Spontaneous S–Si bonding of alkanethiols to Si(111)–H: towards Si–molecule–Si circuits

We report the synthesis of covalently linked self-assembled monolayers (SAMs) on silicon surfaces, using mild conditions, in a way that is compatible with silicon-electronics fabrication technologies. In molecular electronics, SAMs of functional molecules tethered to gold via sulfur linkages dominate, but these devices are not robust in design and not amenable to scalable manufacture. Whereas covalent bonding to silicon has long been recognized as an attractive alternative, only formation processes involving high temperature and/or pressure, strong chemicals, or irradiation are known. To make molecular devices on silicon under mild conditions with properties reminiscent of Au–S ones, we exploit the susceptibility of thiols to oxidation by dissolved O₂, initiating free-radical polymerization mechanisms without causing oxidative damage to the surface. Without thiols present, dissolved O₂ would normally oxidize the silicon and hence reaction conditions such as these have been strenuously avoided in the past. The surface coverage on Si(111)–H is measured to be very high, 75% of a full monolayer, with density-functional theory calculations used to profile spontaneous reaction mechanisms. The impact of the Si–S chemistry in single-molecule electronics is demonstrated using STM-junction approaches by forming Si–hexanedithiol–Si junctions. Si–S contacts result in single-molecule wires that are mechanically stable, with an average lifetime at room temperature of 2.7 s, which is five folds higher than that reported for conventional molecular junctions formed between gold electrodes. The enhanced “ON” lifetime of this single-molecule circuit enables previously inaccessible electrical measurements on single molecules.

Spontaneously formed Si–S bonds enable monolayer and single-molecule Si–molecule–Si circuits.     

Tailor-made thermoplastic elastomers: customisable materials via modulation of molecular weight distributions

The ability to change polymer properties has in the past largely been a factor of modulating the molecular weight, molecular weight distribution breadth, crosslinking, or branching. The use of controlled MWD shape has recently emerged as a promising avenue towards modifying polymer properties. Taking advantage of molecular weight distribution shape, we report a simple and efficient approach for tuning material properties in polystyrene-block-polyisoprene-block-polystyrene (SIS) thermoplastic elastomers (TPEs). We find that the skew of the MWD function governs tensile properties and can be used as a handle to predictably vary polymer toughness while reducing energy dissipation.

Taking advantage of molecular weight distributions shape, we report a simple and efficient approach for predictably tuning material properties for thermoplastic elastomers.     

Multimerized self-assembled caged two-in-one siRNA nanoparticles for photomodulation of RNAi-induced gene silencing

We rationally designed and developed caged siRNA nanoparticles (Multi-Chol-siRNA) self-assembled with cholesterol-modified multimerized caged siRNAs for photomodulation of siRNA gene silencing activity. Strong resistance to serum nuclease and RNase A was observed for these cholesterol-modified caged siRNA nanoparticles due to the formation of nanostructures with high intensity of siRNA. These caged Multi-Chol-siRNA self-assembled nanoparticles were successfully used to achieve photochemical regulation of both exogenous GFP and endogenous Eg5 gene expressions with a GFP/RFP transient transfection system and Eg5-associated assays, respectively. Further, Two-in-One caged Multi-Chol-siGFP/siEg5 self-assembled nanoparticles simultaneously targeting GFP and Eg5 genes were also developed. The caged Multi-Chol-siRNA self-assembled nanoparticles have demonstrated the effectiveness of enhancing photomodulation of multiple RNAi-induced gene silencing activities in cells.

Upon light irradiation, multimerized self-assembled caged Two-in-One siRNA nanoparticles (Multi-Chol-siRNA) were collapsed to release trapped siRNAs for multiple RNAi-induced gene silencing activity.     

Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids

The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression, but tracing their molecular origin has been difficult due to the structural and chemical complexity. We posit that concepts from machine learning can help to tackle this long-standing challenge. Here, we demonstrate the feasibility and advantage of this strategy through developing a structure-mechanics statistical learning scheme to elucidate how local rigidity in double-stranded (ds)DNA and dsRNA may lead to their global flexibility in bend, stretch, and twist. Specifically, the mechanical parameters in a heavy-atom elastic network model are computed from the trajectory data of all-atom molecular dynamics simulation. The results show that the inter-atomic springs for backbone and ribose puckering in dsRNA are stronger than those in dsDNA, but are similar in strengths for base-stacking and base-pairing. Our analysis shows that the experimental observation of dsDNA being easier to bend but harder to stretch than dsRNA comes mostly from the respective B- and A-form topologies. The computationally resolved composition of local rigidity indicates that the flexibility of both nucleic acids is mostly due to base-stacking. But for properties like twist-stretch coupling, backbone springs are shown to play a major role instead. The quantitative connection between local rigidity and global flexibility sets foundation for understanding how local binding and chemical modification of genetic materials effectuate longer-ranged regulatory signals.

The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression. We devise structural mechanics statistical learning method to reveal their molecular origin in terms of chemical interactions.     

Room temperature conductance switching in a molecular iron(iii) spin crossover junction

Herein, we report the first room temperature switchable Fe(iii) molecular spin crossover (SCO) tunnel junction. The junction is constructed from [Fe^III(qsal-I)₂]NTf₂ (qsal-I = 4-iodo-2-[(8-quinolylimino)methyl]phenolate) molecules self-assembled on graphene surfaces with conductance switching of one order of magnitude associated with the high and low spin states of the SCO complex. Normalized conductance analysis of the current–voltage characteristics as a function of temperature reveals that charge transport across the SCO molecule is dominated by coherent tunnelling. Temperature-dependent X-ray absorption spectroscopy and density functional theory confirm the SCO complex retains its SCO functionality on the surface implying that van der Waals molecule—electrode interfaces provide a good trade-off between junction stability while retaining SCO switching capability. These results provide new insights and may aid in the design of other types of molecular devices based on SCO compounds.

Herein, we report the first room temperature switchable Fe(iii) molecular spin crossover (SCO) tunnel junction.     

Coupling molecular rigidity and flexibility on fused backbones for NIR-II photothermal conversion

Great attention is being increasingly paid to photothermal conversion in the near-infrared (NIR)-II window (1000–1350 nm), where deeper tissue penetration is favored. To date, only a limited number of organic photothermal polymers and relevant theory have been exploited to direct the molecular design of polymers with highly efficient photothermal conversion, specifically in the NIR-II window. This work proposes a fused backbone structure locked via an intramolecular hydrogen bonding interaction and double bond, which favors molecular planarity and rigidity in the ground state and molecular flexibility in the excited state. Following this proposal, a particular class of NIR-II photothermal polymers are prepared. Their remarkable photothermal conversion efficiency is in good agreement with our strategy of coupling polymeric rigidity and flexibility, which accounts for the improved light absorption on going from the ground state to the excited state and nonradiative emission on going from the excited state to the ground state. It is envisioned that such a concept of coupling polymeric rigidity and flexibility will offer great inspiration for developing NIR-II photothermal polymers with the use of other chromophores.

Low bandgap and large deformation generally conflict each other. This work couples molecular rigidity and flexibility by intramolecular hydrogen bonds and double bonds to achieve NIR-II light absorption and reinforced internal conversion at the same time.     

Flexible polyfluorinated bis-diazirines as molecular adhesives

Motivated by a desire to develop flexible covalent adhesives that afford some of the same malleability in the adhesive layer as traditional polymer-based adhesives, we designed and synthesized two flexible, highly fluorinated bis-diazirines. Both molecules are shown to function as effective crosslinkers for polymer materials, and to act as strong adhesives when painted between two polymer objects of low surface energy, prior to thermal activation. Data obtained from lap-shear experiments suggests that greater molecular flexibility is correlated with improved mechanical compliance in the adhesive layer.

Flexible, highly fluorinated covalent adhesives are synthesized, and are shown to afford comparable C–H insertion efficiency and adhesion strength relative to a rigid analogue, while providing improved mechanical compliance in the adhesion layer.     

Enhanced voltammetric anion sensing at halogen and hydrogen bonding ferrocenyl SAMs

Halogen bonding mediated electrochemical anion sensing has very recently been established as a potent platform for the selective and sensitive detection of anions, although the principles that govern binding and subsequent signal transduction remain poorly understood. Herein we address this challenge by providing a comprehensive study of novel redox-active halogen bonding (XB) and hydrogen bonding (HB) ferrocene-isophthalamide-(iodo)triazole receptors in solution and at self-assembled monolayers (SAMs). Under diffusive conditions the sensory performance of the XB sensor was significantly superior. In molecular films the XB and HB binding motifs both display a notably enhanced, but similar, response to specific anions. Importantly, the enhanced response of these films is rationalised by a consideration of the (interfacial) dielectric microenvironment. These effects, and the resolved relationship between anion binding and signal transduction, underpin an improved fundamental understanding of anion sensing at redox-active interfaces which will benefit not just the development of more potent, real-life relevant, sensors but also new tools to study host–guest interactions at interfaces.

Surface enhancement effects in the sensing of anions at redox-active molecular films are investigated in detail and rationalised based on a consideration of the dielectric binding microenvironment.     

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.     

Lipase mimetic cyclodextrins

Glycerophospholipids (GPLs) perform numerous essential functions in biology, including forming key structural components of cellular membranes and acting as secondary messengers in signaling pathways. Developing biomimetic molecular devices that can detect specific GPLs would enable modulation of GPL-related processes. However, the compositional diversity of GPLs, combined with their hydrophobic nature, has made it challenging to develop synthetic scaffolds that can react with specific lipid species. By taking advantage of the host–guest chemistry of cyclodextrins, we have engineered a molecular device that can selectively hydrolyze GPLs under physiologically relevant conditions. A chemically modified α-cyclodextrin bearing amine functional groups was shown to hydrolyze lyso-GPLs, generating free fatty acids. Lyso-GPLs are preferentially hydrolyzed when part of a mixture of GPL lipid species, and reaction efficiency was dependent on lyso-GPL chemical structure. These findings lay the groundwork for the development of molecular devices capable of specifically manipulating lipid-related processes in living systems.

Lipase mimetic cyclodextrins (CDs) can selectively hydrolyze native lyso-glycerophospholipids (GPLs) under physiologically relevant conditions.     

Molecularly-tunable nanoelectrode arrays created by harnessing intermolecular interactions

Intermolecular interactions play a critical role in the binding strength of molecular assemblies on surfaces. The ability to harness them enables molecularly-tunable interfacial structures and properties. Herein we report the tuning of the intermolecular interactions in monolayer assemblies derived from organothiols of different structures for the creation of nanoelectrode arrays or ensembles with effective mass transport by a molecular-level perforation strategy. The homo- and hetero-intermolecular interactions can be fully controlled, which is demonstrated not only by thermodynamic analysis of the fractional coverage but also by surface infrared reflection absorption and X-ray photoelectron spectroscopic characterizations. This understanding enables controllable electrochemical perforation for the creation of ensembles or arrays of channels across the monolayer thickness with molecular and nanoscale dimensions. Redox reactions on the nanoelectrode array display molecular tunability with a radial diffusion characteristic in good agreement with theoretical simulation results. These findings have implications for designing membrane-type ion-gating, electrochemical sensing, and electrochemical energy storage devices with molecular level tunability.

Intermolecular interactions in monolayer assembly are harnessed for creating molecularly-tunable nanoelectrode arrays or ensembles.     

Self-healing and shape memory functions exhibited by supramolecular liquid-crystalline networks formed by combination of hydrogen bonding interactions and coordination bonding

We here report a new approach to develop self-healing shape memory supramolecular liquid-crystalline (LC) networks through self-assembly of molecular building blocks via combination of hydrogen bonding and coordination bonding. We have designed and synthesized supramolecular LC polymers and networks based on the complexation of a forklike mesogenic ligand with Ag⁺ ions and carboxylic acids. Unidirectionally aligned fibers and free-standing films forming layered LC nanostructures have been obtained for the supramolecular LC networks. We have found that hybrid supramolecular LC networks formed through metal–ligand interactions and hydrogen bonding exhibit both self-healing properties and shape memory functions, while hydrogen-bonded LC networks only show self-healing properties. The combination of hydrogen bonds and metal–ligand interactions allows the tuning of intermolecular interactions and self-assembled structures, leading to the formation of the dynamic supramolecular LC materials. The new material design presented here has potential for the development of smart LC materials and functional LC membranes with tunable responsiveness.

New supramolecular hybrid liquid-crystalline networks exhibiting self-healing and shape memory properties are developed by self-assembly of small components through hydrogen bonding interactions and coordination bonding.     

Cooperatively assembled liquid crystals enable temperature-controlled Förster resonance energy transfer

Balancing the rigidity of a π-conjugated structure for strong emission and the flexibility of liquid crystals for self-assembly is the key to realizing highly emissive liquid crystals (HELCs). Here we show that (1) integrating organization-induced emission into dual molecular cooperatively-assembled liquid crystals, (2) amplifying mesogens, and (3) elongating the spacer linking the emitter and the mesogen create advanced materials with desired thermal–optical properties. Impressively, assembling the fluorescent acceptor Nile red into its host donor designed according to the aforementioned strategies results in a temperature-controlled Förster resonance energy transfer (FRET) system. Indeed, FRET exhibits strong S-curve dependence as temperature sweeps through the liquid crystal phase transformation. Such thermochromic materials, suitable for dynamic thermo-optical sensing and modulation, are anticipated to unlock new and smart approaches for controlling and directing light in stimuli-responsive devices.

A temperature-sensitive Förster resonance energy transfer system was constructed using a highly emissive liquid crystal co-assembled with Nile red, enabling thermo-optical modulation for controlling and directing light in stimuli-responsive devices.     

Oxidative regulation of the mechanical strength of a C–S bond

The mechanical strength of individual polymer chains is believed to underlie a number of performance metrics in bulk materials, including adhesion and fracture toughness. Methods by which the intrinsic molecular strength of the constituents of a given polymeric material might be switched are therefore potentially useful both for applications in which triggered property changes are desirable, and as tests of molecular theories for bulk behaviors. Here we report that the sequential oxidation of sulfide containing polyesters (PE-S) to the corresponding sulfoxide (PE-SO) and then sulfone (PE-SO2) first weakens (sulfoxide), and then enhances (sulfone), the effective mechanical integrity of the polymer backbone; PE-S ∼ PE-SO2 > PE-SO. The relative mechanical strength as a function of oxidation state is revealed through the use of gem-dichlorocyclopropane nonscissile mechanophores as an internal standard, and the observed order agrees well with the reported bond dissociation energies of C–S bonds in each species and with the results of CoGEF modeling.

The mechanical strength of individual polymer chains is believed to underlie a number of performance metrics in bulk materials, including adhesion and fracture toughness.     

Self-assembled low-molecular-weight gelator injectable microgel beads for delivery of bioactive agents

We report the preparation of hybrid self-assembled microgel beads by combining the low molecular weight gelator (LMWG) DBS-CONHNH₂ and the natural polysaccharide calcium alginate polymer gelator (PG). Microgel formulations based on LMWGs are extremely rare due to the fragility of the self-assembled networks and the difficulty of retaining any imposed shape. Our hybrid beads contain interpenetrated LMWG and PG networks, and are obtained by an emulsion method, allowing the preparation of spherical gel particles of controllable sizes with diameters in the mm or μm range. Microgels based on LMWG/alginate can be easily prepared with reproducible diameters <1 μm (ca. 800 nm). They are stable in water at room temperature for many months, and survive injection through a syringe. The rapid assembly of the LMWG on cooling plays an active role in helping control the diameter of the microgel beads. These LMWG microbeads retained the ability of the parent gel to deliver the bioactive molecule heparin, and in cell culture medium this enhanced the growth of human mesenchymal stem cells. Such microgels may therefore have future applications in tissue repair. This approach to fabricating LMWG microgels is a platform technology, which could potentially be applied to a variety of different functional LMWGs, and hence has wide-ranging potential.

We report microgel beads with diameters of ca. 800 nm based on interpenetrating networks of a low-molecular-weight gelator and a polymer gelator, and demonstrate their use as heparin delivery vehicles to enhance stem cell growth.     

Confined space design by nanoparticle self-assembly

Nanoparticle (NP) self-assembly has led to the fabrication of an array of functional nanoscale systems, having diverse architectures and functionalities. In this perspective, we discuss the design and application of NP suprastructures (SPs) characterized by nanoconfined compartments in their self-assembled framework, providing an overview about SP synthetic strategies reported to date and the role of their confined nanocavities in applications in several high-end fields. We also set to give our contribution towards the formation of more advanced nanocompartmentalized SPs able to work in dynamic manners, discussing the opportunities of further advances in NP self-assembly and SP research.

This perspective gives an outlook on the design of interparticle confined nanocavities in self-assembled NP systems and their functional relevance.     

Tuning energy landscapes and metal–metal interactions in supramolecular polymers regulated by coordination geometry

Herein, we exploit coordination geometry as a new tool to regulate the non-covalent interactions, photophysical properties and energy landscape of supramolecular polymers. To this end, we have designed two self-assembled Pt(ii) complexes 1 and 2 that feature an identical aromatic surface, but differ in the coordination and molecular geometry (linear vs. V-shaped) as a result of judicious ligand choice (monodentate pyridine vs. bidentate bipyridine). Even though both complexes form cooperative supramolecular polymers in methylcyclohexane, their supramolecular and photophysical behaviour differ significantly: while the high preorganization of the bipyridine-based complex 1 enables an H-type 1D stacking with short Pt⋯Pt contacts via a two-step consecutive process, the existence of increased steric effects for the pyridyl-based derivative 2 hinders the formation of metal–metal contacts and induces a single aggregation process into large bundles of fibers. Ultimately, this fine control of Pt⋯Pt distances leads to tuneable luminescence—red for 1vs. blue for 2, which highlights the relevance of coordination geometry for the development of functional supramolecular materials.

In this article, we exploit coordination geometry as a new tool to control the energy landscape and photophysical properties (red vs. blue luminescence) of supramolecular polymers.     

Chemical control of peptide material phase transitions

Progressive solute-rich polymer phase transitions provide pathways for achieving ordered supramolecular assemblies. Intrinsically disordered protein domains specifically regulate information in biological networks via conformational ordering. Here we consider a molecular tagging strategy to control ordering transitions in polymeric materials and provide a proof-of-principle minimal peptide phase network captured with a dynamic chemical network.

Substrate initiated assembly of a dynamic chemical network.     

Targeting structural features of viral genomes with a nano-sized supramolecular drug

RNA targeting is an exciting frontier for drug design. Intriguing targets include functional RNA structures in structurally-conserved untranslated regions (UTRs) of many lethal viruses. However, computational docking screens, valuable in protein structure targeting, fail for inherently flexible RNA. Herein we harness MD simulations with Markov state modeling to enable nanosize metallo-supramolecular cylinders to explore the dynamic RNA conformational landscape of HIV-1 TAR untranslated region RNA (representative for many viruses) replicating experimental observations. These cylinders are exciting as they have unprecedented nucleic acid binding and are the first supramolecular helicates shown to have anti-viral activity in cellulo: the approach developed in this study provides additional new insight about how such viral UTR structures might be targeted with the cylinder binding into the heart of an RNA-bulge cavity, how that reduces the conformational flexibility of the RNA and molecular details of the insertion mechanism. The approach and understanding developed represents a new roadmap for design of supramolecular drugs to target RNA structural motifs across biology and nucleic acid nanoscience.

MD simulations and Markov state modeling explore induced fit binding of metallo-helicates to bulges in dynamic TAR RNA, reproduce experimental data, show how RNA conformational flexibility is reduced, and give mechanistic insight into insertion.     

Defect-engineered surfaces to investigate the formation of self-assembled molecular networks

Herein we report the impact of covalent modification (grafting), inducing lateral nanoconfinement conditions, on the self-assembly of a quinonoid zwitterion derivative into self-assembled molecular networks at the liquid/solid interface. At low concentrations where the compound does not show self-assembly behaviour on bare highly oriented pyrolytic graphite (HOPG), close-packed self-assembled structures are visualized by scanning tunneling microscopy on covalently modified HOPG. The size of the self-assembled domains decreases with increasing the density of grafted molecules, i.e. the molecules covalently bound to the surface. The dynamics of domains are captured with molecular resolution, revealing not only time-dependent growth and shrinkage processes but also the orientation conversion of assembled domains. Grafted pins play a key role in initiating the formation of on-surface molecular self-assembly and their stabilization, providing an elegant route to study various aspects of nucleation and growth processes of self-assembled molecular networks.

We showcase the use of covalently modified HOPG for the investigation of domain size controlled 2D self-assembly, nucleation and growth kinetics, molecular adsorption/desorption thermodynamics, and tip-induced selective recrystallization.