Interplay of Depletion Forces and Biomolecular Recognition in the Hierarchical Assembly of Supramolecular Tubes

Crowding effects have a profound impact on the hierarchical organization of cellular architectures. In the fields of systems chemistry and soft matter, this effect has not received much attention so far. Here, it is explored how poly(ethylene glycol) (PEG) as a crowding agent invokes depletion forces that act on synthetic supramolecular tubes. Hence, supramolecular tubes are pushed from their random orientation into hierarchically assembled bundles due to the PEG-induced crowded environment. The resulting morphology of formed bundled architectures can be tuned by the concentrations of both the supramolecular tubes and the PEG. The introduction of biotin groups at the surface of the tubes allows the engineering of biotin-streptavidin crosslinks between them. The order of introducing PEG and streptavidin in the system further affects the formed hierarchical assemblies, as well as their resistance toward dilution. The strategy described here provides a new route to establish hierarchically organized supramolecular architectures, combining crowding and specific biomolecular interactions, which shows the potential for controlling the structure of supramolecular materials and other soft matter systems.

Molecular Engineering of the Kinetic Barrier in Seeded Supramolecular Polymerization

Seeded supramolecular polymerization (SSP) is a method that enables the controlled synthesis of supramolecular structures. SSP often relies on structures that are capable of self-assembly by interconverting between intramolecular and intermolecular modes of hydrogen bonding, characterized by a given kinetic barrier that is typically low. The control of the polymerization process is thus limited by the propensity of the hydrogen bonds to interconvert between the intramolecular and intermolecular modes of binding. Here, we report on an engineering of the polymerization kinetic barriers by sophisticated molecular design of the building blocks involved in such SSP processes. Our designs include two types of intramolecular hydrogen-bonded rings: on one hand, a central triazine tricarboxamide moiety that prevents self-assembly due to its stable intramolecular hydrogen bonds and on the other hand, three peripheral amide groups that promote self-assembly due to their stable intermolecular hydrogen bonds. We report a series of molecules with increasing bulkiness of the peripheral side chains exhibiting increasing kinetic stability in the monomeric form. Owing to the relative height of the barrier, we were able to observe that the rate constant of seeding is not proportional to the concentration of the seeds used. Based on that, we proposed a new kinetic model in which the rate-determining step is the activation of the monomer, and we provide the detailed energy landscape of the supramolecular polymerization process. Finally, we investigated the hetero-seeding of the building blocks that shows either inhibition or triggering of the polymerization.

Photoswitchable architecture transformation of a DNA-hybrid assembly at the microscopic and macroscopic scale

Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks. Oligonucleotide-based nanotechnology and soft-materials benefit from the high information storage density, self-correction, and memory function of DNA. Here we control these beneficial properties with light in a photoresponsive biohybrid hydrogel, adding an extra level of function to the system. An ssDNA template was combined with a complementary photo-responsive unit to reversibly switch between various functional states of the supramolecular assembly using a combination of light and heat. We studied the structural response of the hydrogel at both the microscopic and macroscopic scale using a combination of UV-vis absorption and CD spectroscopy, as well as fluorescence, transmission electron, and atomic force microscopy. The hydrogels grown from these supramolecular self-assembly systems show remarkable shape-memory properties and imprinting shape-behavior while the macroscopic shape of the materials obtained can be further manipulated by irradiation.

Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks.

Multivalent Noncovalent Interfacing and Cross-Linking of Supramolecular Tubes

Natural supramolecular filaments have the ability to cross-link with each other and to interface with the cellular membrane via biomolecular noncovalent interactions. This behavior allows them to form complex networks within as well as outside the cell, i.e., the cytoskeleton and the extracellular matrix, respectively. The potential of artificial supramolecular polymers to interact through specific noncovalent interactions has so far only seen limited exploration due to the dynamic nature of supramolecular interactions. Here, a system of synthetic supramolecular tubes that cross-link forming supramolecular networks, and at the same time bind to biomimetic surfaces by the aid of noncovalent streptavidin-biotin linkages, is demonstrated. The architecture of the networks can be engineered by controlling the density of the biotin moiety at the exterior of the tubes as well as by the concentration of the streptavidin. The presented strategy provides a pathway for designing adjustable artificial supramolecular superstructures, which can potentially yield more complex biomimetic adaptive materials.

How Defects Control the Out-of-Equilibrium Dissipative Evolution of a Supramolecular Tubule

Supramolecular architectures that work out-of-equilibrium or that can change in specific ways when absorbing external energy are ubiquitous in nature. Gaining the ability to create via self-assembly artificial materials possessing such fascinating behaviors would have a major impact in many fields. However, the rational design of similar dynamic structures requires to understand and, even more challenging, to learn how to master the molecular mechanisms governing how the assembled systems evolve far from the equilibrium. Typically, this represents a daunting challenge due to the limited molecular insight that can be obtained by the experiments or by classical modeling approaches. Here we combine coarse-grained molecular models and advanced simulation approaches to study at submolecular (<5 Å) resolution a supramolecular tubule, which breaks and disassembles upon absorption of light energy triggering isomerization of its azobenzene-containing monomers. Our approach allows us to investigate the molecular mechanism of monomer transition in the assembly and to elucidate the kinetic process for the accumulation of the transitions in the system. Despite the stochastic nature of the excitation process, we demonstrate how these tubules preferentially dissipate the absorbed energy locally via the amplification of defects in their supramolecular structure. We find that this constitutes the best kinetic pathway for accumulating monomer transitions in the system, which determines the dynamic evolution out-of-equilibrium and the brittle behavior of the assembly under perturbed conditions. Thanks to the flexibility of our models, we finally come out with a general principle, where defects explain and control the brittle/soft behavior of such light-responsive assemblies.

Light-fuelled reversible expansion of spiropyran-based vesicles in water

Vesicles formed by a spiropyran-based amphiphile show reversible expansion upon illumination

Electron-Transfer Rates in Host-Guest Assemblies at β-Cyclodextrin Monolayers

The effect of the distance between a β-cyclodextrin (βCD) host core and a conductive substrate on the electron-transfer rate of complexed guests as well as of free-diffusing electrochemically active probes has been studied. First we have evaluated a set of short-tethered βCD adsorbates bearing different anchoring groups in order to get a reliable platform for the study of short-distance electron transfer. An electrochemically active trivalent guest was immobilized on these host monolayers in a selective and reversible manner, providing information about the packing density. Iodine- and nitrile-functionalized βCD monolayers gave coverages close to maximum packing. Electron transfer in the presence of Fe(CN)₆^3-/4- studied by impedance spectroscopy revealed that the electron transfer of the diffusing probe was 3 orders of magnitude faster than when the βCD cores were separated from the surface by undecyl chains. When an electrochemically active guest was immobilized on the surface, electron-transfer rate measurements by cyclic voltammetry and capacitance spectroscopy showed differences of up to a factor of 8 for different βCD monolayers. These results suggest that increasing the distance between the βCD core and the underlying conductive substrate leads to a diminishing of the electron-transfer rate.

Monolayer Contact Doping from a Silicon Oxide Source Substrate

Monolayer contact doping (MLCD) is a modification of the monolayer doping (MLD) technique that involves monolayer formation of a dopant-containing adsorbate on a source substrate. This source substrate is subsequently brought into contact with the target substrate, upon which the dopant is driven into the target substrate by thermal annealing. Here, we report a modified MLCD process, in which we replace the commonly used Si source substrate by a thermally oxidized substrate with a 100 nm thick silicon oxide layer, functionalized with a monolayer of a dopant-containing silane. The thermal oxide potentially provides a better capping effect and effectively prevents the dopants from diffusing back into the source substrate. The use of easily accessible and processable silane monolayers provides access to a general and modifiable process for the introduction of dopants on the source substrate. As a proof of concept, a boron-rich carboranyl-alkoxysilane was used here to construct the monolayer that delivers the dopant, to boost the doping level in the target substrate. X-ray photoelectron spectroscopy (XPS) showed a successful grafting of the dopant adsorbate onto the SiO₂ surface. The achieved doping levels after thermal annealing were similar to the doping levels acessible by MLD as demonstrated by secondary ion mass spectrometry measurements. The method shows good prospects, e.g. for use in the doping of Si nanostructures.

High-Power Actuation from Molecular Photoswitches in Enantiomerically Paired Soft Springs

Motion in plants often relies on dynamic helical systems as seen in coiling tendrils, spasmoneme springs, and the opening of chiral seedpods. Developing nanotechnology that would allow molecular-level phenomena to drive such movements in artificial systems remains a scientific challenge. Herein, we describe a soft device that uses nanoscale information to mimic seedpod opening. The system exploits a fundamental mechanism of stimuli-responsive deformation in plants, namely that inflexible elements with specific orientations are integrated into a stimuli-responsive matrix. The device is operated by isomerization of a light-responsive molecular switch that drives the twisting of strips of liquid-crystal elastomers. The strips twist in opposite directions and work against each other until the pod pops open from stress. This mechanism allows the photoisomerization of molecular switches to stimulate rapid shape changes at the macroscale and thus to maximize actuation power.

Highly doped silicon nanowires by monolayer doping

Controlling the doping concentration of silicon nanostructures is challenging. Here, we investigated three different monolayer doping techniques to obtain silicon nanowires with a high doping dose. These routes were based on conventional monolayer doping, starting from covalently bound dopant-containing molecules, or on monolayer contact doping, in which a source substrate coated with a monolayer of a carborane silane was the dopant source. As a third route, both techniques were combined to retain the benefits of conformal monolayer formation and the use of an external capping layer. These routes were used for doping fragile porous nanowires fabricated by metal-assisted chemical etching. Differences in porosity were used to tune the total doping dose inside the nanowires, as measured by X-ray photoelectron spectroscopy and secondary ion mass spectrometry measurements. The higher the porosity, the higher was the surface available for dopant-containing molecules, which in turn led to a higher doping dose. Slightly porous nanowires could be doped via all three routes, which resulted in highly doped nanowires with (projected areal) doping doses of 10¹⁴-10¹⁵ boron atoms per cm² compared to 10¹² atoms per cm² for a non-porous planar sample. Highly porous nanowires were not compatible with the conventional monolayer doping technique, but monolayer contact doping and the combined route resulted for these highly porous nanowires in tremendously high doping doses up to 10¹⁷ boron atoms per cm².

Boosting the Boron Dopant Level in Monolayer Doping by Carboranes

Monolayer doping (MLD) presents an alternative method to achieve silicon doping without causing crystal damage, and it has the capability of ultrashallow doping and the doping of nonplanar surfaces. MLD utilizes dopant-containing alkene molecules that form a monolayer on the silicon surface using the well-established hydrosilylation process. Here, we demonstrate that MLD can be extended to high doping levels by designing alkenes with a high content of dopant atoms. Concretely, carborane derivatives, which have 10 B atoms per molecule, were functionalized with an alkene group. MLD using a monolayer of such a derivative yielded up to ten times higher doping levels, as measured by X-ray photoelectron spectroscopy and dynamic secondary mass spectroscopy, compared to an alkene with a single B atom. Sheet resistance measurements showed comparably increased conductivities of the Si substrates. Thermal budget analyses indicate that the doping level can be further optimized by changing the annealing conditions.

Controlling the dopant dose in silicon by mixed-monolayer doping

Molecular monolayer doping (MLD) presents an alternative to achieve doping of silicon in a nondestructive way and holds potential for realizing ultrashallow junctions and doping of nonplanar surfaces. Here, we report the mixing of dopant-containing alkenes with alkenes that lack this functionality at various ratios to control the dopant concentration in the resulting monolayer and concomitantly the dopant dose in the silicon substrate. The mixed monolayers were grafted onto hydrogen-terminated silicon using well-established hydrosilylation chemistry. Contact angle measurements, X-ray photon spectroscopy (XPS) on the boron-containing monolayers, and Auger electron spectroscopy on the phosphorus-containing monolayers show clear trends as a function of the dopant-containing alkene concentration. Dynamic secondary-ion mass spectroscopy (D-SIMS) and Van der Pauw resistance measurements on the in-diffused samples show an effective tuning of the doping concentration in silicon.

Bicomponent H-bonded porous molecular networks at the liquid-solid interface: what is the influence of preorganization in solution?

Tailoring the architecture of porous two-dimensional networks formed by molecules is essential for developing functional materials with low dimensionality. Here we present bicomponent porous networks with tunable pore-sizes that were formed by self-assembly of hydrogen-bonding molecules at the liquid/graphite interface. Scanning tunneling microscopy investigations demonstrate the formation and coexistence of three polymorphs. It is found that the occurrence of these polymorphs depends critically on the surface coverage. Further on, atomic force microscopy measurements, spectroscopic studies, and dynamic light scattering investigations show the propensity of one of the two molecular components to form aggregates beyond the monolayer. We discuss how these preorganized aggregates in solution may affect the self-assembly at the interface.

Self-assembled monolayers on gold of β-cyclodextrin adsorbates with different anchoring groups

We designed multivalent β-cyclodextrin-based adsorbates bearing different anchoring groups aiming to yield stable monolayers with improved packing and close contact of the cavity to the gold surface. Toward this end the primary rim of the β-cyclodextrin was decorated with several functional groups, namely iodide, nitrile, amine, isothiocyanate, methyl sulfide, and isocyanide. Monolayers formed by these adsorbates were characterized by contact angle measurements, surface plasmon resonance spectroscopy, polarization modulation infrared reflection adsorption spectroscopy, X-ray photoelectron spectroscopy, and electrochemistry. The nature of the anchoring group influenced the adsorption kinetics, thickness, layer stability, number of anchoring groups bounded to the surface, and packing in the resulting monolayers. Therefore, chemical manipulation of multivalent adsorbates can be used to modify the properties of their monolayers.

Reversible light induced conductance switching of asymmetric diarylethenes on gold: surface and electronic studies

We report on the light-induced switching of conductance of a new generation of diarylethene switches embedded in an insulating matrix of dodecanethiol on Au(111), by using scanning tunneling microscopy (STM). The diarylethene switches we synthesize and study are modified diarylethenes where the thiophene unit at one side of the molecular backbone introduces an intrinsic asymmetry into the switch, which is expected to influence its photo-conductance properties. We show that reversible conversion between two distinguishable conductance states can be controlled via photoisomerisation of the switches by using alternative irradiation with UV (λ = 313 nm) or visible (λ > 420 nm) light. We addressed this phenomenon by using STM in ambient conditions, based on switching of the apparent height of the molecules which convert from 4-6 Å in their closed form to 0-1 Å in their open form. Furthermore, the levels of the frontier molecular orbital levels (HOMO and LUMO) were evaluated for these asymmetric switches by using Scanning Tunneling Spectroscopy at 77 K, which allowed us to determine a HOMO-LUMO energy gap of 2.24 eV.

Electrically driven directional motion of a four-wheeled molecule on a metal surface

Propelling single molecules in a controlled manner along an unmodified surface remains extremely challenging because it requires molecules that can use light, chemical or electrical energy to modulate their interaction with the surface in a way that generates motion. Nature's motor proteins have mastered the art of converting conformational changes into directed motion, and have inspired the design of artificial systems such as DNA walkers and light- and redox-driven molecular motors. But although controlled movement of single molecules along a surface has been reported, the molecules in these examples act as passive elements that either diffuse along a preferential direction with equal probability for forward and backward movement or are dragged by an STM tip. Here we present a molecule with four functional units--our previously reported rotary motors--that undergo continuous and defined conformational changes upon sequential electronic and vibrational excitation. Scanning tunnelling microscopy confirms that activation of the conformational changes of the rotors through inelastic electron tunnelling propels the molecule unidirectionally across a Cu(111) surface. The system can be adapted to follow either linear or random surface trajectories or to remain stationary, by tuning the chirality of the individual motor units. Our design provides a starting point for the exploration of more sophisticated molecular mechanical systems with directionally controlled motion.

STM visualisation of counterions and the effect of charges on self-assembled monolayers of macrocycles

Despite their importance in self-assembly processes, the influence of charged counterions on the geometry of self-assembled organic monolayers and their direct localisation within the monolayers has been given little attention. Recently, various examples of self-assembled monolayers composed of charged molecules on surfaces have been reported, but no effort has been made to prove the presence of counterions within the monolayer. Here we show that visualisation and exact localisation of counterions within self-assembled monolayers can be achieved with scanning tunnelling microscopy (STM). The presence of charges on the studied shape-persistent macrocycles is shown to have a profound effect on the self-assembly process at the liquid-solid interface. Furthermore, preferential adsorption was observed for the uncharged analogue of the macrocycle on a surface.

Large all-hydrocarbon spoked wheels of high symmetry: modular synthesis, photophysical properties, and surface assembly

In a convergent modular synthesis, a very efficient pathway to shape-persistent molecular spoked wheels has been developed and applied according to the covalent-template concept. The structurally defined two-dimensional (2D) oligo(phenylene-ethynylene-butadiynylene)s (OPEBs) presented here are about 8 nm sized hydrocarbons of high symmetry. 48 alkyl chains attached to the molecular plane (hexyl and hexadecyl, respectively) guarantee a high solubility of the compounds. The structure and uniformity of these defined, stable, D(6h) symmetrical compounds is verified by MALDI-MS, GPC analysis, and high-temperature (HT) (1)H and (13)C NMR. Detailed photophysical measurements of nonaggregated molecules in solution (as confirmed by dynamic light scattering (DLS)) focus on the identification of chromophores by comparison with suitable model compounds. Moreover, time-resolved measurements including fluorescence lifetime and depolarization support the chromophore assignment and reveal the occurrence of intramolecular energy transfer. Scanning tunneling microscope (STM) characterization at the solid/liquid interface demonstrates the efficient self-assembly of the OPEBs into hexagonal 2D crystalline layers with a periodicity determined by both the size of the OPEB backbone and the length of peripheral side chains. Atomic force microscope (AFM) studies show a very different assembly behavior of the two spoked wheel molecules, on both graphite and mica. While the hexyl-substituted wheel can form stacked superstructures, hexadecyl groups prevent any ordering in the film aside from the monolayer directly in contact with the surface.

Light-controlled conductance switching of ordered metal-molecule-metal devices

We demonstrate reversible, light-controlled conductance switching of molecular devices based on photochromic diarylethene molecules. These devices consist of ordered, two-dimensional lattices of gold nanoparticles, in which neighboring particles are bridged by switchable molecules. We independently confirm that reversible isomerization of the diarylethenes employed is at the heart of the room-temperature conductance switching. For this, we take full advantage of the possibility to use optical spectroscopy to follow molecular switching in these samples.

Self-organized monolayer of meso-tetradodecylporphyrin coordinated to Au(111)

The structure of molecular monolayers formed at the interface between atomically flat surfaces and a solution of free-base meso-tetradodecylporphyrins (H2Ps) was examined by scanning tunneling microscopy (STM) at the liquid/solid interface. On the surface of graphite (HOPG), H2Ps form a well-ordered monolayer characterized by an oblique unit cell. On Au(111), H2Ps form a self-organized monolayer comprised of two distinct domain types. In both types of domains, the density of the porphyrin cores is increased in comparison to the arrangement observed on HOPG. Also, high-resolution STM images reveal that, in contrast to what is observed on HOPG, physisorption on Au(111) induces a distortion of the porphyrin macrocycle out of planarity. By using X-ray photoelectron spectroscopy, we demonstrate that this is likely to be due to the coordination of the lone pairs of the iminic (-C=N-) nitrogen atoms of the porphyrin macrocycle to Au(111).

Uni- and bi-directional light-induced switching of diarylethenes on gold nanoparticles

Photochromic studies of diarylethenes with their switching unit linked to the surface of gold nanoparticles via a conjugated aromatic spacer show linker-dependent switching behavior.

Oxidative Electrochemical Switching in Dithienylcyclopentenes, Part 1: Effect of Electronic Perturbation on the Efficiency and Direction of Molecular Switching

The electro- and spectroelectrochemical properties of dithienylhexahydro- and dithienyhexafluorocyclopentenes are reported. The large effect of variation in the central cyclopentene moieties on the redox properties of the dithienylcyclopentenes is in striking contrast to the minor effect on their photochemical properties. The electronic properties of the oxidised compounds in the +1 and +2 oxidation state are reported, and the possibility of electrochemical cyclisation and cycloreversion were explored by UV/Vis spectroelectrochemistry. The efficiency of electrochemical switching is found to be dependent both on the central cyclopentene unit and on the nature of the substituents at C5 of the thienyl rings. For the hexahydrocyclopentene-based compounds oxidative ring closure of the ring-open form is observed, while for the hexafluorocyclopentene-based compounds oxidative ring opening of the ring-closed form is observed. However, the introduction of electroactive groups such as methoxyphenyl allows oxidative ring closure to occur in the hexafluoro compounds. The effect of electrolyte, solvent and temperature on the spectroelectrochemical properties were examined, and the switching process was found to be sensitive to the donor properties of the solvent/electrolyte system employed. In addition, thermally activated reversible isomerisation of the dicationic closed form was observed. The driving force for electrochemical ring opening and closure appears to be dependent on the relative stabilisation of the dicationic ring-open and ring-closed states. This study provides insight into the factors which determine the direction of cyclisation.

Oxidative Electrochemical Switching in Dithienylcyclopentenes, Part 2: Effect of Substitution and Asymmetry on the Efficiency and Direction of Molecular Switching and Redox Stability

The electrochemical and spectroelectrochemical properties of a series of C5-substituted dithienylhexahydro- and dithienylhexafluorocyclopentenes are reported. The effect of substitution at C5 of the thienyl moiety on the redox properties is quite dramatic, in contrast to the effect on their photochemical properties. The efficiency of electrochemical switching is dependent both on the central cyclopentene unit and on the nature of the substituents, whereby electron-donating moieties favour oxidative electrochemical ring-closure and vice versa. Asymmetrically substituted dithienylcyclopentenes were investigated to explore the ring-closure process in more detail. The results indicate that electrochemically induced ring-closure occurs via the monocation of the open form. In the presence of electroactive groups at C5 of the thienyl ring (e.g., methoxyphenyl) initial oxidation of these groups is followed by intermolecular electron transfer, which drives ring-closure of the open forms.

One-way optoelectronic switching of photochromic molecules on gold

We investigate photochromic molecular switches that are self-assembled on gold. We use two experimental techniques; namely, the mechanically controllable break-junction technique to measure electronic transport, and UV/Vis spectroscopy to measure absorption. We observe switching of the molecules from the conducting to the insulating state when illuminated with visible light (lambda=546 nm), in spite of the gold surface plasmon absorption present around this wavelength. However, we fail to observe the reverse process which should occur upon illumination with UV light (lambda=313 nm). We attribute this to quenching of the excited state of the molecule in the open form by the presence of gold.