Assembly of functional molecular nanostructures on surfaces

Peptide nucleic acids in materials science

This review highlights the recent methods to prepare PNA-based materials through a combination of self-assembly and self-organization processes. The use of these methods allows easy and versatile preparation of structured hybrid materials showing specific recognition properties and unique physicochemical properties at the nano- and micro-scale levels displaying potential applications in several directions, ranging from sensors and microarrays to nanostructured devices for biochips.

Biosupramolecular nanowires from chlorophyll dyes with exceptional charge-transport properties

Conductive tubes: Self-assembled nanotubes of a bacteriochlorophyll derivative are reminiscent of natural chlorosomal light-harvesting assemblies. After deposition on a substrate that consists of a non-conductive silicon oxide surface (see picture, brown) and contacting the chlorin nanowires to a conductive polymer (yellow), they show exceptional charge-transport properties.

Interplay between H-bonding and alkyl-chain ordering in self-assembly of monodendritic L-alanine derivatives

This paper reports on the synthesis and self-organizing properties of monodendrons consisting of L-alanine at the focal point and alkyl chains with different length at the periphery. The structures of thin films and monolayers are studied by temperature-resolved grazing-incidence X-ray diffraction and scanning force microscopy. The interplay between H-bonding and ordering of the alkyl chains results in a rich temperature-dependent phase behavior. The monodendrons form H-bonded stabilized clusters with the number of molecules depending on the length of the aliphatic chains and temperature. The clusters play the role of constitutive units in the subsequent self-assembly. Short alkyl chains allow the material to form thermodynamically stable crystalline phases. The molecules with longer side groups exhibit additional transitions from the crystalline phase to thermotropic columnar hexagonal or columnar rectangular liquid-crystalline phases. In monolayers deposited on highly ordered pyrolytic graphite, the materials show ordering similar to thin films. However, for the compound bearing hexadecyl chains the affinity of the alkyl groups to graphite dominates the self-assembly and thereby allows epitaxial growth of a 2D lattice with flat-on oriented molecules.

Optical materials based on molecular nanoparticles

A major part of contemporary nanomaterials research is focused on metal and semiconductor nanoparticles, constituted of extended lattices of atoms or ions. Molecular nanoparticles assembled from small molecules through non-covalent interactions are relatively less explored but equally fascinating materials. Their unique and versatile characteristics have attracted considerable attention in recent years, establishing their identity and status as a novel class of nanomaterials. Optical characteristics of molecular nanoparticles capture the essence of their nanoscale features and form the basis of a variety of applications. This review describes the advances made in the field of fabrication of molecular nanoparticles, the wide spectrum of their optical and nonlinear optical characteristics and explorations of the potential applications that exploit their unique optical attributes.

Template-assisted assembly: scanning tunneling microscopy study of solvent-dependent adlattices of alkyl-derivatized tetrathiafulvalene

The self-assembly of an adsorbate as a function of the strength of solvent-substrate adsorption is an important yet relatively unexplored subject. In this study, how the strength of solvent-substrate adsorption and solvent-solvent attraction affects the assembly of tetrakis(octadecylthio)tetrathiafulvalene (1) is scrutinized by scanning tunneling microscopy (STM). For solvents with strong intermolecular interactions and adsorption onto graphite, such as long n-alkanes (C(n)H(2n+2), n ≥ 13), STM reveals that the solvent molecules form lamellae which become a template to direct the assembly of 1 into one-dimensional arrays. The lengths of one of the unit cell vectors for the assemblies are increased and well correlated with the solvent sizes. In situ STM monitoring of 1 introduced onto graphite with preadsorbed n-tetradecane adlattices shows that the developed assemblies of 1 have striped features aligned parallel to the underlying template. In contrast, for solvents with weak adsorption, such as short n-alkanes (C(n)H(2n+2), n ≤ 12), toluene, and 1,2,4-trichlorobenzene, the adlattice structures of 1 are solvent-independent.

Little exchange at the liquid/solid interface: defect-mediated equilibration of physisorbed porphyrin monolayers

The transition from low to high density 2D surface structures of copper porphyrins at a liquid/solid interface requires specific defects at which nearly all exchange of physisorbed molecules with those dissolved in the supernatant occurs.

Controlling the length and location of in situ formed nanowires by means of microfluidic tools

Progress in microelectronics, sensors and optics is strongly dependent on the miniaturization of components, and the integration of nanoscale structures into applicable systems. In this regard, conventional top-down technologies such as lithography have limits concerning the dimensions and the choice of material. Therefore, several bottom-up approaches have been investigated to satisfy the need for structures with large aspect ratios in the nanometre regime. For further implementation, however, it is crucial to find methods to define position, orientation and length of the nanowires. In this study, we present a microchip to trap in situ formed bundles of nanowires in microsized cages and clamps, thereby enabling immobilisation, positioning and cutting-out of desired lengths. The microchip consists of two layers, one of which enables the formation of metal-organic nanowires at the interface of two co-flowing laminar streams. The other layer, separated by a thin and deflectable PDMS membrane, serves as the pneumatic control layer to impress microsized features ("donuts") onto the nanowires. In this way, a piece of the nanowire bundle with a prescribed length is immobilised inside the donut. Furthermore, partly open ring-shaped structures enabled trapping of hybrid wires and subsequent functionalisation with fluorescent beads. We believe that the method is a versatile approach to form and modify nanoscale structures via microscale tools, thereby enabling the construction of fully functional nanowire-based systems.

Thermosolutal self-organization of supramolecular polymers into nanocraters

The ability of two complementary molecular modules bearing H-bonding uracilic and 2,6-(diacetylamino)pyridyl moieties to self-assemble and self-organize into submicrometer morphologies has been investigated by means of spectroscopic, thermogravimetric, and microscopic methods. Using uracilic (3)N-BOC-protected modules, it has been possible to thermally trigger the self-assembly/self-organization process of the two molecular modules, inducing the formation of objects on a mica surface that exhibit crater-like morphology and a very homogeneous size distribution. Confirmation of the presence of the hydrogen-bonding-driven self-assembly/self-organization process in solution was obtained by variable-temperature (VT) steady-state UV-vis absorption and emission measurements. The variation of the geometric and spatial features of the morphologies was monitored at different T by means of atomic force microscopy (AFM) and was interpreted by a nonequilibrium diffusion model for two chemical species in solution. The formation of nanostructures turned out to be affected by the solid substrate (molecular interactions at a solid-liquid interface), by the matter-momentum transport in solution (solute diffusivity D(0) and solvent kinematic viscosity ν), and the thermally dependent cleavage reaction of the BOC functions (T-dependent differential weight loss, θ = θ(Τ)) in a T interval extrapolated to ∼60 K. A scaling function, f = f (νD(0), ν/D(0), θ), relying on the onset condition of a concentration-driven thermosolutal instability has been established to simulate the T-dependent behavior of the structural dimension (i.e., height and radius) of the self-organized nanostructures as ⟨h⟩ ≈ f (T) and ⟨r⟩ ≈ 1/f (T).

From molecular to macroscopic engineering: shaping hydrogen-bonded organic nanomaterials

The self-assembly and self-organization behavior of chromophoric acetylenic scaffolds bearing 2,6-bis(acetylamino)pyridine (1, 2) or uracyl-type (3-9) terminal groups has been investigated by photophysical and microscopic methods. Systematic absorption and luminescence studies show that 1 and 2, thanks to a combination of solvophilic/solvophobic forces and π-π stacking interactions, undergo self-organization in apolar solvents (i.e., cyclohexane) and form spherical nanoparticles, as evidenced by wide-field optical microscopy, TEM, and AFM analysis. For the longer molecular module, 2, a more uniform size distribution is found (80-200 nm) compared to 1 (20-1000 nm). Temperature scans in the range 283-353 K show that the self-organized nanoparticles are reversibly formed and destroyed, being stable at lower temperatures. Molecular modules 1 and 2 were then thoroughly mixed with the complementary triply hydrogen-bonding units 3-9. Depending on the specific geometrical structure of 3-9, different nanostructures are evidenced by microscopic investigations. Combination of modules 1 or 2 with 3, which bears only one terminal uracyl unit, leads to the formation of vesicular structures; instead, when 1 is combined with bis-uracyl derivative 4 or 5, a structural evolution from nanoparticles to nanowires is observed. The length of the wires obtained by mixing 1 and 4 or 1 and 5 can be controlled by addition of 3, which prompts transformation of the wires into shorter rods. The replacement of linear system 5 with the related angular modules 6 and 7 enables formation of helical nanostructures, unambiguously evidenced by AFM. Finally, thermally induced self-assembly was studied in parallel with modules 8 and 9, in which the uracyl recognition sites are protected with tert-butyloxycarbonyl (BOC) groups. This strategy allows further control of the self-assembly/self-organization process by temperature, since the BOC group is completely removed on heating. Microscopy studies show that the BOC-protected ditopic modules 8 self-assemble and self-organize with 1 into ordered linear nanostructures, whereas BOC-protected tritopic system 9 gives rise to extended domains of circular nano-objects in combination with 1.

Organogelators based on TTF supramolecular assemblies: synthesis, characterization, and conductive property

A closely related family of organogelators 1-2 appended one or two electroactive tetrathiafulvalene (TTF) residues, has been designed and readily synthesized by Sonogashira reactions. These compounds can gelate a variety of organic solvents in view of multiple intermolecular interactions, and compounds 2 with two TTF subunits exhibit higher gelation ability than their corresponding 1. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) investigation of the xerogels from toluene gave a visual image showing that fibrillar aggregates are entangled in three-dimensional network structures. The columnar TTF cores stacking in the fiber, evidenced by the mixed-valence states absorption at around 2000 nm in ultraviolet-visible-near-infrared (UV-vis-NIR) spectra, provide an efficient pathway for the electron conduction. Upon oxidized by iodine, these xerogels exhibit semiconductive behaviors with moderate levels of conductivity. Additionally, the electrical conductivity of doped-xerogels 2 is 1 order of magnitude higher than that of 1 under identical conditions.

Two-dimensional structures of anthracene derivatives: photodimerization and host-guest chemistry

By using a simple anthracene derivative with four alkoxy tails, a two-dimensional patterned surface was fabricated. The two-dimensional structures were directly visualized by scanning tunneling microscopy (STM) at the solid/liquid interface. The anthracene derivative formed highly ordered structures displaying cavities into which solvent molecules of 1-phenyloctane were coadsorbed. The functionality of the patterned surface was demonstrated by activating host-guest chemistry as the solvent molecules could be replaced by coronene, whose size is almost identical to the cavities formed by the anthracene derivative. Furthermore, [4 + 4] photodimerization of the anthracene derivative was performed at the solid/liquid interface and revealed that the physical height and electron density of the states were changed, resulting in the increase of an apparent height in the STM images. We demonstrate thus that the porous network of the two-dimensional pattern created by the anthracene derivative can be applied for selectively incorporating guest molecules and for photoprocessing.

Tuning the supramolecular chirality of one- and two-dimensional aggregates with the number of stereogenic centers in the component porphyrins

A synthetic strategy was developed for the preparation of porphyrins containing between one and four stereogenic centers, such that their molecular weights vary only as a result of methyl groups which give the chiral forms. The low-dimensional nanoscale aggregates of these compounds reveal the profound effects of this varying molecular chirality on their supramolecular structure and optical activity. The number of stereogenic centers influences significantly the self-assembly and chiral structure of the aggregates of porphyrin molecules described here. A scanning tunneling microscopy study of monolayers on graphite shows that the degree of structural chirality with respect to the surface increases almost linearly with the number of stereogenic centers, and only one handedness is formed in the monolayers, whereas the achiral compound forms a mixture of mirror-image domains at the surface. In solution, four hydrogen bonds induce the formation of an H-aggregate, and circular dichroism measurements and theoretical studies indicate that the compounds self-assemble into helical structures. Both the chirality and stability of the aggregates depend critically on the number of stereocenters. The chiral porphyrin derivatives gelate methylcyclohexane at concentrations dependent on the number and position of chiral groups at the periphery of the aromatic core, reflecting the different aggregation forces of the molecules in solution. Increasing the number of stereogenic centers requires more material to immobilize the solvent, in all likelihood because of the greater solubility of the porphyrins. The vibrational circular dichroism spectra of the gels show that all compounds have a chiral environment around the amide bonds, confirming the helical model proposed by calculations. The morphologies of the xerogels (studied by scanning electron microscopy and scanning force microscopy) are similar, although more fibrous features are present in the molecules with fewer stereogenic centers. Importantly, the presence of only one stereogenic center, bearing a methyl group as the desymmetrizing ligand, in a molecule of considerable molecular weight is enough to induce single-handed chirality in both the one- and two-dimensional supramolecular self-assembled structures.

Immobilization of zinc porphyrin complexes on pyridine-functionalized glass surfaces

In order to immobilize sublimable and fluorescent dye molecules on transparent surfaces for the detection of far field molecular interference experiments, we investigate the potential of pyridine-functionalized glass substrates as coordination sites for the zinc complex of tetraphenylporphyrin (ZnTPP). Borosilicate glass is functionalized with 4-(6-(ethoxydimethylsilyl)hexyloxy)pyridine in order to cover the glass surface with pyridine subunits. ZnTPP molecules are deposited by sublimation through mechanical masks of various sizes in a high-vacuum chamber. The resulting micropatterns are analyzed using epifluorescence microscopy which also allows us to define a measure for the quality of molecular immobilization. We observe a reduced mobility and an increased efficiency for the trapping of ZnTPP on pyridine-functionalized surfaces.

Bipyridine derivatives at a solid/liquid interface: effects of the number and length of peripheral alkyl chains

Bipyridine derivatives (bpys) with various number and length of peripheral alkyl chains (with carbon numbers of n = 11-17) were synthesized, and their self-assembled monolayers were observed by scanning tunneling microscopy (STM) at a 1-phenyloctane/highly oriented pyrolytic graphite (HOPG) interface. The effects of the number, the substitution position, and the length of alkyl chains on the two-dimensional structures were systematically studied. Bpys substituted by a single alkyl chain in the p-position on each side adopted an almost linear form with zigzag-type alignment of the pi-conjugated unit, whereas, in the case of m-substitution, the bpys showed Z-shaped morphology with interdigitated alkyl chains. In both cases, no odd-even alkyl chain length effects were observed. The bpys with double alkyl chains at m- and p-positions displayed odd-even alkyl chain effects, suggesting that the formation of two-dimensional structure is dominated by the interactions between alkyl chains. Bpys with triple alkyl chains at o-, m-, and p-positions also showed odd-even alkyl chain effects, but only for the higher number of carbon atoms in the alkyl chain unit (n = 14-17). These results indicate that concerted intermolecular interactions of the alkyl chain unit introduce the odd-even chain length effect on the self-assembled two-dimensional structure. After coordination of PdCl(2), odd-even effects were quenched, and bpys were converged into the same lamellar structure, in which the molecules are almost linear. All the structural differences due to the odd-even alkyl chain length effect were explained in terms of intermolecular and molecule-substrate interactions.

Modulated self-assembly of 4,4'-diphenyltetrathiafulvalene molecules on highly oriented pyrolytic graphite by n-tetradecane solvent

We report the formation of a binary-component self-assembled monolayer (SAM) comprising 4,4'-diphenyltetrathiafulvalene (DP-TTF) and n-tetradecane (n-C(14)H(30)) molecules with periodic strip-like phase separation structures on a highly oriented pyrolytic graphite (HOPG) surface. Scanning tunneling microscopy (STM) imaging reveals that ordered DP-TTF single- and double-lamella are periodically tuned by ordered n- C(14)H(30) single- and double-lamella, respectively. This finding can be qualitatively understood in terms of a phase field model, in which the interplay of three ingredients, including free energy of the binary-component solution monolayer, phase boundary energy and surface stress, determines the final equilibrium sizes of the ordered DP-TTF and n- C(14)H(30) phases in the binary-component SAM. Furthermore, anisotropy of the surface stress breaks the symmetry of the substrate and causes the n- C(14)H(30) molecules to arrange along preferential substrate 010 directions. The orientation of the n-C(14)H(30) molecule stripes further guides the directions of the DP-TTF lamellar structures. In addition, scanning tunneling spectra (STS) of the individual DP-TTF and n- C(14)H(30) molecules in the ordered monolayer show a remarkable difference in I(V) curves on the HOPG substrate.

Supramolecular chemistry at interfaces: molecular recognition on nanopatterned porous surfaces

Through the illustration of key examples that have recently appeared in the literature, the intention of this review is to provide a perspective of current advances on the molecular recognition at the interfaces aimed at the engineering of multifunctional organic-based materials. The great interest in such systems has been motivated by the need to fabricate smaller and smaller components in order to improve, for example, the information storage capabilities of classical silicon-based devices. Although great progress has been achieved on the exploitation of "top-down" approaches, strong hope is now put on the development of hybrid devices in which the elementary components are replaced with single organic molecules. Nevertheless, the drive towards such devices is restricted by both their stability and difficulties to precisely control and manipulate the structural organisation at the molecular level. To overcome these restrictions, the use of nanotemplated surfaces featuring porous domains in which responsive functional molecules can be precisely accommodated at the single-molecule level is one of the most promising approaches. In the first part of this manuscript, we therefore illustrate the main engineering strategies [1) through non-covalent interactions, 2) surface-confined covalent reactions and 3) assembly of pre-organised cavities such as synthetic macrocycles] currently in use to create two-dimensional (2D) patterned surfaces displaying porous structures at the nanoscale level. Such networks, featuring periodic hollow domains (controllable both in shape and size), are of particular significance as their cavities can be used as receptors for the recognition of remotely controllable functional molecules. In the second part, the confinement of molecular guests within the cavities is discussed, emphasising the selectivity and dynamics of key assemblies, with a particular focus on the biomolecular recognition and post-assembly covalent functionalisation, which could provide the opportunity to fabricate devices currently beyond our reach on an unprecedented precision and efficiency. All the examples will be discussed in terms of structural organisation as studied by scanning tunnelling microscopy (STM) techniques.

Lyomesophases of C3-symmetrical bipyridine-based discs in alkanes: an X-ray diffraction study

The importance of the role of alkane solvents in the self-assembly process of pi-conjugated molecules is well recognized but hardly understood. Here we present our results on the X-ray diffraction studies that we conducted to gain insight into the supramolecular structure of mixtures of a bipyridine-based molecule (1) with alkanes. Independent of the alkane used (linear or branched), above x(w) > 0.06 (with x(w) being the weight fraction of 1) the mixtures show lyotropic liquid-crystalline behavior. The nature of the lyomesophase depends only on x(w) and not on the nature of the alkane (linear or branched). A columnar rectangular phase is present when x(w) > 0.66. Upon dilution of 1, a columnar hexagonal phase is assigned first (0.50 < x(w) < 0.65), and finally a columnar nematic phase is observed when x(w) < 0.50. Concentration-dependent SAXD measurements revealed that the dilution of 1 can be viewed as a swelling process. First, solvent molecules occupy space between the columns formed by 1, which are not disrupted. This process can quantitatively be described by a 2D swelling model. Only at lower concentrations does 3D swelling start as the columns start breaking into shorter fragments.

Robust supramolecular network on Ag(111): hydrogen-bond enhancement through partial alcohol dehydrogenation

Alcohol oxidation and self-assembly: the in situ oxidation of hydroxyl functional groups to quinone groups promotes the formation of enhanced hydrogen bonds and allows reorganization of the resulting supramolecular self-assemblies, which evolve from a weakly bound dense phase to a strongly bound nanoporous open structure (see picture).

Dipole effects on molecular and electronic structures in a novel conjugate of oligo(phenyleneethynylene) and helical peptide

A novel conjugate of a helical nonapeptide and an oligo(phenyleneethynylene) (OPE) having a nitro group at a molecular terminal was synthesized. Both components have a dipole. The peptide has a disulfide group at the N-terminal for immobilization on gold. In order to investigate the electric field effect of the helical peptide dipole on the OPE and molecular structure by the dipole-dipole interaction between the two components, the electronic structure of the OPE was spectroscopically studied in solution, the self-assembled monolayer on gold, and Langmuir-Blodgett (LB) layers on a fused quartz surface. The absorption maximum (lambda(max)) of the OPE component in chloroform is red-shifted by 4 nm from the reference OPE derivative without the helical peptide component. The red shifts of the OPE component are also observed in the LB monolayer and bilayer compared with that of the self-assembled monolayer. The observed dipole effect of the peptide on the OPE electronic structure was quantitatively discussed with ab initio calculations. Antiparallel orientation on the dipole directions of the peptide and the OPE components is considered to explain the red shifts via the dipole effect on the electronic structure of the OPE.

Surface confined metallosupramolecular architectures: formation and scanning tunneling microscopy characterization

Metallosupramolecular compounds have attracted a great deal of attention over the past two decades largely because of their unique, highly complex structural characteristics and their potential electronic, magnetic, optical, and catalytic properties. These molecules can be prepared with relative ease using coordination-driven self-assembly techniques. In particular, the use of electron-poor square-planar Pt(II) transition metals in conjunction with rigid, electron-rich pyridyl donors has enabled the spontaneous self-assembly of a rich library of 2D metallacyclic and 3D metallacage assemblies via the directional-bonding approach. With this progress in the preparation and characterization of metallosupramolecules, researchers have now turned their attention toward fully exploring and developing their materials properties. Assembling metallosupramolecular compounds on solid supports represents a vitally important step toward developing their materials properties. Surfaces provide a means of uniformly aligning and orienting these highly symmetric metallacycles and metallacages. This uniformity increases the level of coherence between molecules above that which can be achieved in the solution phase and provides a way to integrate adsorbed layers, or adlayers, into a solid-state materials setting. The dynamic nature of kinetically labile Pt(II)-N coordination bonds requires us to adjust deposition and imaging conditions to retain the assemblies' stability. Toward these aims, we have used scanning tunneling microscopy (STM) to image these adlayers and to understand the factors that govern surface self-assembly and the interactions that influence their structure and stability. This Account describes our efforts to deposit 2D rectangular and square metallacycles and 3D trigonal bipyramidal and chiral trigonal prism metallacages on highly oriented pyrolytic graphite (HOPG) and Au(111) substrates to give intact assemblies and ordered adlayers. We have investigated the effects of varying the size, symmetry, and dimensionality of supramolecular adsorbates, the choice of substrate, the use of a molecular template, and the effects of chirality. Our systematic investigations provide insights into the various adsorbate-adsorbate and substrate-adsorbate interactions that largely determine the architecture of each assembly and affect their performance in a materials setting. Rational control over adlayer formation and structure will greatly enhance the potential of these supramolecules to be used in a variety of applications such as host-guest sensing/diagnostic systems, molecular electronic devices, and heterogeneous stereoselective synthesis and catalysis.