Energy propagation throughout chemical networks

Emergent Behavior of a Photoswitchable Solute in a Biphasic Solvent System

Due to thermal E/Z isomerization, hydrazones in solution typically exist in thermodynamic equilibria between their isomers. Irradiation of such solutions leads to photostationary states that may differ from the equilibrium distribution. Operating such switchable hydrazones in a biphasic system of two immiscible solvents introduces three new degrees of freedom: the E/Z equilibrium in the second solvent and two equilibria for distribution of each of the isomers between the solvents. Irradiation of such a system can be performed in three different ways - the first solvent only, the second solvent only, and both solvents at once - all yielding distinct outcomes. Depending on the choice of materials and the mode of irradiation, such setup may lead to different emergent behaviors that are not immediately intuitive, including net cyclic transport or the accumulation of one photoswitched product in one of the phases, beyond what is reachable by irradiating a simple solution of the same photoswitch.

Cell-Like Synthetic Supramolecular Soft Materials Realized in Multicomponent, Non-/Out-of-Equilibrium Dynamic Systems

Living cells are complex, nonequilibrium supramolecular systems capable of independently and/or cooperatively integrating multiple bio-supramolecules to execute intricate physiological functions that cannot be accomplished by individual biomolecules. These biological design strategies offer valuable insights for the development of synthetic supramolecular systems with spatially controlled hierarchical structures, which, importantly, exhibit cell-like responses and functions. The next grand challenge in supramolecular chemistry is to control the organization of multiple types of supramolecules in a single system, thus integrating the functions of these supramolecules in an orthogonal and/or cooperative manner. In this perspective, the recent progress in constructing multicomponent supramolecular soft materials through the hybridization of supramolecules, such as self-assembled nanofibers/gels and coacervates, with other functional molecules, including polymer gels and enzymes is highlighted. Moreover, results show that these materials exhibit bioinspired responses to stimuli, such as bidirectional rheological responses of supramolecular double-network hydrogels, temporal stimulus pattern-dependent responses of synthetic coacervates, and 3D hydrogel patterning in response to reaction-diffusion processes are presented. Autonomous active soft materials with cell-like responses and spatially controlled structures hold promise for diverse applications, including soft robotics with directional motion, point-of-care disease diagnosis, and tissue regeneration.

Progressive Local Accumulation of Self-Assembled Nanoreactors in a Hydrogel Matrix through Repetitive Injections of ATP

Cellular functions are regulated with high spatial control through the local activation of chemical processes in a complex inhomogeneous matrix. The development of synthetic macroscopic systems with a similar capacity allows fundamental studies aimed at understanding the relationship between local molecular events and the emergence of functional properties at the macroscopic level. Here, we show that a kinetically stable inhomogeneous hydrogel matrix is spontaneously formed upon the local injection of ATP. Locally, ATP templates the self-assembly of amphiphiles into large nanoreactors with a much lower diffusion rate compared to unassembled amphiphiles. The local depletion of unassembled amphiphiles near the injection point installs a concentration gradient along which unassembled amphiphiles diffuse from the surroundings to the center. This allows for a progressive local accumulation of self-assembled nanoreactors in the matrix upon repetitive cycles of ATP injection separated by time intervals during which diffusion of unassembled amphiphiles takes place. Contrary to the homogeneous matrix containing the same components, in the inhomogeneous matrix the local upregulation of a chemical reaction occurs. Depending on the way the same amount of injected ATP is administered to the hydrogel matrix different macroscopic distributions of nanoreactors are obtained, which affect the location in the matrix where the chemical reaction is upregulated.

Light-driven dissipative self-assembly of a peptide hydrogel

Light energy provides an attractive fuel source for energy dissipating systems because of the lack of waste production, wavelength tunability and the potential for spatial and temporal resolution. In this work, we describe a peptide-spiropyran conjugate that assembled into a transient nanofiber hydrogel in the presence of visible light, and dissociated when the light source was removed.

Enhanced catalytic activity under non-equilibrium conditions

The development of non-equilibrium synthetic systems provides access to innovative materials with life-like properties. Non-equilibrium systems require a continuous input of energy to retain their functional state, which makes for a fundamental difference to systems that operate at thermodynamic equilibrium. Kinetic asymmetry in the energy consumption pathway is required to drive systems out of equilibrium. This understanding has permitted chemists to design dissipative synthetic molecular machines and high-energy materials. Here we show that kinetic asymmetry also emerges at the macroscopic level by demonstrating that local energy delivery in the form of light to a hydrogel containing gold nanoparticles installs a non-equilibrium steady state. The instalment and maintenance of the macroscopic non-equilibrium state is facilitated by the gel matrix in which motion is governed by diffusion rather than convection. The non-equilibrium state is characterized by a persistent gradient in the surface composition of the nanoparticles embedded in the gel, which affects the fluorescent and catalytic properties of the system. We show that the overall catalytic performance of the system is enhanced under these non-equilibrium conditions. In perspective it will be possible to develop out-of-equilibrium matrices in which functional properties emerge as a result of spatially controlled energy delivery and spatially controlled chemistries.

Light-controlled switchable complexation by a non-photoresponsive hydrogen-bonded amide macrocycle

A light controlled switchable host–guest system based on a non-photoresponsive H-bonded macrocycle and pyridinium salts was developed using a photoacid.

A chemically encoded timer for dual molecular delivery at tailored ranges and concentrations

Spatiotemporal control of molecular distribution is much in demand in many fields of chemistry. To address this goal, we exploit a low molecular weight branched self-immolative architecture, which acts as a triggerable chemically encoded timer for autonomous sequential release of two chemicals. Using a light-activated model liberating two distinct fluorophores, we generated a tunable spatially contrasted molecular distribution.

Do dihydroxymagnesium carboxylates form Grignard-type reagents? A theoretical investigation on decarboxylative fragmentation

Dihydroxymagnesium carboxylates [(OH)₂MgO₂CR] were probed for decarboxylation on a theoretical level, by utilizing both Møller-Plesset perturbation theory (MP2) and density functional theory (B3LYP-DFT) computations. This study is connected to the question of whether this recently introduced, astrobiologically relevant chemical class may form Grignard-type reagent molecules. To extract trends for a broad molecular mass range, different linear alkyl chain lengths between C₄ and C₁₁ were computed. The forward energy barrier for decarboxylation reactions increases linearly as a function of the ligand's chain length. Decarboxylation-type fragmentations of these organomagnesium compounds seem to be improbable in non-catalytic, low energetic environments. A high forward energy barrier (E_MP2 > 55 kcal mol^-1) towards a described transition state restricts the release of CO₂. Nevertheless, we propose the release of CO₂ on a theoretical level, as been revealed via an intramolecular nucleophilic attack mechanism. Once the challenging transition state for decarboxylation is overcome, a stable Mg-C bond is formed. These mechanistic insights were gained by help of natural bond orbital analysis. The Cα atom (first carbon atom in the ligand chain attached to the carboxyl group) is thought to prefer binding towards the electrophilic magnesium coordination center, rather than towards the electrophilic CO₂-carbon atom. Additionally, the putatively formed Grignard-type OH-bearing product molecules possess a more polarized Mg-C bond in comparison to RMgCl species. Therefore, carbanion formation from OH-bearing Grignard-type molecules is made feasible for triggering C-C bond formation reactions. Graphical abstract This study asks whether recently introduced, astrobiologically dihydroxymagnesium carboxylates form Grignard-type reagent molecules via decarboxylative fragmentation.

Proton gradients and pH oscillations emerge from heat flow at the microscale

Proton gradients are essential for biological systems. They not only drive the synthesis of ATP, but initiate molecule degradation and recycling inside lysosomes. However, the high mobility and permeability of protons through membranes make pH gradients very hard to sustain in vitro. Here we report that heat flow across a water-filled chamber forms and sustains stable pH gradients. Charged molecules accumulate by convection and thermophoresis better than uncharged species. In a dissociation reaction, this imbalances the reaction equilibrium and creates a difference in pH. In solutions of amino acids, phosphate, or nucleotides, we achieve pH differences of up to 2 pH units. The same mechanism cycles biomolecules by convection in the created proton gradient. This implements a feedback between biomolecules and a cyclic variation of the pH. The finding provides a mechanism to create a self-sustained proton gradient to drive biochemical reactions.

Emergence of a New Self-Replicator from a Dynamic Combinatorial Library Requires a Specific Pre-Existing Replicator

Our knowledge regarding the early steps in the formation of evolvable life and what constitutes the minimal molecular basis of life remains far from complete. The recent emergence of systems chemistry reinvigorated the investigation of systems of self-replicating molecules to address these questions. Most of these studies focus on single replicators and the effects of replicators on the emergence of other replicators remains under-investigated. Here we show the cross-catalyzed emergence of a novel self-replicator from a dynamic combinatorial library made from a threonine containing peptide building block, which, by itself, only forms trimers and tetramers that do not replicate. Upon seeding of this library with different replicators of different macrocycle size (hexamers and octamers), we observed the emergence of hexamer replicator consisting of six units of the threonine peptide only when it is seeded with an octamer replicator containing eight units of a serine building block. These results reveal for the first time how a new replicator can emerge in a process that relies critically on the assistance by another replicator through cross-catalysis and that replicator composition is history dependent.

Redox Control over Acyl Hydrazone Photoswitches

Photoisomerization provides a clean and efficient way of reversibly altering physical properties of chemical systems and injecting energy into them. These effects have been applied in development of systems such as photoresponsive materials, molecular motors, and photoactivated drugs. Typically, switching from more to less stable isomer(s) is performed by irradiation with UV or visible light, while the reverse process proceeds thermally or by irradiation using another wavelength. In this work we developed a method of rapid and tunable Z→E isomerization of C═N bond in acyl hydrazones, using aromatic thiols as nucleophilic catalysts. As thiols can be oxidized into catalytically inactive disulfides, the isomerization rates can be controlled via the oxidation state of the catalyst, which, together with the UV irradiation, provides orthogonal means to control the E/Z state of the system. As a proof of this concept, we have applied this method to control the diversity of acyl hydrazone based dynamic combinatorial libraries.

Antiparallel Dynamic Covalent Chemistries

The ability to design reaction networks with high, but addressable complexity is a necessary prerequisite to make advanced functional chemical systems. Dynamic combinatorial chemistry has proven to be a useful tool in achieving complexity, however with some limitations in controlling it. Herein we introduce the concept of antiparallel chemistries, in which the same functional group can be channeled into one of two reversible chemistries depending on a controllable parameter. Such systems allow both for achieving complexity, by combinatorial chemistry, and addressing it, by switching from one chemistry to another by controlling an external parameter. In our design the two antiparallel chemistries are thiol-disulfide exchange and thio-Michael addition, sharing the thiol as the common building block. By means of oxidation and reduction the system can be reversibly switched from predominantly thio-Michael chemistry to predominantly disulfide chemistry, as well as to any intermediate state. Both chemistries operate in water, at room temperature, and at mildly basic pH, which makes them a suitable platform for further development of systems chemistry.

Transient self-assembly of molecular nanostructures driven by chemical fuels

Over the past decades, chemists have mastered the art of assembling small molecules into complex nanostructures using non-covalent interactions. The driving force for self-assembly is thermodynamics: the self-assembled structure is more stable than the separate components. However, biological self-assembly processes are often energetically uphill and require the consumption of chemical energy. This allows nature to control the activation and duration of chemical functions associated with the assembled state. Synthetic chemical systems that operate in the same way are essential for creating the next generation of intelligent, adaptive materials, nanomachines and delivery systems. This review focuses on synthetic molecular nanostructures which self-assemble under dissipative conditions. The chemical function associated with the transient assemblies is operational as long as chemical fuel is present.

Fluctuations in reactive networks subject to extrinsic noise studied in the framework of the chemical Langevin equation

Theoretical and experimental studies have shown that the fluctuations of in vivo systems break the fluctuation-dissipation theorem. One can thus ask what information is contained in the correlation functions of protein concentrations and how they relate to the response of the reactive network to a perturbation. Answers to these questions are of prime importance to extract meaningful parameters from the in vivo fluorescence correlation spectroscopy data. In this paper we study the fluctuations of the concentration of a reactive species involved in a cyclic network that is in a nonequilibrium steady state perturbed by a noisy force, taking into account both the breaking of detailed balance and extrinsic noises. Using a generic model for the network and the extrinsic noise, we derive a chemical Langevin equation that describes the dynamics of the system, we determine the expressions of the correlation functions of the concentrations, and we estimate the deviation of the fluctuation-dissipation theorem and the range of parameters in which an effective temperature can be defined.

Dual stimuli-induced formation of a μ-hydroxido bridged [Zn9L5(μ-OH)6]12+ half-pipe

Low-symmetry metal–organic architectures that feature unusual binding motifs are useful for exploring new modes of guest recognition.

Low-symmetry metal–organic architectures that feature unusual binding motifs are useful for exploring new modes of guest recognition. Such structures remain difficult to create using current rational design principles. One approach to constructing such architectures is to employ ligands with coordination vectors oriented to preclude the formation of simple, low nuclearity molecular assemblies upon complexation to metal ions. Here we report two new supramolecular assemblies generated from such a ligand: a simple metastable [Zn₃L₃]⁶⁺ assembly, which was observed to convert to a more complex [Zn₉L₅(μ-OH)₆]¹²⁺ twisted half-pipe architecture. Two chemically distinct stimuli—an anionic template and a base—must be applied for the conversion to occur. Perchlorate, perrhenate, trifluoromethanesulfonate and 2-naphthalenesulfonate were found to act as competent templates for the [Zn₉L₅(μ-OH)₆]¹²⁺ structure.

An Autocatalytic System of Photooxidation-Driven Substitution Reactions on a Fe(II)4L6 Cage Framework

The functions of life are accomplished by systems exhibiting nonlinear kinetics: autocatalysis, in particular, is integral to the signal amplification that allows for biological information processing. Novel synthetic autocatalytic systems provide a foundation for the design of artificial chemical networks capable of carrying out complex functions. Here we report a set of Fe(II)4L6 cages containing BODIPY chromophores having tuneable photosensitizing properties. Electron-rich anilines were observed to displace electron-deficient anilines at the dynamic-covalent imine bonds of these cages. When iodoaniline residues were incorporated, heavy-atom effects led to enhanced (1)O2 production. The incorporation of (methylthio)aniline residues into a cage allowed for the design of an autocatalytic system: oxidation of the methylthio groups into sulfoxides make them electron-deficient and allows their displacement by iodoanilines, generating a better photocatalyst and accelerating the reaction.

Coupled Oscillations and Circadian Rhythms in Molecular Replication Networks

Living organisms often display rhythmic and oscillatory behavior. We investigate here a challenge in contemporary Systems Chemistry, that is, to construct "bottom-up" molecular networks that display such complex behavior. We first describe oscillations during self-replication by applying kinetic parameters relevant to peptide replication in an open environment. Small networks of coupled oscillators are then constructed in silico, producing various functions such as logic gates, integrators, counters, triggers, and detectors. These networks are finally utilized to simulate the connectivity and network topology of the Kai proteins circadian clocks from the S. elongatus cyanobacteria, thus producing rhythms whose constant frequency is independent of the input intake rate and robust toward concentration fluctuations. We suggest that this study helps further reveal the underlying principles of biological clocks and may provide clues into their emergence in early molecular evolution.

Chemical reactivity drives spatiotemporal organisation of bacterial metabolism

In this review, we examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects.