Comparison of numerical calculations and ALOHA modeling in consequence assessment of chlorine gas emissions from ethylene dichloride reactors.

Incidents involving chemical storage tanks in the petrochemical industry are significant events with severe consequences. Within the petrochemical industry, EDC is a sector that produces ethylene dichloride through the reaction of chlorine and ethylene. The present research was conducted to evaluate the consequences of chlorine gas released from the EDC reactor in a petrochemical industry in southern Iran. Data regarding reactor specifications were obtained from the factory's technical office, while climatic data was acquired from the Meteorological Organization. The consequences of chlorine gas release from the reactor were assessed in four predefined scenarios using numerical calculation methods and modeling with the ALOHA software. The numerical calculation method involved thermodynamic fluid path analysis, discharge coefficient calculations, and wind speed impact analysis. The hazard radius was determined based on the ERPG1-2-3 index. Results showed that in the scenario of chlorine gas release from EDC reactors, according to the ALOHA model, an increase in wind speed from 3 to 7 m/h led to an expanded dispersion radius. At a radius of 700 m from the reactor, the maximum outdoor concentration reached 3.12 ppm, decreasing to 2.27 ppm at 800 m and further to 1.53 ppm at 1000 m. The comparison of numerical calculations and modeling using the ALOHA software indicates the desirable conformity of the results with each other. The R2 coefficient for evaluating the conformity of the results was 0.9964, indicating the desired efficiency of the model in evaluating the consequences of the release of toxic gasses from the EDC tank. The results of this research can be useful in designing the site and emergency response plan.

Effect of calcium and phosphorus on ammonium and nitrate nitrogen adsorption onto iron (hydr)oxides surfaces: CD-MUSIC model and DFT computation.

Calcium (Ca2+) and phosphorous (PO43-) significantly influence the form and effectiveness of nitrogen (N), however, the precise mechanisms governing the adsorption of ammonium nitrogen (NH4+-N) and nitrate nitrogen (NO3--N) are still lacking. This study employed batch adsorption experiments, charge distribution and multi-site complexation (CD-MUSIC) models and density functional theory (DFT) calculations to elucidate the mechanism by which Ca2+ and PO43- affect the adsorption of NH4+-N and NO3--N on the goethite (GT) surface. The results showed that the adsorption of NH4+-N on the GT exhibited an initial increase followed by a decrease as pH increased, peaking at a pH of 8.5. Conversely, the adsorption of NO3--N decreased with rising pH. According to the CD-MUSIC model, Ca2+ minimally affected the NH4+-N adsorption on the GT but enhanced NO3--N adsorption via electrostatic interaction, promoting the adsorption of ≡FeOH-NO3- and ≡Fe3O-NO3- species. Similarly, PO43- inhibited the adsorption of ≡FeOH-NO3- and ≡Fe3O-NO3- species. However, PO43- boosted NH4+-N adsorption by facilitating the formation of ≡Fe3O-NH4+ via electrostatic interaction and site competition. DFT calculations indicates that although bidentate phosphate (BP) was beneficial to stabilize NH4+-N than monodentate phosphate (SP), SP-NH4+ was the main adsorption configuration at pH 5.5-9.5 owing the prevalence of SP on the GT surface under site competition of NH4+-N. The results of CD-MUSIC model and DFT calculation were verified mutually, and provide novel insights into the mechanisms underlying N fixation and migration in soil.

Modeling the degradation of polypropylene and polystyrene under shock compression and mechanical cleaving using the ReaxFF force field.

Polypropylene (PP) and polystyrene (PS) underwent a comprehensive investigation into their mechanical and chemical degradation through reactive molecular dynamics simulations. The simulations utilized the ReaxFF force field for CHO (carbon-hydrogen-oxygen) systems in the combustion branch. The study included equilibrium simulations to determine densities and melting temperatures, non-equilibrium simulations for stress-strain and Young moduli determination, mechanical cleaving to identify surface species resulting from material fragmentation, and shock compression simulations to elucidate chemical reactions activated by some external energy sources. The results indicate that material properties such as densities, phase transition temperatures, and Young moduli are accurately reproduced by the ReaxFF-CHO force field. The reactive dynamics analysis yielded crucial insights into the surface composition of fragmented polymers. Both polymers exhibited backbone breakage, leaving -CH2· and -CH·- radicals as terminals. PP demonstrated substantial fragmentation, while PS showed a tendency to develop crosslinks. A detailed analysis of chemical reactions resulting from increasing activation due to increasing value of compression pressure is presented and discussed.

Insights into the hydrolysis/alcoholysis/ammonolysis mechanisms of ethylene naphthalate dimer using density functional theory (DFT) method.

Hydrolysis, alcoholysis and ammonolysis are viable routes for the efficient degradation and recycling of polyethylene naphthalate (PEN) plastic waste. Various possible hydrolysis/alcoholysis/ammonolysis reaction pathways for the degradation mechanism of the ethylene naphthalate dimer were investigated using the density functional theory (DFT) B3P86/6-31++G(d,p). To determine the thermodynamic and kinetic parameters, geometric structure optimization and frequency calculation were performed on a range of intermediates, transition states, and products associated with the reaction. The calculation results show that the highest energy barrier of the main element reaction step in hydrolysis is about 169.0 kJ/mol, the lowest is about 151.0 kJ/mol for ammonolysis, and the second is about 155.0 kJ/mol for alcoholysis. The main hydrolysis products of the ethylene naphthalate dimer are 2,6-naphthalenedicarboxylic acid and ethylene glycol; the main products of alcoholysis are dimethyl naphthalene-2,6-dicarboxylate and ethylene glycol, and the main products of ammonolysis are naphthalene-2,6-dicarboxamide and ethylene glycol. Furthermore, in the process of ethylene naphthalate dimer hydrolysis/alcoholysis/ammonolysis, the decomposition reaction in the NH3 atmosphere is better than that in methanol, and the reaction in CH3OH is better than that in the H2O molecular environment, and the increase in reaction temperature can increase its spontaneity. Our study presents the molecular mechanism of PEN hydrolysis/alcoholysis/ammonolysis and provides a reference for studying the degradation of other plastic wastes.

Improving benzene catalytic oxidation on Ag/Co3O4 by regulating the chemical states of Co and Ag.

Silver (9 wt.%) was loaded on Co3O4-nanofiber using reduction and impregnation methods, respectively. Due to the stronger electronegativity of silver, the ratios of surface Co3+/Co2+ on Ag/Co3O4 were higher than on Co3O4, which further led to more adsorbed oxygen species as a result of the charge compensation. Moreover, the introducing of silver also obviously improved the reducibility of Co3O4. Hence the Ag/Co3O4 showed better catalytic performance than Co3O4 in benzene oxidation. Compared with the Ag/Co3O4 synthesized via impregnation method, the one prepared using reduction method (named as AgCo-R) exhibited higher contents of surface Co3+ and adsorbed oxygen species, stronger reducibility, as well as more active surface lattice oxygen species. Consequently, AgCo-R showed lowest T90 value of 183°C, admirable catalytic stability, largest normalized reaction rate of 1.36 × 10-4 mol/(h·m2) (150°C), and lowest apparent activation energy (Ea) of 63.2 kJ/mol. The analyzing of in-situ DRIFTS indicated benzene molecules were successively oxidized to phenol, o-benzoquinone, small molecular intermediates, and finally to CO2 and water on the surface of AgCo-R. At last, potential reaction pathways including five detailed steps were proposed.

The Adipokinetic Hormone (AKH) and the Adipokinetic Hormone/Corazonin-Related Peptide (ACP) Signalling Systems of the Yellow Fever Mosquito Aedes aegypti: Chemical Models of Binding.

Neuropeptides are the main regulators of physiological, developmental, and behavioural processes in insects. Three insect neuropeptide systems, the adipokinetic hormone (AKH), corazonin (Crz), and adipokinetic hormone/corazonin-related peptide (ACP), and their cognate receptors, are related to the vertebrate gonadotropin (GnRH) system and form the GnRH superfamily of peptides. In the current study, the two signalling systems, AKH and ACP, of the yellow fever mosquito, Aedes aegypti, were comparatively investigated with respect to ligand binding to their respective receptors. To achieve this, the solution structure of the hormones was determined by nuclear magnetic resonance distance restraint methodology. Atomic-scale models of the two G protein-coupled receptors were constructed with the help of homology modelling. Thereafter, the binding sites of the receptors were identified by blind docking of the ligands to the receptors, and models were derived for each hormone system showing how the ligands are bound to their receptors. Lastly, the two models were validated by comparing the computational results with experimentally derived data available from the literature. This mostly resulted in an acceptable agreement, proving the models to be largely correct and usable. The identification of an antagonist versus a true agonist may, however, require additional testing. The computational data also explains the exclusivity of the two systems that bind only the cognate ligand. This study forms the basis for further drug discovery studies.

A systematic study on the chemical model of polycyclic aromatic hydrocarbons formation from nutrients (glucose, amino acids, fatty acids) in food.

Polycyclic aromatic hydrocarbons (PAHs), prominent carcinogens formed during food processing, pose health risks through long-term consumption. This study focuses on 16 priority PAHs in the European Union, investigating their formation during pyrolysis. Glucose, amino acids and fatty acids are important food nutrients. To further explore whether these nutrients in food form PAHs during heating, a single chemical model method was used to heat these nutrients respectively, and GC-MS/MS was used to identify and quantify the obtained components. Glucose is the most basic nutrient in food, so the influence of water, pH, temperature and other factors on the formation of PAHs was studied in the glucose model. At the same time, the models of amino acids and fatty acids were used to assist in improving the entire nutrient research system. According to our results, some previously reported mechanisms of PAHs formation by fatty acids heating were confirmed. In addition, glucose and amino acids could also produce many PAHs after heating, and some conclusions were improved by comparing the intermediates of PAHs from three types of nutrients.

Analysis of Poly(ethylene terephthalate) degradation kinetics of evolved IsPETase variants using a surface crowding model.

Poly(ethylene terephthalate) (PET) is a major plastic polymer utilized in the single-use and textile industries. The discovery of PET-degrading enzymes (PETases) has led to an increased interest in the biological recycling of PET in addition to mechanical recycling. IsPETase from Ideonella sakaiensis is a candidate catalyst, but little is understood about its structure-function relationships with regards to PET degradation. To understand the effects of mutations on IsPETase productivity, we develop a directed evolution assay to identify mutations beneficial to PET film degradation at 30 °C. IsPETase also displays enzyme concentration-dependent inhibition effects, and surface crowding has been proposed as a causal phenomenon. Based on total internal reflectance fluorescence microscopy and adsorption experiments, IsPETase is likely experiencing crowded conditions on PET films. Molecular dynamics simulations of IsPETase variants reveal a decrease in active site flexibility in free enzymes and reduced probability of productive active site formation in substrate-bound enzymes under crowding. Hence, we develop a surface crowding model to analyze the biochemical effects of three hit mutations (T116P, S238N, S290P) that enhanced ambient temperature activity and/or thermostability. We find that T116P decreases susceptibility to crowding, resulting in higher PET degradation product accumulation despite no change in intrinsic catalytic rate. In conclusion, we show that a macromolecular crowding-based biochemical model can be used to analyze the effects of mutations on properties of PETases and that crowding behavior is a major property to be targeted for enzyme engineering for improved PET degradation.

Investigation of the Formaldehyde-Catalyzed NNitrosation of Dialkyl Amines: An Automated Experimental and Kinetic Modelling Study Using Dibutylamine.

The potential for drug substances and drug products to contain low levels of N-nitrosamines is of continued interest to the pharmaceutical industry and regulatory authorities. Acid-promoted nitrosation mechanisms in solution have been investigated widely in the literature and are supported by kinetic modelling studies. Carbonyl compounds, particularly formaldehyde, which may be present as impurities in excipients and drug product packaging components or introduced during drug substance manufacturing processes are also known to catalyze nitrosation, but their impact on the risk of N-nitrosamine formation has not been systematically investigated to date. In this study, we experimentally investigated the multivariate impact of formaldehyde, nitrite and pH on N-nitrosation in aqueous solution using dibutylamine as a model amine. We augmented a published kinetic model by adding formaldehyde-catalyzed nitrosation reactions. We validated the new kinetic model vs. the experimental data and then used the model to systematically investigate the impact of formaldehyde levels on N-nitrosamine formation. Simulations of aqueous solution systems show that at low formaldehyde levels the formaldehyde-catalyzed mechanisms are insignificant in comparison to other routes. However, formaldehyde-catalyzed mechanisms can become more significant at neutral and high pH under higher formaldehyde levels. Model-based sensitivity analysis demonstrated that under high nitrite levels and low formaldehyde levels (where the rate of formaldehyde-catalyzed nitrosation is low compared to the acid-promoted pathways) the model can be used with kinetic parameters for model amines in the literature without performing additional experiments to fit amine-specific parameters. For other combinations of reaction parameters containing formaldehyde, the formaldehyde-catalyzed kinetics are non-negligible, and thus it is advised that, under such conditions, additional experiments should be conducted to reliably use the model.

Leucine Motifs Stabilize Residual Helical Structure in Disordered Proteins.

Many examples are known of regions of intrinsically disordered proteins that fold into α-helices upon binding to their targets. These helical binding motifs (HBMs) can be partially helical also in the unbound state, and this so-called residual structure can affect binding affinity and kinetics. To investigate the underlying mechanisms governing the formation of residual helical structure, we assembled a dataset of experimental helix contents of 65 peptides containing HBM that fold-upon-binding. The average residual helicity is 17% and increases to 60% upon target binding. The helix contents of residual and target-bound structures do not correlate, however the relative location of helix elements in both states shows a strong overlap. Compared to the general disordered regions, HBMs are enriched in amino acids with high helix preference and these residues are typically involved in target binding, explaining the overlap in helix positions. In particular, we find that leucine residues and leucine motifs in HBMs are the major contributors to helix stabilization and target-binding. For the two model peptides, we show that substitution of leucine motifs to other hydrophobic residues (valine or isoleucine) leads to reduction of residual helicity, supporting the role of leucine as helix stabilizer. From the three hydrophobic residues only leucine can efficiently stabilize residual helical structure. We suggest that the high occurrence of leucine motifs and a general preference for leucine at binding interfaces in HBMs can be explained by its unique ability to stabilize helical elements.

Temporal control by cofactors prevents kinetic trapping in retroviral Gag lattice assembly.

For retroviruses like HIV to proliferate, they must form virions shaped by the self-assembly of Gag polyproteins into a rigid lattice. This immature Gag lattice has been structurally characterized and reconstituted in vitro, revealing the sensitivity of lattice assembly to multiple cofactors. Due to this sensitivity, the energetic criterion for forming stable lattices is unknown, as are their corresponding rates. Here, we use a reaction-diffusion model designed from the cryo-ET structure of the immature Gag lattice to map a phase diagram of assembly outcomes controlled by experimentally constrained rates and free energies, over experimentally relevant timescales. We find that productive assembly of complete lattices in bulk solution is extraordinarily difficult due to the large size of this ∼3700 monomer complex. Multiple Gag lattices nucleate before growth can complete, resulting in loss of free monomers and frequent kinetic trapping. We therefore derive a time-dependent protocol to titrate or "activate" the Gag monomers slowly within the solution volume, mimicking the biological roles of cofactors. This general strategy works remarkably well, yielding productive growth of self-assembled lattices for multiple interaction strengths and binding rates. By comparing to the in vitro assembly kinetics, we can estimate bounds on rates of Gag binding to Gag and the cellular cofactor IP6. Our results show that Gag binding to IP6 can provide the additional time delay necessary to support smooth growth of the immature lattice with relatively fast assembly kinetics, mostly avoiding kinetic traps. Our work provides a foundation for predicting and disrupting formation of the immature Gag lattice via targeting specific protein-protein binding interactions.

Response of Arctic Black Carbon Contamination and Climate Forcing to Global Supply Chain Relocation.

Black carbon (BC) plays a vital role in Arctic warming. Extensive investigations have been conducted to elucidate the source-receptor relationships of BC between the Arctic and mid-/high-latitude sources. However, it is unclear to what extent source relocation under globalization could disturb Arctic BC contamination and climate forcing from anthropogenic BC emissions. Here, we show that the global supply chain (GSC) relocation featured by the southward shift of industries from high-latitude developed countries to low-latitude developing countries markedly reduces the BC burden in the Arctic using a global chemical transport model (GEOS-Chem) and a multiregional input-output analysis (MRIO). We find that Arctic annual mean BC concentration associated with the GSC relocation drops by ∼15% from the case without the GSC relocation. The total net BC level declines 7% over the entire Arctic and 16% in the European Arctic. We also observed markedly declining BC deposition as well as direct and snow albedo radiative forcing in the Arctic. We show that the Arctic BC burden would be further reduced by decreasing BC emissions in China, attributable to its emission reduction and ongoing shift of the GSC from China to southern and southeastern Asia.

Tensor network construction for lattice gas models: Hard-core and triangular lattice models.

The representation of complex lattice models in the form of a tensor network is a promising approach to the analysis of the thermodynamics of such systems. Once the tensor network is built, various methods can be used to calculate the partition function of the corresponding model. However, it is possible to build the initial tensor network in different ways for the same model. In this work, we have proposed two ways of constructing tensor networks and demonstrated that the construction process affects the accuracy of calculations. For demonstration purposes, we have done a brief study of the 4 nearest-neighbor (NN) and 5NN models, where adsorbed particles exclude all sites up to the fourth and fifth nearest neighbors from being occupied by another particle. In addition, we have studied a 4NN model with finite repulsions with a fifth neighbor. In a sense, this model is intermediate between 4NN and 5NN models, so algorithms designed for systems with hard-core interactions may experience difficulties. We have obtained adsorption isotherms, as well as graphs of entropy and heat capacity for all models. The critical values of the chemical potential were determined from the position of the heat capacity peaks. As a result, we were able to improve our previous estimate of the position of the phase transition points for the 4NN and 5NN models. And in the model with finite interactions, we found the presence of two first-order phase transitions and made an estimate of the critical values of the chemical potential for them.

Mitochondrial dysfunction, oxidative stress, ER stress and mitochondria-ER crosstalk alterations in a chemical rat model of Huntington's disease: Potential benefits of bezafibrate.

Redox homeostasis, mitochondrial functions, and mitochondria-endoplasmic reticulum (ER) communication were evaluated in the striatum of rats after 3-nitropropionic acid (3-NP) administration, a recognized chemical model of Huntington's disease (HD). 3-NP impaired redox homeostasis by increasing malondialdehyde levels at 28 days, decreasing glutathione (GSH) concentrations at 21 and 28 days, and the activities of glutathione peroxidase (GPx), superoxide dismutase (SOD) and glutathione S-transferase at 7, 21, and 28 days, catalase at 21 days, and glutathione reductase at 21 and 28 days. Impairment of mitochondrial respiration at 7 and 28 days after 3-NP administration was also observed, as well as reduced activities of succinate dehydrogenase (SDH) and respiratory chain complexes. 3-NP also impaired mitochondrial dynamics and the interactions between ER and mitochondria and induced ER-stress by increasing the levels of mitofusin-1, and of DRP1, VDAC1, Grp75 and Grp78. Synaptophysin levels were augmented at 7 days but reduced at 28 days after 3-NP injection. Finally, bezafibrate prevented 3-NP-induced alterations of the activities of SOD, GPx, SDH and respiratory chain complexes, DCFH oxidation and on the levels of GSH, VDAC1 and synaptophysin. Mitochondrial dysfunction and synaptic disruption may contribute to the pathophysiology of HD and bezafibrate may be considered as an adjuvant therapy for this disorder.

Formation of spread-out Bragg peak for helium-ion beam using microdosimetric kinetic model.

PURPOSE: To evaluate the applicability of microdosimetric kinetic model (MKM) to helium-ion therapy by forming a spread-out Bragg peak (SOBP) of a helium-ion beam using the MKM developed for carbon-ion radiotherapy and confirming the predictions in biological experiments. METHODS: Using a ridge filter, a 90-mm wide SOBP for a 210 MeV/u helium-ion beam was created in a broad beam delivery system. The ridge filter was designed such that a uniform biological response was achieved with a cell survival rate of 7% over the SOBP region. Biological experiments were then performed using the SOBP beam in a human salivary gland (HSG) cell line to measure the cell survival rates. RESULTS: The biological responses were uniform in the SOBP region, as expected by the MKM; however, the mean of the measured cell survival rates was (11.2 ± 0.6) % in the SOBP region, which was 60% higher than the designed rate. When investigating the biological parameters of the HSG cell line used in the experiments, we found that they were altered slightly from the MKM parameters used for carbon-ion radiotherapy. The new ß parameter reproduced the measured survival rates within 6.5% in the SOBP region. CONCLUSION: We produced biologically uniform SOBP using MKM for carbon-ion radiotherapy. The measured survival rates in the SOBP region were higher than expected, and the survival rates were reproduced by modifying the MKM parameter. This study was limited to one SOBP, and further investigations are required to prove that MKM is generally applicable to helium-ion radiotherapy.

Modeling and optimization of the coagulation/flocculation process in turbidity removal from water using poly aluminum chloride and rice starch as a natural coagulant aid.

The application of the coagulation/flocculation process is very important due to its simplicity in removing turbidity. Due to the disadvantages of using chemical coagulants in water and the lack of sufficient effect of natural materials alone in removing turbidity for proper performance, the simultaneous use of chemical and natural coagulants is the best way to reduce the harmful effects of chemical coagulants in water. In this study, the application of poly aluminum chloride (PAC) as a chemical coagulant and rice starch as a natural coagulant aid to remove turbidity from aqueous solutions was investigated. Effects of the above coagulants on the four main factors, coagulant dose (0-10 mg/L), coagulant adjuvant dose (0-0.1 mg/L), pH (5-9), turbidity (NTU 0-50), and each five levels were assessed using a central composite design (CCD). Under the optimized conditions, the maximum turbidity elimination efficiency was found to be 96.6%. The validity and adequacy of the proposed model (quadratic model) were confirmed by the corresponding statistics (i.e., F-value of 23.3, p-values of 0.0001, and lack of fit of 0.877 for the model, respectively, R2 = 0.88, R2adj. = 0.84, R2 pred = 0.79, AP = 22.04).

A bivalent ß-carboline derivative inhibits macropinocytosis-dependent entry of pseudorabies virus by targeting the kinase DYRK1A.

Pseudorabies virus (PRV) has become a "new life-threatening zoonosis" since the human-originated PRV strain was first isolated in 2020. To identify novel anti-PRV agents, we screened a total of 107 ß-carboline derivatives and found 20 compounds displaying antiviral activity against PRV. Among them, 14 compounds showed better antiviral activity than acyclovir. We found that compound 45 exhibited the strongest anti-PRV activity with an IC50 value of less than 40 nM. Our in vivo studies showed that treatment with 45 significantly reduced the viral loads and protected mice challenged with PRV. To clarify the mode of action of 45, we conducted a time of addition assay, an adsorption assay, and an entry assay. Our results indicated that 45 neither had a virucidal effect nor affected viral adsorption while significantly inhibiting PRV entry. Using the FITC-dextran uptake assay, we determined that 45 inhibits macropinocytosis. The actin-dependent plasma membrane protrusion, which is important for macropinocytosis, was also suppressed by 45. Furthermore, the kinase DYRK1A (dual-specificity tyrosine phosphorylation-regulated kinase 1A) was predicted to be a potential target for 45. The binding of 45 to DYRK1A was confirmed by drug affinity responsive target stability and cellular thermal shift assay. Further analysis revealed that knockdown of DYRK1A by siRNA suppressed PRV macropinocytosis and the tumor necrosis factor alpha-TNF-induced formation of protrusions. These results suggested that 45 could restrain PRV macropinocytosis by targeting DYRK1A. Together, these findings reveal a unique mechanism through which ß-carboline derivatives restrain PRV infection, pointing to their potential value in the development of anti-PRV agents.

Peptide-based chemical models for lytic polysaccharide monooxygenases.

Copper(II) complexes of HPH-NH2 (L1) and HPHPY-NH2 (L2) peptides have been studied as small molecular models of lytic polysaccharide monooxygenases by pH-potentiometry and UV-vis, CD and EPR spectroscopy. The coordination properties of these ligands are fundamentally different from those of other non-protected N-terminal HXH-sequences concerning the metal binding ability of amide nitrogens. The proline units prevent the formation of fused chelates with the participation of amide nitrogens; therefore, instead of ATCUN-type {NH2,2N-,Nim} coordination, dimer complexes (Cu2HxL2, where x = -1, -2, and -3 for L1 and 1, 0, and -1 for L2) are formed in equimolar systems above pH 5. Using H2O2 as the oxidant and PNPG as the activated substrate, these dimer complexes were proved to be relevant functional models of LPMOs, even at neutral pH. Although the tyrosine residue in L2 participates in the coordination at pH 7-9.6, it does not seem to play a role in the oxidation process. In the presence of H2O2, the dimer complexes partially dissociate to form mononuclear hydroperoxo complexes, which are stable for 1-2 hours in equimolar concentrations of H2O2. On the other hand, with excess H2O2 both their formation and their decomposition are faster. The decay of (hydro)peroxo complexes, after longer reaction times, results in the evolution of dioxygen bubbles and the formation of Cu(I) (probably through catalytic disproportionation). However, in the presence of PNPG, the formation of dioxygen bubbles was not observed. Therefore, we assumed that the formed Cu(I) complexes bind H2O2 and enter into a similar catalytic cycle as suggested recently for native LPMOs.

Thioester synthesis by a designed nickel enzyme models prebiotic energy conversion.

The formation of carbon-carbon bonds from prebiotic precursors such as carbon dioxide represents the foundation of all primordial life processes. In extant organisms, this reaction is carried out by the carbon monoxide dehydrogenase (CODH)/acetyl coenzyme A synthase (ACS) enzyme, which performs the cornerstone reaction in the ancient Wood-Ljungdahl metabolic pathway to synthesize the key biological metabolite, acetyl-CoA. Despite its significance, a fundamental understanding of this transformation is lacking, hampering efforts to harness analogous chemistry. To address these knowledge gaps, we have designed an artificial metalloenzyme within the azurin protein scaffold as a structural, functional, and mechanistic model of ACS. We demonstrate the intermediacy of the NiI species and requirement for ordered substrate binding in the bioorganometallic carbon-carbon bond-forming reaction from the one-carbon ACS substrates. The electronic and geometric structures of the nickel-acetyl intermediate have been characterized using time-resolved optical, electron paramagnetic resonance, and X-ray absorption spectroscopy in conjunction with quantum chemical calculations. Moreover, we demonstrate that the nickel-acetyl species is chemically competent for selective acyl transfer upon thiol addition to biosynthesize an activated thioester. Drawing an analogy to the native enzyme, a mechanism for thioester generation by this ACS model has been proposed. The fundamental insight into the enzymatic process provided by this rudimentary ACS model has implications for the evolution of primitive ACS-like proteins. Ultimately, these findings offer strategies for development of highly active catalysts for sustainable generation of liquid fuels from one-carbon substrates, with potential for broad applications across diverse fields ranging from energy storage to environmental remediation.

The optimal docking strength for reversibly tethered kinases.

Many kinases use reversible docking interactions to augment the specificity of their catalytic domains. Such docking interactions are often structurally independent of the catalytic domain, which allow for a flexible combination of modules in evolution and in bioengineering. The affinity of docking interactions spans several orders of magnitude. This led us to ask how the affinity of the docking interaction affects enzymatic activity and how to pick the optimal interaction module to complement a given substrate. Here, we develop equations that predict the optimal binding strength of a kinase docking interaction and validate it using numerical simulations and steady-state phosphorylation kinetics for tethered protein kinase A. We show that a kinase-substrate pair has an optimum docking strength that depends on their enzymatic constants, the tether architecture, the substrate concentration, and the kinetics of the docking interactions. We show that a reversible tether enhances phosphorylation rates most when 1) the docking strength is intermediate, 2) the substrate is nonoptimal, 3) the substrate concentration is low, 4) the docking interaction has rapid exchange kinetics, and 5) the tether optimizes the effective concentration of the intramolecular reaction. This work serves as a framework for interpreting mutations in kinase docking interactions and as a design guide for engineering enzyme scaffolds.