The emerging landscape of single-molecule protein sequencing technologies.

Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.

Redox-Controlled Shunts in a Synthetic Chemical Reaction Cycle.

Shunts, alternative pathways in chemical reaction networks (CRNs), are ubiquitous in nature, enabling adaptability to external and internal stimuli. We introduce a CRN in which the recovery of Michael-accepting species is driven by oxidation chemistry. Using weak oxidants can enable access to two shunts within this CRN with different kinetics and a reduced number of side reactions compared to the main cycle that is driven by strong oxidants. Furthermore, we introduce a strategy to recycle one of the main products under flow conditions to partially reverse the CRN and control product speciation throughout time. These findings introduce new levels of control over artificial CRNs, driven by redox chemistry, narrowing the gap between synthetic and natural systems.

Naked-Eye Thiol Analyte Detection via Self-Propagating, Amplified Reaction Cycle.

We present an approach for detecting thiol analytes through a self-propagating amplification cycle that triggers the macroscopic degradation of a hydrogel scaffold. The amplification system consists of an allylic phosphonium salt that upon reaction with the thiol analyte releases a phosphine, which reduces a disulfide to form two thiols, closing the cycle and ultimately resulting in exponential amplification of the thiol input. When integrated in a disulfide cross-linked hydrogel, the amplification process leads to physical degradation of the hydrogel in response to thiol analytes. We developed a numerical model to predict the behavior of the amplification cycle in response to varying concentrations of thiol triggers and validated it with experimental data. Using this system, we were able to detect multiple thiol analytes, including a small molecule probe, glutathione, DNA, and a protein, at concentrations ranging from 132 to 0.132 µM. In addition, we discovered that the self-propagating amplification cycle could be initiated by force-generated molecular scission, enabling damage-triggered hydrogel destruction.

On-Demand Release of Secondary Amine Bases for the Activation of Catalysts and Crosslinkers.

Dynamic covalent (DCv) ureas have been used abundantly to design self-healing materials. We demonstrate that apart from self-healing materials, the species present in the equilibrium of DCv ureas can be employed as responsive organocatalysts. Easily controllable stimuli like heat or addition of water shift the equilibrium towards isocyanate and free base which can function as an in situ released reagent. We demonstrate this application of DCv ureas with two examples. Firstly, we use the liberated base to catalytically activate a latent organocatalyst for acylhydrazone formation. Secondly, this base can be employed in an equimolar manner to trigger the release of nitrile-N-oxides from chlorooximes, which react with acrylate-terminated polymers to form an isoxazoline polymer gel.

Enhancing the ROS Sensitivity of a Responsive Supramolecular Hydrogel Using Peroxizyme Catalysis.

Hydrogels that can disintegrate upon exposure to reactive oxygen species (ROS) have the potential for targeted drug delivery to tumor cells. In this study, we developed a diphenylalanine (FF) derivative with a thioether phenyl moiety attached to the N-terminus that can form supramolecular hydrogels at neutral and mildly acidic pH. The thioether can be oxidized by ROS to the corresponding sulfoxide, which makes the gelator hydrolytically labile. The resulting oxidation and hydrolysis products alter the polarity of the gelator, leading to disassembly of the gel fibers. To enhance ROS sensitivity, we incorporated peroxizymes in the gels, namely, chloroperoxidase CiVCPO and the unspecific peroxygenase rAaeUPO. Both enzymes accelerated the oxidation process, enabling the hydrogels to collapse with 10 times lower H2O2 concentrations than those required for enzyme-free hydrogel collapse. These ROS-responsive hydrogels could pave the way toward optimized platforms for targeted drug delivery in the tumor microenvironment.

Switching the Mode of Drug Release from a Reaction-Coupled Low-Molecular-Weight Gelator System by Altering Its Reaction Pathway.

Low-molecular-weight hydrogels are attractive scaffolds for drug delivery applications because of their modular and facile preparation starting from inexpensive molecular components. The molecular design of the hydrogelator results in a commitment to a particular release strategy, where either noncovalent or covalent bonding of the drug molecule dictates its rate and mechanism. Herein, we demonstrate an alternative approach using a reaction-coupled gelator to tune drug release in a facile and user-defined manner by altering the reaction pathway of the low-molecular-weight gelator (LMWG) and drug components through an acylhydrazone-bond-forming reaction. We show that an off-the-shelf drug with a reactive handle, doxorubicin, can be covalently bound to the gelator through its ketone moiety when the addition of the aldehyde component is delayed from 0 to 24 h, or noncovalently bound with its addition at 0 h. We also examine the use of an l-histidine methyl ester catalyst to prepare the drug-loaded hydrogels under physiological conditions. Fitting of the drug release profiles with the Korsmeyer-Peppas model corroborates a switch in the mode of release consistent with the reaction pathway taken: increased covalent ligation drives a transition from a Fickian to a semi-Fickian mode in the second stage of release with a decreased rate. Sustained release of doxorubicin from the reaction-coupled hydrogel is further confirmed in an MTT toxicity assay with MCF-7 breast cancer cells. We demonstrate the modularity and ease of the reaction-coupled approach to prepare drug-loaded self-assembled hydrogels in situ with tunable mechanics and drug release profiles that may find eventual applications in macroscale drug delivery.

Dynamic Growth of Macroscopically Structured Supramolecular Hydrogels through Orchestrated Reaction-Diffusion.

Living organisms are capable of dynamically changing their structures for adaptive functions through sophisticated reaction-diffusion processes. Here we show how active supramolecular hydrogels with programmable lifetimes and macroscopic structures can be created by relying on a simple reaction-diffusion strategy. Two hydrogel precursors (poly(acrylic acid) PAA/CaCl2 and Na2 CO3 ) diffuse from different locations and generate amorphous calcium carbonate (ACC) nanoparticles at the diffusional fronts, leading to the formation of hydrogel structures driven by electrostatic interactions between PAA and ACC nanoparticles. Interestingly, the formed hydrogels are capable of autonomously disintegrating over time because of a delayed influx of electrostatic-interaction inhibitors (NaCl). The hydrogel growth process is well explained by a reaction-diffusion model which offers a theoretical means to program the dynamic growth of structured hydrogels. Furthermore, we demonstrate a conceptual access to dynamic information storage in soft materials using the developed reaction-diffusion strategy. This work may serve as a starting point for the development of life-like materials with adaptive structures and functionalities.

Transient Host-Guest Complexation To Control Catalytic Activity.

Signal transduction mechanisms are key to living systems. Cells respond to signals by changing catalytic activity of enzymes. This signal responsive catalysis is crucial in the regulation of (bio)chemical reaction networks (CRNs). Inspired by these networks, we report an artificial signal responsive system that shows signal-induced temporary catalyst activation. We use an unstable signal to temporarily activate an out of equilibrium CRN, generating transient host-guest complexes to control catalytic activity. Esters with favorable binding toward the cucurbit[7]uril (CB[7]) supramolecular host are used as temporary signals to form a transient complex with CB[7], replacing a CB[7]-bound guest. The esters are hydrolytically unstable, generating acids and alcohols, which do not bind to CB[7], leading to guest reuptake. We demonstrate the feasibility of the concept using signal-controlled temporary dye release and reuptake. The same signal controlled system was then used to tune the reaction rate of aniline catalyzed hydrazone formation. Varying the ester structure and concentration gave access to different catalyst liberation times and free catalyst concentration, regulating the overall reaction rate. With temporary signal controlled transient complex formation we can tune the kinetics of a second chemical reaction, in which the signal does not participate. This system shows promise for building more complex nonbiological networks, to ultimately arrive at signal transduction in organic materials.

Light-Sensitive Phenacyl Crosslinked Dextran Hydrogels for Controlled Delivery.

Stimuli-responsive soft materials enable controlled release of loaded drug molecules and biomolecules. Controlled release of potent chemotherapeutic or immunotherapeutic agents is crucial to reduce unwanted side effects. In an effort to develop controlled release strategies that can be triggered by using Cerenkov luminescence, we have developed polymer hydrogels that can release bovine serum albumin and immunoglobulin G by using light (254 nm-375 nm) as a trigger. We describe the synthesis and photochemical characterization of two light sensitive phenacyl bis-azide crosslinkers that are used to prepare transparent self-supporting hydrogel patches. One crosslinker was designed to optimize the overlap with the Cerenkov luminescence emission window, bearing an π-extended phenacyl core, resulting in a high quantum yield (14 %) of photocleavage when irradiated with 375 nm light. We used the extended phenacyl crosslinker for the preparation of protein-loaded dextran hydrogel patches, which showed efficient and selective dosed release of bovine serum albumin or immunoglobulin G after irradiation with 375 nm light. Cerenkov-triggered release is as yet inconclusive due to unexpected side-reactivity. Based on the high quantum yield, efficient release and large overlap with the Cerenkov window, we envision application of these photosensitive soft materials in radiation targeted drug release.

Tuneable Control of Organocatalytic Activity through Host-Guest Chemistry.

Dynamic regulation of chemical reactivity is important in many complex chemical reaction networks, such as cascade reactions and signal transduction processes. Signal responsive catalysts could play a crucial role in regulating these reaction pathways. Recently, supramolecular encapsulation was reported to regulate the activities of artificial catalysts. We present a host-guest chemistry strategy to modulate the activity of commercially available synthetic organocatalysts. The molecular container cucurbit[7]uril was successfully applied to change the activity of four different organocatalysts and one initiator, enabling up- or down-regulation of the reaction rates of four different classes of chemical reactions. In most cases CB[7] encapsulation results in catalyst inhibition, however in one case catalyst activation by binding to CB[7] was observed. The mechanism behind this unexpected behavior was explored by NMR binding studies and pKa measurements. The catalytic activity can be instantaneously switched during operation, by addition of either supramolecular host or competitive binding molecules, and the reaction rate can be predicted with a kinetic model. Overall, this signal responsive system proves a promising tool to control catalytic activity.

Out-of-Equilibrium Colloidal Assembly Driven by Chemical Reaction Networks.

Transient assembled structures play an indispensable role in a wide variety of processes fundamental to living organisms including cellular transport, cell motility, and proliferation. Typically, the formation of these transient structures is driven by the consumption of molecular fuels via dissipative reaction networks. In these networks, building blocks are converted from inactive precursor states to active (assembling) states by (a set of) irreversible chemical reactions. Since the activated state is intrinsically unstable and can be maintained only in the presence of sufficient fuel, fuel depletion results in the spontaneous disintegration of the formed superstructures. Consequently, the properties and behavior of these assembled structures are governed by the kinetics of fuel consumption rather than by their thermodynamic stability. This fuel dependency endows biological systems with unprecedented spatiotemporal adaptability and inherent self-healing capabilities. Fascinated by these unique material characteristics, coupling the assembly behavior to molecular fuel or light-driven reaction networks was recently implemented in synthetic (supra)molecular systems. In this invited feature article, we discuss recent studies demonstrating that dissipative assembly is not limited to the molecular world but can also be translated to building blocks of colloidal dimensions. We highlight crucial guiding principles for the successful design of dissipative colloidal systems and illustrate these with the current state of the art. Finally, we present our vision on the future of the field and how marrying nonequilibrium self-assembly with the functional properties associated with colloidal building blocks presents a promising route for the development of next-generation materials.

Transient supramolecular hydrogels formed by catalytic control over molecular self-assembly.

The present work shows how transient supramolecular hydrogels can be formed by catalytically controlled molecular self-assembly. Catalysis formation of molecular gelators leads the self-assembly along a kinetically favored pathway, resulting in transient hydrogels. This work demonstrates an effective approach towards pathway-dependent supramolecular materials.

Single-molecule functionality in electronic components based on orbital resonances.

In recent years, a wide range of single-molecule devices has been realized, enabled by technological advances combined with the versatility offered by synthetic chemistry. In particular, single-molecule diodes have attracted significant attention with an ongoing effort to increase the rectification ratio between the forward and reverse current. Various mechanisms have been investigated to improve rectification, either based on molecule-intrinsic properties or by engineering the coupling of the molecule to the electrodes. In this perspective, we first provide an overview of the current experimental approaches reported in literature to achieve rectification at the single-molecule level. We then proceed with our recent efforts in this direction, exploiting the internal structure of multi-site molecules, yielding the highest rectification ratio based on a molecule-intrinsic mechanism. We introduce the theoretical framework for multi-site molecules and infer general design guidelines from this. Based on these guidelines, a series of two-site molecules have been developed and integrated into devices. Using two- and three-terminal mechanically controllable break junction measurements, we show that depending on the on-site energies, which are tunable by chemical design, the devices either exhibit pronounced negative differential conductance, or behave as highly-efficient rectifiers. Finally, we propose a design of a single-molecule diode with a theoretical rectification ratio exceeding a million.

Organocatalytic Control over a Fuel-Driven Transient-Esterification Network*.

Signal transduction in living systems is the conversion of information into a chemical change, and is the principal process by which cells communicate. In nature, these functions are encoded in non-equilibrium (bio)chemical reaction networks (CRNs) controlled by enzymes. However, man-made catalytically controlled networks are rare. We incorporated catalysis into an artificial fuel-driven out-of-equilibrium CRN, where the forward (ester formation) and backward (ester hydrolysis) reactions are controlled by varying the ratio of two organocatalysts: pyridine and imidazole. This catalytic regulation enables full control over ester yield and lifetime. This fuel-driven strategy was expanded to a responsive polymer system, where transient polymer conformation and aggregation are controlled through fuel and catalyst levels. Altogether, we show that organocatalysis can be used to control a man-made fuel-driven system and induce a change in a macromolecular superstructure, as in natural non-equilibrium systems.

Conditional Copper-Catalyzed Azide-Alkyne Cycloaddition by Catalyst Encapsulation.

Supramolecular encapsulation is known to alter chemical properties of guest molecules. We have applied this strategy of molecular encapsulation to temporally control the catalytic activity of a stable copper(I)-carbene catalyst. Encapsulation of the copper(I)-carbene catalyst by the supramolecular host cucurbit[7]uril (CB[7]) resulted in the complete inactivation of a copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction. The addition of a chemical signal achieved the near instantaneous activation of the catalyst, by releasing the catalyst from the inhibited CB[7] catalyst complex. To broaden the scope of our on-demand CuAAC reaction, we demonstrated the protein labeling of vinculin with the copper(I)-carbene catalyst, to inhibit its activity by encapsulation with CB[7] and to initiate labeling at any moment by adding a specific signal molecule. Ultimately, this strategy allows for temporal control over copper-catalyzed click chemistry, on small molecules as well as protein targets.

Biomimetic Strain-Stiffening Self-Assembled Hydrogels.

Supramolecular structures with strain-stiffening properties are ubiquitous in nature but remain rare in the lab. Herein, we report on strain-stiffening supramolecular hydrogels that are entirely produced through the self-assembly of synthetic molecular gelators. The involved gelators self-assemble into semi-flexible fibers, which thereby crosslink into hydrogels. Interestingly, these hydrogels are capable of stiffening in response to applied stress, resembling biological intermediate filaments system. Furthermore, strain-stiffening hydrogel networks embedded with liposomes are constructed through orthogonal self-assembly of gelators and phospholipids, mimicking biological tissues in both architecture and mechanical properties. This work furthers the development of biomimetic soft materials with mechanical responsiveness and presents potentially enticing applications in diverse fields, such as tissue engineering, artificial life, and strain sensors.

Hierarchically Compartmentalized Supramolecular Gels through Multilevel Self-Sorting.

Hierarchical compartmentalization through the bottom-up approach is ubiquitous in living cells but remains a formidable task in synthetic systems. Here we report on hierarchically compartmentalized supramolecular gels that are spontaneously formed by multilevel self-sorting. Two types of molecular gelators are formed in situ from nonassembling building blocks and self-assemble into distinct gel fibers through a kinetic self-sorting process; interestingly, these distinct fibers further self-sort into separated microdomains, leading to microscale compartmentalized gel networks. Such spontaneously multilevel self-sorting systems provide a "bottom-up" approach toward hierarchically structured functional materials and may play a role in intracellular organization.

Controlled Fabrication of Micropatterned Supramolecular Gels by Directed Self-Assembly of Small Molecular Gelators.

Herein, the micropatterning of supramolecular gels with oriented growth direction and controllable spatial dimensions by directing the self-assembly of small molecular gelators is reported. This process is associated with an acid-catalyzed formation of gelators from two soluble precursor molecules. To control the localized formation and self-assembly of gelators, micropatterned poly(acrylic acid) (PAA) brushes are employed to create a local and controllable acidic environment. The results show that the gel formation can be well confined in the catalytic surface plane with dimensions ranging from micro- to centimeter. Furthermore, the gels show a preferential growth along the normal direction of the catalytic surface, and the thickness of the resultant gel patterns can be easily controlled by tuning the grafting density of PAA brushes. This work shows an effective "bottom-up" strategy toward control over the spatial organization of materials and is expected to find promising applications in, e.g., microelectronics, tissue engineering, and biomedicine.

Control over the formation of supramolecular material objects using reaction-diffusion.

Controlled diffusion, reaction and assembly of hydrogelator precursors can be used to create soft hydrogel objects of defined shape and size. In this study we show that controlling local reaction kinetics by means of pH, diffusion length and the concentrations of reactants allows control over the dimensions of formed supramolecular structures. By correlating a reaction diffusion model to experimental results, we show that the influence of all these control parameters can be unified using the Damköhler number, thus providing an easy-to-use relation between experimental parameters and structure dimensions. Finally, our study suggests that control over concentration gradients and chemical reactivity in combination with supramolecular chemistry is a promising platform for the design of soft matter objects of defined sizes, a concept that has received little attention up until now.

Access to Metastable Gel States Using Seeded Self-Assembly of Low-Molecular-Weight Gelators.

Here we report on how metastable supramolecular gels can be formed through seeded self-assembly of multicomponent gelators. Hydrazone-based gelators decorated with non-ionic and anionic groups are formed in situ from hydrazide and aldehyde building blocks, and lead through multiple self-sorting processes to the formation of heterogeneous gels approaching thermodynamic equilibrium. Interestingly, the addition of seeds composing of oligomers of gelators bypasses the self-sorting processes and accelerates the self-assembly along a kinetically favored pathway, resulting in homogeneous gels of which the network morphologies and gel stiffness are markedly different from the thermodynamically more stable gel products. Importantly, over time, these metastable homogeneous gel networks are capable of converting into the thermodynamically more stable state. This seeding-driven formation of out-of-equilibrium supramolecular structures is expected to serve as a simple approach towards functional materials with pathway-dependent properties.