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.

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Catalysis is an essential function in living systems and provides a way to control complex reaction networks. In natural out-of-equilibrium chemical reaction networks (CRNs) driven by the consumption of chemical fuels, enzymes provide catalytic control over pathway kinetics, giving rise to complex functions. Catalytic regulation of man-made fuel-driven systems is far less common and mostly deals with enzyme catalysis instead of synthetic catalysts. Here, we showviasimulations, illustrated by literature examples, how any catalyst can be incorporated in a non-equilibrium CRN and what their effect is on the behavior of the system. Alteration of the catalysts' concentrations in batch and flow gives rise to responses in maximum conversion, lifetime (i.e.product half-lives andt90 - time to recover 90% of the reactant) and steady states.In situup or downregulation of catalysts' levels temporarily changes the product steady state, whereas feedback elements can give unusual concentration profiles as a function of time and self-regulation in a CRN. We show that simulations can be highly effective in predicting CRN behavior. In the future, shifting the focus from enzyme catalysis towards small molecule and metal catalysis in out-of-equilibrium systems can provide us with new reaction networks and enhance their application potential in synthetic materials, overall advancing the design of man-made responsive and interactive systems.

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The entire research described in this thesis is part of the larger field of Systems Chemistry. This field of chemistry deals with the understanding of the complexity of biology by mimicking biochemical reaction networks with emergent properties attributed to the entire system. In particular, this research focuses on the design of artificial non-equilibrium chemical reaction networks (CRNs) inspired by signal transduction pathways in living organisms. Specific attention is given to catalysis in such networks. For the design of the catalytic CRNs, organocatalysts are considered as the ideal candidates as they are simple, cheap, recyclable and robust compared to enzymes and frequently less toxic catalysts than metals. On top of that, since organocatalysts can operate under mild conditions, it can pave the way for future applications in biological environments.@en

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.

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Acylhydrazones formation has been widely applied in materials science and biolabeling. However, their sluggish condensation rate under neutral conditions limits its application. Herein, indolines with electron-donating groups are reported as a new catalyst scaffold, which can catalyze acylhydrazone, hydrazone, and oxime formation via an iminium ion intermediate. This new type of catalyst showed up to 15-fold rate enhancement over the traditional aniline-catalyzed reaction at neutral conditions. The identified indoline catalyst was successfully applied in hydrogel formation.

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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.

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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.

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Enzymes are supreme catalysts when it comes to high enantiopurities and their immobilization will pave the way for continuous operation. In this context, we show the covalent immobilization of hydroxynitrile lyases HbHNL (from Hevea brasiliensis) and MeHNL (from Manihot esculenta) in a siliceous monolithic microreactor for continuous operation. A thorough characterization of the immobilized HNLs on mesoporous silicates indicated the conditions essential for a successful immobilization. Their application in a continuous flow system enabled a remarkably fast (3.2 min) production of chiral cyanohydrins with high conversion (97%) and high ee (98%) using minimal enzyme loading (STY = 71 g L ^-1 h ^-1 mg _protein ^-1 ). MeHNL showed increased operational stability, possibly due to a structural difference. The continuous flow microreactor outperformed batch systems, demonstrating the advantage of the mesoporous/macroporous environment for the expression of enzyme activity and the favorable characteristics of the microreactor. Overall, the system shows great potential for future industrial application of biocatalytic asymmetric syntheses.

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In the main text, a citation to Ref 55 has been changed to Ref 182 (and vice versa). In the Supplementary information, corrections were made to reactions 16–18, and Refs 4, 5 and 42. Compounds numbers in the text have been styled to emphasize they represent chemical species..

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Even though enzymes are the cornerstones of living systems, it has so far proven difficult to deploy artificial catalysts in a biological setting. Organocatalysts are arguably well-suited artificial catalysts for this purpose because, compared with enzymes and inorganic catalysts, they are simpler, often less toxic and widely accessible. This Review describes how organocatalysts that operate in aqueous media might enable us to selectively access new chemical transformations and provide new possibilities for chemical biology and biomedicine. Organocatalysts can be categorized according to the mechanisms by which they activate substrates, drawing comparisons with enzymes. We describe the characteristics of a catalyst that are necessary for biological compatibility and in vivo applicability, and use these to evaluate a selection of organocatalytic reactions. The attributes of the catalyst (such as functional groups and pK_a values) and the reaction (such as the microenvironment surrounding intermediates) are key considerations when developing efficient organocatalysis in aqueous media. Although we only know of a limited set of organocatalytic reactions with biological potential, on the basis of recent developments we expect a bright future for organocatalysis in biology, to the benefit of chemical biology and biomedicine.

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Rhodococcus strains are ubiquitous in nature and known to metabolise a wide variety of compounds. At the same time, asymmetric reduction of C=C bonds is important in the production of high-valued chiral building blocks. In order to evaluate if Rhodococci can be used for this task, we have probed several Rhodococcus rhodochrous and R. erythropolis strains for ene-reductase activity. A series of substrates including activated ketones, an aldehyde, an imide and nitro-compound were screened using whole cells of seven Rhodococcus strains. This revealed that whole cells of all Rhodococcus strains showed apparent (S)-selectivity towards ketoisophorone, while most other organisms show (R)-selectivity for this compound. Three putative ene-reductases from R. rhodochrous ATCC 17895 were heterologously expressed in Escherichia coli. One protein was purified and its biocatalytic and biochemical properties were characterised, showing typical (enantioselective) properties for class 3 ene-reductases of the old yellow enzyme family.

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