nanotubes by Using Organic Molecule Supramolecular Structures

Supramolecular structures of organic molecules on planar nanocarbon surfaces, such as highly oriented pyrolytic graphite (HOPG), have been extensively studied and the factors that control them are generally well-established. In contrast, the properties of supramolecular structures on curved nanocarbon surfaces like carbon nanotubes remain challenging to predict and/or to understand. This paper reports an investigation into the first study of the supramolecular structures of 5,15-bisdodecylporphyrin (C12P) on chiral, concentrated single-walled carbon nanotubes (SWNTs; with right-handed helix P- and left-handed helix M-) surfaces using STM. Furthermore, the study is the first of its kind to experimentally assign the absolute-handedness chirality of SWNTs, as well as to understand their effect on the supramolecular structures of organic molecules on their surfaces. Interestingly, these SWNT enantiomers resulted in supramolecular structures of opposite chirality based on the handedness chirality. With molecular modelling, we predicted the absolute-handedness chirality of SWNTs, before demonstrating this experimentally.     

Photochemical Reactions in Self‐Assembled Organic Monolayers Characterized by using Scanning Tunneling Microscopy

Research on the supramolecular self‐assembly behavior at interfaces is of great importance to improving the performance of nanodevices that are based on optical functional materials. In this Minireview, several photoinduced isomerization and polymerization reactions in self‐assembled organic monolayers on surfaces are discussed. Typical organic molecules contain azobenzene, alkynyl, or olefins groups. The feature surface base is a highly oriented pyrolytic graphite (HOPG) surface or a gold surface. Scanning tunneling microscopy (STM) is used as a strong tool to characterize new species’ structures before and after illumination.     

Bilayer Molecular Assembly at a Solid/Liquid Interface as Triggered by a Mild Electric Field

The construction of a spatially defined assembly of molecular building blocks, especially in the vertical direction, presents a great challenge for surface molecular engineering. Herein, we demonstrate that an electric field applied between an STM tip and a substrate triggered the formation of a bilayer structure at the solid–liquid interface. In contrast to the typical high electric‐field strength (10⁹ V m^?1) used to induce structural transitions in supramolecular assemblies, a mild electric field (10⁵ V m^?1) triggered the formation of a bilayer structure of a polar molecule on top of a nanoporous network of trimesic acid on graphite. The bilayer structure was transformed into a monolayer kagome structure by changing the polarity of the electric field. This tailored formation and large‐scale phase transformation of a molecular assembly in the perpendicular dimension by a mild electric field opens perspectives for the manipulation of surface molecular nanoarchitectures.     

2D supramolecular structures of a shape-persistent macrocycle and co-deposition with fullerene on HOPG

Two 2D supramolecular structures of macrocycle 1 and 1/C60 have been obtained on HOPG by self-assembly under ambient conditions and investigated by high-resolution STM. The monolayers of 1 are characterized by structures with perfect ordering over relatively large areas. In the case of 1/C60, the size of the macrocycle 1 and the presence of two individual bithiophene units per ring lead in the final superstructure to a 1:2 stoichiometry. The fullerenes are not trapped at the graphite surface inside the macrocyclic holes but are located around the periphery of the bithiophene units. This clearly shows that the donor-acceptor interaction between C60 and the electron-rich units of the ring is the dominant factor for the structure formation.     

Incorporation and manipulation of coronene in an organic template structure

A two-dimensional molecular template structure of 1,3,5-benzenetricarboxylic acid (trimesic acid, TMA) was formed on a highly oriented pyrolytic graphite surface (HOPG) by self-assembly at the liquid-solid interface. Scanning tunneling microscopy (STM) investigations show high-resolution images of the porous structure on the surface. After the host structure was created, coronene molecules were inserted as guest molecules into the pores. STM results indicate that some of the guest molecules rotate inside their molecular bearing. Further investigations show that single coronene molecules can be directly kicked out of their pores by means of STM.