Selenium catalysis enables negative feedback organic oscillators

Abstract

The construction of materials regulated by chemical reaction networks requires regulatory motifs that can be stacked together into systems with desired properties. Multiple autocatalytic reactions producing thiols are known. However, negative feedback loop motifs are unavailable for thiol chemistry. Here, we develop a negative feedback loop based on the selenocarbonates. In this system, thiols induce the release of aromatic selenols that catalyze the oxidation of thiols by organic peroxides. This negative feedback loop has two important features. First, catalytic oxidation of thiols follows Michaelis-Menten-like kinetics, thus increasing nonlinearity for the negative feedback. Second, the strength of the negative feedback can be tuned by varying substituents in selenocarbonates. When combined with the autocatalytic production of thiols in a flow reactor, this negative feedback loop induces sustained oscillations. The availability of this negative feedback motif enables the future construction of oscillatory, homeostatic, adaptive, and other regulatory circuits in life-inspired systems and materials.

Fig. 1. Network topologies.

The difference in network topologies of all previously published oscillators based on small organic molecules (a) and oscillators presented in this work (b). Red, blue, and green colors represent autocatalysts, substrates, and inhibitors correspondingly. Sharp arrows represent activation; dull arrows represent inhibition.

Fig. 2. Generic mechanism for the oxidation of thiols catalyzed by selenols.

The scheme neglects mixed seleno-sulfide (RSSeR) and other intermediates of selenide oxidation.

Fig. 3. Selenium derivatives used in this study and their reactions with thiols.

a Derivatives of 4-carboxyselenophenol that were used as catalysts in this study. b Reaction of selenocarbonates 3–5 with 6 and its kinetics. Second-order rate constants are calculated based on three independent ¹H NMR kinetic measurements (Supplementary Figs. 5–7). Errors represent standard deviations based on three independent experiments.

Fig. 4. Selenium-catalyzed oxidation-based oscillators.

a A schematic representation of the CSTR experimental set-up and the downstream derivatization with Ellman’s reagent. The UV–Vis spectrometer detects the absorption of 4-nitro-3-carboxythiophenolate at 412 nm. b The reaction networks of selenium-catalyzed oxidation-based oscillators. The scheme describes oscillators with negative feedback consisting of the thiol-induced release of 7 from 3, 4, or 5. The oscillator with catalyst 2 has 2 in place of 7 and does not have a closed negative feedback loop. Colors represent key elements of the oscillatory network: blue—substrates, red—autocatalysts, and green – inhibitor. Bold plus and minus signs represent positive and negative feedback loops correspondingly.

Fig. 5. Kinetic studies of the oscillators.

Experimental conditions shared by all experiments: H₂O, 1 M Tris-buffer pH 7.7, at 25 °C; other parameters are indicated for specific experiments. a. Experimental data showing sustained oscillations in the system with catalyst 2. [8] = 64 mM; [9] = 114 mM; [1] = 83.2 mM; [2] = 0.14 mM; f/V = 1.46·10⁻³ s⁻¹. b. Experimental data showing sustained oscillations in the system with catalyst 3. [8] = 56 mM; [9] = 100 mM; [1] = 72.8 mM; [3] = 0.5 mM; f/V = 1.67·10⁻³s⁻¹ c. Experimental data showing sustained oscillations in the system with catalyst 4. [8] = 56 mM; [9] = 100 mM; [1] = 72.8 mM; [4] = 1 mM; f/V = 1.67·10⁻³s⁻¹ d. Experimental data showing sustained oscillations in the system with catalyst 5. [8] = 56 mM; [9] = 100 mM; [1] = 72.8 mM; [5] = 2 mM; f/V = 1.67^.10⁻³s⁻¹. RSH stands for the sum of the concentrations of all three thiols in the system. Chemical structures of catalysts 2-4 are shown above corresponding plots.

Fig. 6. Kinetic studies of the oxidation of 6 by 1 catalyzed by 2. [Se] = 2^.[2].

All experiments were conducted in 1 M Tris pH 7.5, at 25 °C. a Dependence of the reaction rate from [Se]. [1] = 7.5 mM, [6] = 5 mM, [Se] = 0.1–1 mM. The dependence in logarithmic coordinates was fit linearly by equation y = a + bx; a = −3.0 ± 0.2, b = 0.84 ± 0.02. b Dependence of the reaction rate on the concentration of 6 in experiments with different [Se] concentrations. [1] = 7.5 mM, [6] = 0.5–10 mM, [Se] are shown above each graph. Data for each set were fitted by equation r = V_max^.S/(K_M + S): [Se] = 0.05 mM, V_max = 1.5 ± 0.1·10⁻⁵M s⁻¹, K_M = 7.8 ± 1.6·10⁻⁴ M; [Se] = 0.1 mM, V_max = 2.8 ± 0.2·10⁻⁵M s⁻¹, K_M = 11 ± 1.6·10⁻⁴M; [Se] = 0.2 mM, V_max = 4.5 ± 0.2·10⁻⁵M s⁻¹, K_M = 8.4 ± 1.5·10⁻⁴M. (See Supplementary Fig. 11 for the full range of [Se].) c Dependence of the reaction rate on the concentration of 6 in experiments with different concentrations of 1. [Se] = 0.2 mM, [6] = 0.5–10 mM, [1] is shown above each graph. Data for each set were fitted by equation r = V_max^.S/(K_M + S): [1] = 3 mM, V_max = 1.9 ± 0.1·10^-5M s⁻¹, K_M = 3.8 ± 0.8^.10^-4M; [1] = 7.5 mM, V_max = 4.5 ± 0.2^.10⁻⁵ M s⁻¹, K_M = 8.4 ± 1.5·10⁻⁴M; [1] = 12 mM, V_max = 6.9 ± 0.3·10⁻⁵M s⁻¹, K_M = 14.5 ± 1.0·10⁻⁴M. d Inhibition of the reaction by [9]. [1] = 7.5 mM, [6] = 5 mM, [Se] = 0.2 mM, [9] = 0–100 mM. Data were fitted by equation y = 2.2·10⁻⁷/(0.006 + ax), a = 0.11 ± 0.01. Error bars in all plots represent standard deviations based on three independent experiments.

Fig. 7. Mechanistic proposal.

Proposed mechanism for the oxidation of thiols with tert-butyl hydroperoxide catalyzed by selenophenoles.

Fig. 8. Kinetic studies of the oxidation of thiocholine by 1 catalyzed by 2. [Se] = 2^.[2].

All experiments were conducted in 1 M Tris pH 7.5, at 25 ^oC, [Se] = 0.2 mM, [1] = 7.5 mM, [thiocholine] = 0.5–10 mM. Data were fitted by equation r = V_max^.S/(K_M + S): V_max = 3.73 ± 0.08^.10⁻⁵M s⁻¹, K_M = 7.8 ± 2.2·10⁻⁵M. This fitting is approximate because the rate of catalytic oxidation showed no significant drop even at 0.5 mM concentration of thiocholine, and lowering the concentration even more is experimentally challenging. Nevertheless, the data show clearly that K_M for thiocholine oxidation is significantly lower than for oxidation of 6. Error bars represent standard deviations based on three independent experiments.

Fig. 9. Modeling of the oscillators.

a Simulations of the oscillations with catalyst 2. The concentrations of reagents and the flow rate are as in the experiment shown in Fig. 4a. b Simulations of the oscillations with catalyst 5. The concentrations of reagents and the flow rate are as in the experiment shown in Fig. 4d. Details of the model and the rate constants used can be found in Section 6 of Supplementary Information. RSH stands for the sum of concentrations of all three thiols in the system.