Parasitic behavior in competing chemically fueled reaction cycles

Suppressing catalyst poisoning in the carbodiimide-fueled reaction cycle

In biology, cells regulate the function of molecules using catalytic reaction cycles that convert reagents with high chemical potential (fuel) to waste molecules. Inspired by biology, synthetic analogs of such chemical reaction cycles have been devised, and a widely used catalytic reaction cycle uses carboxylates as catalysts to accelerate the hydration of carbodiimides. The cycle is versatile and easy to use, so it is widely applied to regulate motors, pumps, self-assembly, and phase separation. However, the cycle suffers from side reactions, especially the formation of N-acylurea. In catalytic reaction cycles, side reactions are disastrous as they decrease the fuel's efficiency and, more importantly, destroy the molecular machinery or assembling molecules. Therefore, this work tested how to suppress N-acylurea by screening precursor concentration, its structure, carbodiimide structure, additives, temperature, and pH. It turned out that the combination of low temperature, low pH, and 10% pyridine as a fraction of the fuel could significantly suppress the N-acylurea side product and keep the reaction cycle highly effective to regulate successful assembly. We anticipate that our work will provide guidelines for using carbodiimide-fueled reaction cycles to regulate molecular function and how to choose optimal conditions.

Prolinyl Nucleotides Drive Enzyme-Free Genetic Copying of RNA

Proline is one of the proteinogenic amino acids. It is found in all kingdoms of life. It also has remarkable activity as an organocatalyst and is of structural importance in many folded polypeptides. Here, we show that prolinyl nucleotides with a phosphoramidate linkage are active building blocks in enzyme- and ribozyme-free copying of RNA in the presence of monosubstituted imidazoles as organocatalysts. Both dinucleotides and mononucleotides are incorporated at the terminus of RNA primers in aqueous buffer, as instructed by the template sequence, in up to eight consecutive extension steps. Our results show that condensation products of amino acids and ribonucleotides can act like nucleoside triphosphates in media devoid of enzymes or ribozymes. Prolinyl nucleotides are metastable building blocks, readily activated by catalysts, helping to explain why the combination of α-amino acids and nucleic acids was selected in molecular evolution.

Chemically Fueled Supramolecular Materials

In biology, the function of many molecules is regulated through nonequilibrium chemical reaction cycles. The prototypical example is the phosphorylation of an amino acid in an enzyme which induces a functional change, e.g., it folds or unfolds, assembles or disassembles, or binds a substrate. Such phosphorylation does not occur spontaneously but requires a phosphorylating agent with high chemical potential (for example, adenosine triphosphate (ATP)) to be converted into a molecule with lower chemical potential (adenosine diphosphate (ADP)). When this energy is used to regulate an assembly, we speak of chemically fueled assemblies; i.e., the molecule with high potential, the fuel, is used to regulate a self-assembly process. For example, the binding of guanosine triphosphate (GTP) to tubulin induces self-assembly. The bound GTP is hydrolyzed to guanosine diphosphate (GDP) upon assembly, which induces tubulin disassembly. The result is a dynamic assembly endowed with unique characteristics, such as time-dependent behavior and the ability to self-heal. These intriguing, unique properties have inspired supramolecular chemists to create similar chemically fueled molecular assemblies from the bottom up. While examples have been designed, they remain scarce partly because chemically fueled reaction cycles are rare and often complex. Thus, we recently developed a carbodiimide-driven reaction cycle that is versatile and easy to use, quantitatively understood, and does not suffer from side reactions. In the reaction cycle, a carboxylate precursor reacts with a carbodiimide to form an activated species like an anhydride or ester. The activated state reacts with water and thereby reverts to its precursor state; i.e., the activated state is deactivated. Effectively, the precursor catalyzes carbodiimides' conversion into waste and forms a transient activated state. We designed building blocks to regulate a range of assemblies and supramolecular materials at the expense of carbodiimide fuel. The simplicity and versatility of the reaction cycles have democratized and popularized the field of chemically fueled assemblies. In this Account, we describe what we have "learned" on our way. We introduce the field exemplified by biological nonequilibrium self-assembly. We describe the design of the carbodiimide-driven reaction cycle. Using examples from our group and others, we offer design rules for the building block's structure and strategies to create the desired morphology or supramolecular materials. The discussed morphologies include fibers, colloids, crystals, and oil- and coacervate-based droplets. We then demonstrate how these assemblies form supramolecular materials with unique material properties like the ability to self-heal. Besides, we discuss the concept of reciprocal coupling in which the assembly exerts feedback on its reaction cycle and we also offer examples of such feedback mechanisms. Finally, we close the Account with a discussion and an outlook on this field. This Account aims to provide our fundamental understanding and facilitate further progress toward conceptually new supramolecular materials.

Chemical Kinetics and Mass Action in Coexisting Phases

The kinetics of chemical reactions are determined by the law of mass action, which has been successfully applied to homogeneous, dilute mixtures. At nondilute conditions, interactions among the components can give rise to coexisting phases, which can significantly alter the kinetics of chemical reactions. Here, we derive a theory for chemical reactions in coexisting phases at phase equilibrium. We show that phase equilibrium couples the rates of chemical reactions of components with their diffusive exchanges between the phases. Strikingly, the chemical relaxation kinetics can be represented as a flow along the phase equilibrium line in the phase diagram. A key finding of our theory is that differences in reaction rates between coexisting phases stem solely from phase-dependent reaction rate coefficients. Our theory is key to interpreting how concentration levels of reactive components in condensed phases control chemical reaction rates in synthetic and biological systems.

Carbodiimide-fueled catalytic reaction cycles to regulate supramolecular processes

Using molecular self-assembly, supramolecular chemists can create Gigadalton-structures with angstrom precision held together by non-covalent interactions. However, despite relying on the same molecular toolbox for self-assembly, these synthetic structures lack the complexity and sophistication of biological assemblies. Those assemblies are non-equilibrium structures that rely on the constant consumption of energy transduced from the hydrolysis of chemical fuels like ATP and GTP, which endows them with dynamic properties, e.g., temporal and spatial control and self-healing ability. Thus, to synthesize life-like materials, we have to find a reaction cycle that converts chemical energy to regulate self-assembly. We and others recently found that this can be done by a reaction cycle that hydrates carbodiimides. This feature article aims to provide an overview of how the energy transduced from carbodiimide hydration can alter the function of molecules and regulate molecular assemblies. The goal is to offer the reader design considerations for carbodiimide-driven reaction cycles to create a desired morphology or function of the assembly and ultimately to push chemically fueled self-assembly further towards the bottom-up synthesis of life.

Spatiotemporal dynamics of self-assembled structures in enzymatically induced agonistic and antagonistic conditions

Predicting and designing systems with dynamic self-assembly properties in a spatiotemporal fashion is an important research area across disciplines ranging from understanding the fundamental non-equilibrium features of life to the fabrication of next-generation materials with life-like properties. Herein, we demonstrate a spatiotemporal dynamics pattern in the self-assembly behavior of a surfactant from an unorganized assembly, induced by adenosine triphosphate (ATP) and enzymes responsible for the degradation or conversion of ATP. We report the different behavior of two enzymes, alkaline phosphatase (ALP) and hexokinase (HK), towards adenosine triphosphate (ATP)-driven surfactant assembly, which also results in contrasting spatiotemporal dynamic assembly behavior. Here, ALP acts antagonistically, resulting in transient self-assemblies, whereas HK shows agonistic action with the ability to sustain the assemblies. This dynamic assembly behavior was then used to program the time-dependent emergence of a self-assembled structure in a two-dimensional space by maintaining concentration gradients of the enzymes and surfactant at different locations, demonstrating a new route for obtaining 'spatial' organizational adaptability in a self-organized system of interacting components for the incorporation of programmed functionality.

Droplet Formation by Chemically Fueled Self-Assembly: The Role of Precursor Hydrophobicity

We investigate active droplets that form at the expense of a chemical fuel in aqueous buffer and vanish autonomously. Dynamic light scattering reveals the scattered intensity, the hydrodynamic radius, and the width of the size distribution with high precision as well as high temporal and spatial resolutions. Comparing the resulting time-dependent behavior of the droplet characteristics with the time-dependent concentration of the anhydrides, the roles of the chemical reaction cycle and of colloidal growth processes are elucidated. The droplet sizes and lifetimes depend strongly on the hydrophobicity of the precursor, and the growth rate is found to correlate with the deactivation rate of the product.

Space and Time Crystal Engineering in Developing Futuristic Chemical Technology

In the coming years, multipurpose catalysts for delivering different products under the same chemical condition will be required for developing smart devices for industrial or household use. In order to design such multipurpose devices with two or more specific roles, we need to incorporate a few independent but externally controllable catalytically active centers. Through space crystal engineering, such an externally controllable multipurpose MOF-based photocatalyst could be designed. In a chemical system, a few mutually independent secondary reaction cycles nested within the principal reaction cycle can be activated externally to yield different competitive products. Each reaction cycle can be converted into a time crystal, where the time consuming each reaction step could be converted as an event and all the reaction steps or events could be connected by a circle to build a time crystal. For fractal reaction cycles, a time polycrystal can be generated. By activating a certain fractal event based nested time crystal branch, we can select one of the desired competitive products according to our needs. This viewpoint intends to bring together the ideas of (spatial) crystal engineering and time crystal engineering in order to make use of the time–space arrangement in reaction–catalysis systems and introduce new aspects to futuristic chemical engineering technology.

Chemically fueled materials with a self-immolative mechanism: transient materials with a fast on/off response

There is an increasing demand for transient materials with a predefined lifetime like self-erasing temporary electronic circuits or transient biomedical implants. Chemically fueled materials are an example of such materials; they emerge in response to chemical fuel, and autonomously decay as they deplete it. However, these materials suffer from a slow, typically first order decay profile. That means that over the course of the material's lifetime, its properties continuously change until it is fully decayed. Materials that have a sharp on-off response are self-immolative ones. These degrade rapidly after an external trigger through a self-amplifying decay mechanism. However, self-immolative materials are not autonomous; they require a trigger. We introduce here materials with the best of both, i.e., materials based on chemically fueled emulsions that are also self-immolative. The material has a lifetime that can be predefined, after which it autonomously and rapidly degrades. We showcase the new material class with self-expiring labels and drug-delivery platforms with a controllable burst-release.

Spinodal decomposition of chemically fueled polymer solutions

Out-of-equilibrium phase transitions driven by dissipation of chemical energy are a common mechanism for morphological organization and temporal programming in biology. Inspired by this, dissipative self-assembly utilizes chemical reaction networks (CRNs) that consume high-energy molecules (chemical fuels) to generate transient structures and functionality. While a wide range of chemical fuels and building blocks are now available for chemically fueled systems, so far little attention has been paid to the phase-separation process itself. Herein, we investigate the chemically fueled spinodal decomposition of poly(norbornene dicarboxylic acid) (PNDAc) solution, which is driven by a cyclic chemical reaction network. Our analysis encompasses both the molecular level in terms of the CRN, but also the phase separation process. We investigate the morphology of formed domains, as well as the kinetics and mechanism of domain growth, and develop a kinetic/thermodynamic hybrid model to not only rationalize the dependence of the system on fuel concentration and pH, but also open pathways towards predictive design of future fueled polymer systems.