Development of a Five-Chemical-Probe Method to Determine Multiple Radicals Simultaneously in Hydroxyl and Sulfate Radical-Mediated Advanced Oxidation Processes

Advanced oxidation processes (AOPs), such as hydroxyl radical (HO•)- and sulfate radical (SO4•-)-mediated oxidation, are attractive technologies used in water and wastewater treatments. To evaluate the treatment efficiencies of AOPs, monitoring the primary radicals (HO• and SO4•-) as well as the secondary radicals generated from the reaction of HO•/SO4•- with water matrices is necessary. Therefore, we developed a novel chemical probe method to examine five key radicals simultaneously, including HO•, SO4•-, Cl•, Cl2•-, and CO3•-. Five probes, including nitrobenzene, para-chlorobenzoic acid, benzoic acid, 2,4,6-trimethylbenzoic acid, and 2,4,6-trimethylphenol, were selected in this study. Their bimolecular reaction rate constants with diverse radicals were first calibrated under the same conditions to minimize systematic errors. Three typical AOPs (UV/H2O2, UV/S2O82-, and UV/HSO5-) were tested to obtain the radical steady-state concentrations. The effects of dissolved organic matter, Br-, and the probe concentration were inspected. Our results suggest that the five-probe method can accurately measure radicals in the HO•- and SO4•--mediated AOPs when the concentration of Br- and DOM are less than 4.0 μM and 15 mgC L-1, respectively. Overall, the five-probe method is a practical and easily accessible method to determine multiple radicals simultaneously.

Investigation of Flame Structures of Double-Base Propellant and Modified Double-Base Propellant Containing Nitramine Using OH-PLIF and Kinetic Simulation

The combustion behavior of various propellant samples, including double-base propellants, pressed nitramine powders, and modified double-base propellants containing nitramine, was examined using OH-PLIF technology. The combustion process took place within a combustion chamber, and images capturing the flame at the moment of stable combustion were selected for further analysis. The distribution and production rate of OH radicals in both the double-base propellant and the nitramine-modified double-base propellant were simulated using Chemkin-17.0 software. The outcomes from both the experimental and simulation studies revealed that the concentration of OH radicals increased with a higher content of NG in the double-base propellant. In the modified double-base propellant containing RDX, the OH radical concentration decreased as the RDX content increased, with these tendencies of change aligning closely with the simulation results.

Dynamic Transcription Machineries Guide the Synthesis of Temporally Operating DNAzymes, Gated and Cascaded DNAzyme Catalysis

Transient transcription machineries play important roles in the dynamic modulation of gene expression and the sequestered regulation of cellular networks. The present study emulates such processes by designing artificial reaction modules consisting of transcription machineries that guide the transient synthesis of catalytic DNAzymes, the transient operation of gated DNAzymes, and the temporal activation of an intercommunicated DNAzyme cascade. The reaction modules rely on functional constituents that lead to the triggered activation of transcription machineries in the presence of the nucleoside triphosphates oligonucleotide fuel, yielding the transient formation and dissipative depletion of the intermediate DNAzyme(s) products. The kinetics of the transient DNAzyme networks are computationally simulated, allowing to predict and experimentally validate the performance of the systems under different auxiliary conditions. The study advances the field of systems chemistry by introducing transcription machinery-based networks for the dynamic control over transient catalysis─a primary step toward life-like cellular assemblies.

Evolution of Molar Mass Distributions Using a Method of Partial Moments: Initiation of RAFT Polymerization

We describe a method of partial moments devised for accurate simulation of the time/conversion evolution of polymer composition and molar mass. Expressions were derived that enable rigorous evaluation of the complete molar mass and composition distribution for shorter chain lengths (e.g., degree of polymerization, Xn = N < 200 units) while longer chains (Xn ≥ 200 units) are not neglected, rather they are explicitly considered in terms of partial moments of the molar mass distribution, μxN(P)=∑n=N+1∞nx[Pn] (where P is a polymeric species and n is its’ chain length). The methodology provides the exact molar mass distribution for chains Xn < N, allows accurate calculation of the overall molar mass averages, the molar mass dispersity and standard deviations of the distributions, provides closure to what would otherwise be an infinite series of differential equations, and reduces the stiffness of the system. The method also allows for the inclusion of the chain length dependence of the rate coefficients associated with the various reaction steps (in particular, termination and propagation) and the various side reactions that may complicate initiation or initialization. The method is particularly suited for the detailed analysis of the low molar mass portion of molar mass distributions of polymers formed by radical polymerization with reversible addition-fragmentation chain transfer (RAFT) and is relevant to designing the RAFT-synthesis of sequence-defined polymers. In this paper, we successfully apply the method to compare the behavior of thermally initiated (with an added dialkyldiazene initiator) and photo-initiated (with a RAFT agent as a direct photo-iniferter) RAFT-single-unit monomer insertion (RAFT-SUMI) and oligomerization of N,N-dimethylacrylamide (DMAm).

Electron Signatures of Reconnection in a Global eVlasiator Simulation

Geospace plasma simulations have progressed toward more realistic descriptions of the solar wind-magnetosphere interaction from magnetohydrodynamic to hybrid ion-kinetic, such as the state-of-the-art Vlasiator model. Despite computational advances, electron scales have been out of reach in a global setting. eVlasiator, a novel Vlasiator submodule, shows for the first time how electromagnetic fields driven by global hybrid-ion kinetics influence electrons, resulting in kinetic signatures. We analyze simulated electron distributions associated with reconnection sites and compare them with Magnetospheric Multiscale (MMS) spacecraft observations. Comparison with MMS shows that key electron features, such as reconnection inflows, heated outflows, flat-top distributions, and bidirectional streaming, are in remarkable agreement. Thus, we show that many reconnection-related features can be reproduced despite strongly truncated electron physics and an ion-scale spatial resolution. Ion-scale dynamics and ion-driven magnetic fields are shown to be significantly responsible for the environment that produces electron dynamics observed by spacecraft in near-Earth plasmas.

Cotranscriptional Kinetic Folding of RNA Secondary Structures Including Pseudoknots

Computational prediction of ribonucleic acid (RNA) structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence, however, has shown that RNA folds concurrently with its elongation. We investigate RNA secondary structure formation, including pseudoknots, that takes into account the cotranscriptional effects. We propose a single-nucleotide resolution kinetic model of the folding process of RNA molecules, where the polymerase-driven elongation of an RNA strand by a new nucleotide is included as a primitive operation, together with a stochastic simulation method that implements this folding concurrently with the transcriptional synthesis. Numerical case studies show that our cotranscriptional RNA folding model can predict the formation of conformations that are favored in actual biological systems. Our new computational tool can thus provide quantitative predictions and offer useful insights into the kinetics of RNA folding.

Identifying Phase-Dependent Electrochemical Stripping Performance of FeOOH Nanorod: Evidence from Kinetic Simulation and Analyte-Material Interactions

Metal hydroxide nanomaterials are widely applied in the energy and environment fields. The electrochemical performance of such materials is strongly dependent on their crystal phases. However, as there are always multiple factors relating to the phase-dependent electrochemistry, it is still difficult to identify the determining one. The well-defined crystal phases of α- and β-FeOOH nanorods are characterized through the transmission electron microscopy by a series of rotation toward one rod, where the cross-section shape and the growth direction along the [001] crystalline are first verified for 1D FeOOH nanostructures. The electrosensitivity of the two materials toward Pb(II) is tested, where α-FeOOH performs an outstanding sensitivity whilst it is only modest for β-FeOOH. Experiments via Fourier transform infrared spectroscopy, X-ray absorption fine structure (XAFS), etc., show that α-FeOOH presents a larger Pb(II) adsorption capacity due to more surficial hydroxyl groups and weaker PbO bond strength. The reaction kinetics are simulated and the adsorption capacity is found to be the determining factor for the distinct Pb(II) sensitivities. Combining experiment with simulation, this work reveals the physical insights of the phase-dependent electrochemistry for FeOOH and provides guidelines for the functional application of metal hydroxide nanomaterials.

Evolution of Nucleic-Acid-Based Constitutional Dynamic Networks Revealing Adaptive and Emergent Functions

The evolution of networks is a fundamental unresolved issue in developing the area of systems chemistry. We introduce a versatile rewiring mechanism that leads to the emergence of nucleic-acid-based constitutional dynamic networks (CDNs). A two-component constituent AA' functionalized with a Mg²⁺ -ion-dependent DNAzyme activator unit forms a complex with an intact hairpin H_BB' composed of B and B' sequences. Cleavage of H_BB' leads to the two-component constituent BB', and its rewiring with AA' yields CDN X composed of the equilibrated constituents AA', AB', BA', and BB'. In analogy, subjecting AA' to an intact hairpin H_CC' leads to the formation of CDN Y consisting of AA', AC', CA', and CC'. Subjecting AA' to the mixture of H_BB' and H_CC' evolves the [3×3] CDN Z, composed of nine constituents, thus demonstrating hierarchical adaptive properties. Furthermore, the DNAzyme units associated with the constituents are applied to tailor emerging catalytic functions from the different CDNs.

Kinetic Models for the Role of Protein Thiols during Oxidation in Beer

Thiol-containing proteins have been suggested to have antioxidative properties in beer. A kinetic model has been setup for the reactivity of thiols during early stages of oxidative degradation of beer. Kinetic analysis based on the proposed reaction mechanism allowed evaluation of the relative reactivity of beer components, such as bitter acids from hops and polyphenols. The rate constants for the reaction of 1-hydroxyethyl radicals, which are generated during radical mediated oxidation of ethanol in beer, with hop bitter acids and thiols were very similar, and the concentration of these compounds in beer is therefore essential for the relative reactivity. For a standard pilsner beer with 35 international bitter units with typical concentrations of thiols and hop bitter acids, thiols were found to react with ca. 9% of 1-hydroxyethyl radicals, while bitter acids from hops accounted for ca. 88% of the reaction with 1-hydroxyethyl radicals. Polyphenols were not found to account for any major part of the reaction with 1-hydroxyethyl radicals due to low reaction rates and low concentrations in pilsner beer compared to the other components. The kinetic model suggests that the concentration of thiols has to be increased in order to contribute with any significant antioxidative protection and that the fate of thiols during oxidation must be considered since some thiol oxidation products may induce further damage.

Full rate constant matrix contraction method for obtaining branching ratio of unimolecular decomposition

The branching ratio of unimolecular decomposition can be evaluated by solving the rate equations. Recent advances in automated reaction path search methods have enabled efficient construction of the rate equations based on quantum chemical calculations. However, it is still difficult to solve the rate equations composed of hundreds or more elementary steps. This problem is especially serious when elementary steps that occur in highly different timescales coexist. In this article, we introduce an efficient approach to obtain the branching ratio from a given set of rate equations. It has been derived from a recently proposed rate constant matrix contraction (RCMC) method, and termed full-RCMC (f-RCMC). The f-RCMC gives the branching ratio without solving the rate equations. Its performance was tested numerically for unimolecular decomposition of C₃ H₅ and C₄ H₅ . Branching ratios obtained by the f-RCMC precisely reproduced the values obtained by numerically solving the rate equations. It took about 95 h to solve the rate equations of C₄ H₅ consisting of 234 elementary steps. In contrast, the f-RCMC gave the branching ratio in less than 1 s. The f-RCMC would thus be an efficient alternative of the conventional kinetic simulation approach. © 2016 Wiley Periodicals, Inc.

Reactive oxygen species and energy machinery: an integrated dynamic model

The role of several important reactive oxygen species (ROS) on the Krebs cycle, the electron transport chain (ETC) and the two important shuttles has been modelled. Major part of the ROS is produced during oxygen reduction in the ETC, which has been kinetically simulated, and the changes in the final concentrations of several important metabolites were found. The simulation is based on chemical kinetics equation, and the associated set of differential equations was solved by the ordinary differential equation package in Octave. The validity of the model is checked by comparing the experimental results available in the literature with the simulations when a part of the ETC is blocked (80%) in the script. The present approach is versatile and flexible and has potential applications in various simulations. It is easy to study the change in concentrations of various metabolites when a particular enzyme or pathway is blocked (say by a drug). The Octave script is presented in the text.

Acetyl Radical Generation in Cigarette Smoke: Quantification and Simulations

Free radicals are present in cigarette smoke and can have a negative effect on human health. However, little is known about their formation mechanisms. Acetyl radicals were quantified in tobacco smoke and mechanisms for their generation were investigated by computer simulations. Acetyl radicals were trapped from the gas phase using 3-amino-2, 2, 5, 5-tetramethyl-proxyl (3AP) on solid support to form stable 3AP adducts for later analysis by high performance liquid chromatography (HPLC), mass spectrometry/tandem mass spectrometry (MS-MS/MS) and liquid chromatography-mass spectrometry (LC-MS). Simulations were performed using the Master Chemical Mechanism (MCM). A range of 10-150 nmol/cigarette of acetyl radical was measured from gas phase tobacco smoke of both commerial and research cigarettes under several different smoking conditions. More radicals were detected from the puff smoking method compared to continuous flow sampling. Approximately twice as many acetyl radicals were trapped when a glass filber particle filter (GF/F specifications) was placed before the trapping zone. Simulations showed that NO/NO₂ reacts with isoprene, initiating chain reactions to produce hydroxyl radical, which abstracts hydrogen from acealdehyde to generate acetyl radical. These mechanisms can account for the full amount of acetyl radical detected experimentally from cigarette smoke. Similar mechanisms may generate radicals in second hand smoke.

A tethered delivery mechanism explains the catalytic action of a microtubule polymerase

Stu2p/XMAP215 proteins are essential microtubule polymerases that use multiple αβ-tubulin-interacting TOG domains to bind microtubule plus ends and catalyze fast microtubule growth. We report here the structure of the TOG2 domain from Stu2p bound to yeast αβ-tubulin. Like TOG1, TOG2 binds selectively to a fully 'curved' conformation of αβ-tubulin, incompatible with a microtubule lattice. We also show that TOG1-TOG2 binds non-cooperatively to two αβ-tubulins. Preferential interactions between TOGs and fully curved αβ-tubulin that cannot exist elsewhere in the microtubule explain how these polymerases localize to the extreme microtubule end. We propose that these polymerases promote elongation because their linked TOG domains concentrate unpolymerized αβ-tubulin near curved subunits already bound at the microtubule end. This tethering model can explain catalyst-like behavior and also predicts that the polymerase action changes the configuration of the microtubule end.

Modeling the Mechanism of GR/c-Jun/Erg Crosstalk in Apoptosis of Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia (ALL) is one of the most common forms of malignancy that occurs in lymphoid progenitor cells, particularly in children. Synthetic steroid hormones glucocorticoids (GCs) are widely used as part of the ALL treatment regimens due to their apoptotic function, but their use also brings about various side effects and drug resistance. The identification of the molecular differences between the GCs responsive and resistant cells therefore are essential to decipher such complexity and can be used to improve therapy. However, the emerging picture is complicated as the activities of genes and proteins involved are controlled by multiple factors. By adopting the systems biology framework to address this issue, we here integrated the available knowledge together with experimental data by building a series of mathematical models. This rationale enabled us to unravel molecular interactions involving c-Jun in GC induced apoptosis and identify Ets-related gene (Erg) as potential biomarker of GC resistance. The results revealed an alternative possible mechanism where c-Jun may be an indirect GR target that is controlled via an upstream repressor protein. The models also highlight the importance of Erg for GR function, particularly in GC sensitive C7 cells where Erg directly regulates GR in agreement with our previous experimental results. Our models describe potential GR-controlled molecular mechanisms of c-Jun/Bim and Erg regulation. We also demonstrate the importance of using a systematic approach to translate human disease processes into computational models in order to derive information-driven new hypotheses.