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Saidqulov, Sanjar H. "MECHANISM OF PROPANE-BUTANE FRACTION DECOMPOSITION PROCESS INTO LOW MOLECULAR SATURATED AND UNSATURATED HYDROCARBONS." International Journal of Advance Scientific Research 05, no. 12 (2024): 336–48. https://doi.org/10.37547/ijasr-04-12-52.
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The decomposition of propane-butane fractions into low molecular weight saturated and unsaturated hydrocarbons is a key process in petrochemical production. This study explores the kinetic parameters and reaction mechanisms using reactors designed for impulse and continuous flow operations. The results indicate that the decomposition reactions follow first-order kinetics under specific experimental conditions. Conducted at temperatures ranging from 400°C to 700°C with catalysts, the experiments reveal that the process occurs at two distinct active catalytic sites (Z and Z). The mechanism involves the formation of surface radical complexes (C-Z), which govern the reaction pathways. Depending on the stability of these complexes, the process proceeds through either sequential hydrogen detachment, leading to carbon formation on the catalyst surface, or hydrogen recombination from the gas phase with the C-Z complex, resulting in methane production. This study provides valuable insights into the decomposition mechanisms of propane-butane fractions and lays the groundwork for optimizing catalytic processes to enhance the yield of desired low molecular weight hydrocarbons.
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Hirst, Judy. "Towards the molecular mechanism of respiratory complex I." Biochemical Journal 425, no. 2 (2009): 327–39. http://dx.doi.org/10.1042/bj20091382.
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Complex I (NADH:quinone oxidoreductase) is crucial to respiration in many aerobic organisms. In mitochondria, it oxidizes NADH (to regenerate NAD+ for the tricarboxylic acid cycle and fatty-acid oxidation), reduces ubiquinone (the electrons are ultimately used to reduce oxygen to water) and transports protons across the mitochondrial inner membrane (to produce and sustain the protonmotive force that supports ATP synthesis and transport processes). Complex I is also a major contributor to reactive oxygen species production in the cell. Understanding the mechanisms of energy transduction and reactive oxygen species production by complex I is not only a significant intellectual challenge, but also a prerequisite for understanding the roles of complex I in disease, and for the development of effective therapies. One approach to defining a complicated reaction mechanism is to break it down into manageable parts that can be tackled individually, before being recombined and integrated to produce the complete picture. Thus energy transduction by complex I comprises NADH oxidation by a flavin mononucleotide, intramolecular electron transfer from the flavin to bound quinone along a chain of iron–sulfur clusters, quinone reduction and proton translocation. More simply, molecular oxygen is reduced by the flavin, to form the reactive oxygen species superoxide and hydrogen peroxide. The present review summarizes and evaluates experimental data that pertain to the reaction mechanisms of complex I, and describes and discusses contemporary mechanistic hypotheses, proposals and models.
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Sakamoto, Naonari, Keita Sekizawa, Soichi Shirai, et al. "(Digital Presentation) Investigate the Reaction Mechanism in the C3H7OH Electrochemical Reduction Reaction from CO2 Using Dinuclear Cuprous Molecular Catalyst." ECS Meeting Abstracts MA2024-02, no. 62 (2024): 4256. https://doi.org/10.1149/ma2024-02624256mtgabs.
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The urgent global challenge of climate change and the depletion of energy resources have spotlighted the technology of converting carbon dioxide (CO2) into valuable carbon-based products. The CO2 reduction reaction (CO2RR) via metal complex molecules is expected to improve and enhance the electronic/chemical environment of the catalytic active sites through control with freely modulable organic ligands. The selectivity for the formation of formic acid and carbon monoxide from CO2 in organic solvents has been successfully controlled in some molecular catalysts by small structural differences in the ligands. For catalytic reactions in organic solvents, NMR and other common analytical methods can be used to follow structural changes and reaction intermediates during the reaction of unimolecular molecular catalysts. The study of detailed reaction processes has led to ligand design guidelines that contribute to higher reaction rates and improved selectivity. However, analytical methods still need to be developed for heterogeneous molecular catalysts used in water on electrodes. Catalysts capable of producing C2 products, such as ethylene and ethanol, require methods to detect intermediates in multi-electron reduction processes involving C-C coupling reactions. Current C2 producing molecular catalysts are known to decompose during reactions, turning into metals and not fully utilizing their precisely controlled active sites. Therefore, developing structurally stable molecular catalysts during reactions is critical to understanding these mechanisms. In this study, we have demonstrated a Br-bridged copper dinuclear molecular catalyst with high robustness for CO2/CO reduction reactions, producing C3+ products including C3H7OH beyond C2 products. Operando XAFS and various spectroscopic analyses show that the dinuclear molecular catalyst maintains a stable Cu(I) state during the reduction reaction, preventing decomposition. Operando spectroscopic analysis using localized surface plasmon resonance identifies key C2 and C3 coupling intermediates essential for C3 production. Reaction intermediates obtained by 13CO2-labeled operando analysis were also corroborated. DFT calculations propose a mechanism where the reaction proceeds at room temperature to form C3 coupling species. The transition state structures resulting from this mechanistic analysis suggest that the progression of C-C coupling in the Cu dinuclear molecular metal complex is facilitated by the formation of a CO2/CO-reduced intermediate species that bridges the two Cu active sites. The bridging intermediate can adjust the Cu-Cu distance during the reaction, attracting reducing species to one Cu side and accepting substrate to the other Cu side. C3H7OH is formed through C-C coupling at the bridging site in flexible Cu binuclear structures. The discovery of a robust molecular catalyst for C3+ production provides a molecular design guideline for developing next-generation catalysts for multicarbon CO2 reduction products.
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Kulakova, A. M., M. G. Khrenova, and A. V. Nemukhin. "Molecular mechanism of chromogenic substrate hydrolysis in the active site of human carboxylesterase-1." Biomeditsinskaya Khimiya 67, no. 3 (2021): 300–305. http://dx.doi.org/10.18097/pbmc20216703300.
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Human carboxylesterases are involved in the protective processes of detoxification during the hydrolytic metabolism of xenobiotics. Knowledge of the molecular mechanisms of substrates hydrolysis in the enzymes active site is necessary for the rational drug design. In this work, the molecular mechanism of the hydrolysis reaction of para-nitrophenyl acetate in the active site of human carboxylesterase was determined using modern methods of molecular modeling. According to the combined method of quantum mechanics/molecular mechanics calculations, the chemical reaction occurs within four elementary steps, including two steps of the acylation stage, and two steps of the deacylation stage. All elementary steps have low energy barriers, with the gradual lowering of the intermediate energies that stimulates reaction in the forward direction. The molecular docking was used to estimate the binding constants of the enzyme-substrate complex and the dissociation constant of enzyme-product complexes. The effective kinetic parameters of the enzymatic hydrolysis in the active site of carboxylesterase are determined by numerical solution of the differential kinetic equations.
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Zhang, Lanjun, Yujia Han, Dexin Xu, et al. "Study on the Reaction Path of -CH3 and -CHO Functional Groups during Coal Spontaneous Combustion: Quantum Chemistry and Experimental Research." Energies 15, no. 13 (2022): 4891. http://dx.doi.org/10.3390/en15134891.
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Coal spontaneous combustion (CSC) is a disaster that seriously threatens safe production in coal mines. Revealing the mechanism of CSC can provide a theoretical basis for its prevention and control. Compared with experimental research is limited by the complexity of coal molecular structure, the quantum chemical calculation method can simplify the complex molecular structure and realize the exploration of the mechanism of CSC from the micro level. In this study, toluene and phenylacetaldehyde were used as model compounds, and the quantum chemical calculation method was adopted. The reaction processes of the methyl and aldehyde groups with oxygen were investigated with the aid of the Gaussian 09 software, using the B3LYP functional and the 6-311 + G(d,p) basis set and including the D3 dispersion correction. On this basis, the generation mechanisms of CO and CO2, two important indicator gases in the process of CSC, were explored. The calculation results show that the Gibbs free energy changes and enthalpy changes in the two reaction systems are both of negative values. Accordingly, it is judged that the reactions belong to spontaneous exothermic reactions. In the reaction processes, the activation energy of CO is less than that of CO2, indicating that CO is formed more easily in the above-two reaction processes. In addition, the variations in concentrations of important oxidation products (CO and CO2) and main active functional groups (such as methyl, carboxyl and carbonyl) with temperature were revealed through a low-temperature oxidation experiment. The experimental results verify the accuracy of the above quantum chemical reaction path. Moreover, it is also found that the generation mechanisms of CO and CO2 in coal samples with different metamorphic degrees are different. To be specific, for low-rank coal (HYH), CO and CO2 mainly come from the oxidation of alkyl side chains; for high-rank coal (CQ), CO is produced by the oxidation of alkyl side chains, and CO2 is attributed to the inherent oxygen-containing structure.
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Zedler, Linda, Sven Krieck, Stephan Kupfer, and Benjamin Dietzek. "Resonance Raman Spectro-Electrochemistry to Illuminate Photo-Induced Molecular Reaction Pathways." Molecules 24, no. 2 (2019): 245. http://dx.doi.org/10.3390/molecules24020245.
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Electron transfer reactions play a key role for artificial solar energy conversion, however, the underlying reaction mechanisms and the interplay with the molecular structure are still poorly understood due to the complexity of the reaction pathways and ultrafast timescales. In order to investigate such light-induced reaction pathways, a new spectroscopic tool has been applied, which combines UV-vis and resonance Raman spectroscopy at multiple excitation wavelengths with electrochemistry in a thin-layer electrochemical cell to study [RuII(tbtpy)2]2+ (tbtpy = tri-tert-butyl-2,2′:6′,2′′-terpyridine) as a model compound for the photo-activated electron donor in structurally related molecular and supramolecular assemblies. The new spectroscopic method substantiates previous suggestions regarding the reduction mechanism of this complex by localizing photo-electrons and identifying structural changes of metastable intermediates along the reaction cascade. This has been realized by monitoring selective enhancement of Raman-active vibrations associated with structural changes upon electronic absorption when tuning the excitation wavelength into new UV-vis absorption bands of intermediate structures. Additional interpretation of shifts in Raman band positions upon reduction with the help of quantum chemical calculations provides a consistent picture of the sequential reduction of the individual terpyridine ligands, i.e., the first reduction results in the monocation [(tbtpy)Ru(tbtpy•)]+, while the second reduction generates [(tbtpy•)Ru(tbtpy•)]0 of triplet multiplicity. Therefore, the combination of this versatile spectro-electrochemical tool allows us to deepen the fundamental understanding of light-induced charge transfer processes in more relevant and complex systems.
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Kondyli, Aikaterini, and Wolfgang Schrader. "Investigation of the Behavior of Hydrocarbons during Crude Oil Fouling by High-Resolution Electrospray Ionization Mass Spectrometry." Energies 17, no. 6 (2024): 1299. http://dx.doi.org/10.3390/en17061299.
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Crude oil is probably the most complex natural chemical mixture processed in various ways to make fuel and fine chemicals among a wide range of products in industrial processing. The conditions of those industrial processes often include high temperatures, which often cause undesired chemical reactions. One of those reaction sequences is crude oil fouling, which finally results in the formation of undesired solid deposits of carbon material, a calamity that costs millions of dollars worldwide each year and produces toxic waste. However, the compounds involved in fouling, let alone the underlying reaction mechanisms, are not understood to date. Here, in order to investigate chemical fouling, the process was simulated under laboratory conditions, focusing on hydrocarbons as the main constituents of crude oil. The results demonstrate large differences within the hydrocarbon class of compounds before and after thermal treatment, even for a very light crude oil fraction, which initially does not contain any bigger or heavier compounds. Here, the fouling reaction is simulated and studied on the molecular level using high-resolution mass spectrometry. After thermal treatment, new, higher molecular weight hydrocarbon compounds with high aromaticity were detected. Results indicate that a radical reaction leads to the formation of larger and more aromatic compounds. The findings were verified by the use of a model hydrocarbon compound to study the mechanism.
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Zhang, Enhao, Xiumin Chen, Jie Zhou, et al. "Modeling the Carbothermal Chlorination Mechanism of Titanium Dioxide in Molten Salt Using a Deep Neural Network Potential." Materials 18, no. 3 (2025): 659. https://doi.org/10.3390/ma18030659.
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The molten salt chlorination method is one of the two main methods for producing titanium tetrachloride, an important intermediate product in the titanium industry. To effectively improve chlorination efficiency and reduce unnecessary waste salt generation, it is necessary to understand the mechanism of the molten salt chlorination reaction, and consequently this paper conducted studies on the carbon chlorination reaction mechanism in molten salts by combining ab initio molecular dynamics (AIMD) and deep potential molecular dynamics (DeePMD) methods. The use of DeePMD allowed for simulations on a larger spatial and longer time scale, overcoming the limitations of AIMD in fully observing complex reaction processes. The results comprehensively revealed the mechanism of titanium dioxide transforming into titanium tetrachloride. In addition, the presence form and conversion pathways of chlorine in the system were elucidated, and it was observed that chloride ions derived from NaCl can chlorinate titanium dioxide to yield titanium tetrachloride, which was validated through experimental studies. Self-diffusion coefficients of chloride ions in pure NaCl which were acquired by DeePMD showed good agreement with the experimental data.
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Couture, Christiane, and Anthony James Paine. "Mechanisms and models for homogeneous copper mediated ligand exchange reactions of the type: CuNu + ArX → ArNu + CuX." Canadian Journal of Chemistry 63, no. 1 (1985): 111–20. http://dx.doi.org/10.1139/v85-019.
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The title reactions are an important class of copper mediated nucleophilic aromatic substitution processes, which constitute a useful tool in the molecular design and synthesis of small molecules. We report the results of extensive investigation of these processes, primarily focussing on cyanodeiodination (ArI + CuCN → CuI + ArCN). Among the interesting features of these processes are: (a) an unusual rate equation involving autocatalysis by CuI product; (b) retardation by both excess nucleophile (as KCN) and excess leaving group (as KI), which compete with ArX to complex with CuNu; (c) only cuprous nucleophiles are active (ligand exchanged products from cupric salts arise from prior redox equilibria which form CuNu); (d) the halogen effect is large (kI ~ 40–100 kBr ~ 300–5000kCl) but the Hammett ρ value is zero; (e) ortho-alkyl groups do not hinder the reaction (and actually cause mild acceleration by relief of steric strain). Finally, the introduction of an ortho-COO− group accelerates the reaction by a factor of 104–105, but the general features of the accelerated reactions are also the same, again indicating a common mechanism, with entropic acceleration by ortho-carboxylate. Both kinetic and thermodynamic factors were considered in detail, the latter apparently for the first time. Applications to practical syntheses are considered, and novel mechanistic models for these interesting processes are discussed.
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Miller, RJ Dwayne. "2000 John C. Polanyi Award LectureMother Nature and the molecular Big Bang." Canadian Journal of Chemistry 80, no. 1 (2002): 1–24. http://dx.doi.org/10.1139/v01-199.
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Biological molecules are mesoscopic systems that bridge the quantum and classical worlds. At the single molecule level, there are often more than 1 × 104 degrees of freedom that are involved in protein-mediated processes. These molecules are sufficiently large that the bath coordinate convolved to the reaction at an active site is defined by the surrounding protein tertiary structure. In this context, the very interatomic forces that determine the active protein structures create a strongly associated system. Thus, the bath fluctuations leading to reactive crossings involve highly hindered motions within a myriad of local minima that would act to cast the reaction dynamics into the high viscosity limit appropriate to glasses. However, the time scales observed for biological events are orders of magnitude too fast to meet this anticipated categorization. In this context, the apparent deterministic nature of biological processes represents an enormous challenge to our understanding of chemical processes. Somehow Nature has discovered a molecular scaffolding that enables minute amounts of energy to be efficiently channeled to perform biological functions without becoming entrapped in local minima. Clearly, energy derived from chemical processes is highly directed in biological systems. To understand this problem, we must first understand how energy is redistributed among the different degrees of freedom and fully characterize the protein relaxation processes along representative reaction coordinates in relation to these dissipative processes. This paper discusses the development of new nonlinear spectroscopic methods that have enabled interferometric sensitivity to protein motions on femtosecond time scales appropriate to the very fastest motions (i.e., bond breaking or the molecular "Big Bang") out to the slowest relaxation steps. This work has led to the Collective Mode Coupling Model as an explanation of the required reduced dimensionality in biological systems. Within this model, the largest coupling coefficients of the reaction coordinate are to the damped inertial collective modes of the protein defined by the strongly correlated secondary structures. These modes act to guide the reaction along the correct seam(s) in an otherwise highly complex potential energy surface. The mechanism by which biological molecules have been able to harness chemical energy over meso-length scales represents the first step towards higher levels of organization. The new insight afforded by the collective mode mechanism may prove important in understanding this larger issue of scaling in biological systems.Key words: biodynamics, energy transduction, ultrafast spectroscopy, nonlinear spectroscopy, primary processes in biology.
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Ilyin, Daniil V., William A. Goddard, Julius J. Oppenheim, and Tao Cheng. "First-principles–based reaction kinetics from reactive molecular dynamics simulations: Application to hydrogen peroxide decomposition." Proceedings of the National Academy of Sciences 116, no. 37 (2018): 18202–8. http://dx.doi.org/10.1073/pnas.1701383115.
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This paper presents our vision of how to use in silico approaches to extract the reaction mechanisms and kinetic parameters for complex condensed-phase chemical processes that underlie important technologies ranging from combustion to chemical vapor deposition. The goal is to provide an analytic description of the detailed evolution of a complex chemical system from reactants through various intermediates to products, so that one could optimize the efficiency of the reactive processes to produce the desired products and avoid unwanted side products. We could start with quantum mechanics (QM) to ensure an accurate description; however, to obtain useful kinetics we need to average over ∼10-nm spatial scales for ∼1 ns, which is prohibitively impractical with QM. Instead, we use the reactive force field (ReaxFF) trained to fit QM to carry out the reactive molecular dynamics (RMD). We focus here on showing that it is practical to extract from such RMD the reaction mechanisms and kinetics information needed to describe the reactions analytically. This analytic description can then be used to incorporate the correct reaction chemistry from the QM/ReaxFF atomistic description into larger-scale simulations of ∼10 nm to micrometers to millimeters to meters using analytic approaches of computational fluid dynamics and/or continuum chemical dynamics. In the paper we lay out the strategy to extract the mechanisms and rate parameters automatically without the necessity of knowing any details of the chemistry. We consider this to be a proof of concept. We refer to the process as RMD2Kin (reactive molecular dynamics to kinetics) for the general approach and as ReaxMD2Kin (ReaxFF molecular dynamics to kinetics) for QM-ReaxFF–based reaction kinetics.
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Tolasa, Diriba. "Molecular Dynamics Simulations: Unraveling the Complexities of Chemical Reactions at the Atomic Level." American Journal of Physics and Applications 13, no. 3 (2025): 46–58. https://doi.org/10.11648/j.ajpa.20251303.11.
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Molecular dynamics (MD) simulations have emerged as a cornerstone computational technique within the realms of chemistry and materials science, offering profound insights into the intricate behaviors of molecular systems at the atomic scale. By leveraging the principles of classical mechanics and statistical physics, MD simulations afford researchers a detailed, time-resolved perspective on the dynamical behavior of molecules, thereby facilitating the exploration of reaction mechanisms that often elude conventional experimental methodologies. This paper provides a comprehensive overview of the methodologies and diverse applications of molecular dynamics simulations in elucidating the complex processes that underpin chemical reactions. We delve into the fundamental principles of MD, encompassing force field parameterization, integration algorithms, and boundary conditions, underscoring their critical roles in accurately modeling molecular interactions. The selection of potential energy functions, including empirical force fields and abilities methods, is scrutinized, as it significantly impacts the fidelity of the simulations and the reliability of the resultant data. A notable advantage of MD simulations lies in their capacity to capture the temporal evolution of molecular systems, enabling the observation of transient states and intermediates that are pivotal in reaction pathways. Through the analysis of trajectory data, researchers can extract invaluable information regarding reaction coordinates, energy barriers, and the influence of solvent dynamics on reaction kinetics. Furthermore, advanced techniques such as umbrella sampling and meta dynamics are employed to enhance the exploration of conformational space, allowing for the investigation of rare events and transition states that are crucial in determining reaction outcomes. The applicability of MD simulations transcends traditional chemical reactions; they are instrumental in the investigation of biomolecule processes, catalysis, and materials design. For instance, the dynamics of enzyme-substrate interactions can be elucidated through MD, yielding insights into catalytic mechanisms and informing the design of more efficient catalysts. Similarly, the behavior of polymers and nanomaterial’s under varying conditions can be meticulously examined, paving the way for the development of novel materials with tailored properties.
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Bunik, Victoria I., and Alisdair R. Fernie. "Metabolic control exerted by the 2-oxoglutarate dehydrogenase reaction: a cross-kingdom comparison of the crossroad between energy production and nitrogen assimilation." Biochemical Journal 422, no. 3 (2009): 405–21. http://dx.doi.org/10.1042/bj20090722.
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Mechanism-based inhibitors and both forward and reverse genetics have proved to be essential tools in revealing roles for specific enzymatic processes in cellular function. Here, we review experimental studies aimed at assessing the impact of OG (2-oxoglutarate) oxidative decarboxylation on basic cellular activities in a number of biological systems. After summarizing the catalytic and regulatory properties of the OGDHC (OG dehydrogenase complex), we describe the evidence that has been accrued on its cellular role. We demonstrate an essential role of this enzyme in metabolic control in a wide range of organisms. Targeting this enzyme in different cells and tissues, mainly by its specific inhibitors, effects changes in a number of basic functions, such as mitochondrial potential, tissue respiration, ROS (reactive oxygen species) production, nitrogen metabolism, glutamate signalling and survival, supporting the notion that the evolutionary conserved reaction of OG degradation is required for metabolic adaptation. In particular, regulation of OGDHC under stress conditions may be essential to overcome glutamate excitotoxicity in neurons or affect the wound response in plants. Thus, apart from its role in producing energy, the flux through OGDHC significantly affects nitrogen assimilation and amino acid metabolism, whereas the side reactions of OGDHC, such as ROS production and the carboligase reaction, have biological functions in signalling and glyoxylate utilization. Our current view on the role of OGDHC reaction in various processes within complex biological systems allows us a far greater fundamental understanding of metabolic regulation and also opens up new opportunities for us to address both biotechnological and medical challenges.
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Capurso, Matías, Rodrigo Gette, Gabriel Radivoy, and Viviana Dorn. "The Sn2 Reaction: A Theoretical-Computational Analysis of a Simple and Very Interesting Mechanism." Proceedings 41, no. 1 (2019): 81. http://dx.doi.org/10.3390/ecsoc-23-06514.
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Bimolecular nucleophilic substitution (SN2) reaction is one of the most frequently processes chosen as model mechanism to introduce undergraduate chemistry students to computational chemistry methodology. In this work, we performed a computational analysis for the ionic SN2 reaction, where the nucleophile charged (X−; X=F, Cl, Br, I) attacks the carbon atom of the substrate (CH3Cl) through a backside pathway, and simultaneously, the leaving group is displaced (Cl−). The calculations were performed applying DFT methods with the Gaussian09 program, the B3LYP functional, the 6-31+G* basis set for all atoms except iodine (6-311G*), and the solvents effects (acetonitrile and cyclohexane) were evaluated with the PCM model. We evaluated the potential energy surface (PES) for the mentioned reaction considering the reactants, the formation of an initial complex between the nucleophile and the substrate, the transition state, a final complex where the leaving group is still bound to the substrate and the products. We analyzed the atomic charge (ESP) and the bond distance throughout the process. Gas phase and solvent studies were performed in order to analyze the solvation effects on the reactivity of the different nucleophiles. We observed that increasing solvent polarity, decreases reaction rates. On the other hand, we thought it would be enriching, to carry out a reactivity analysis from the point of view of molecular orbitals. Therefore, we analyzed the MOs HOMO and the MOs LUMO of the different stationary states on PES, both in a vacuum (gas phase) and in acetonitrile as the solvent.
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Doddipatla, Srinivas, Chao He, Ralf I. Kaiser, et al. "A chemical dynamics study on the gas phase formation of thioformaldehyde (H2CS) and its thiohydroxycarbene isomer (HCSH)." Proceedings of the National Academy of Sciences 117, no. 37 (2020): 22712–19. http://dx.doi.org/10.1073/pnas.2004881117.
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Complex organosulfur molecules are ubiquitous in interstellar molecular clouds, but their fundamental formation mechanisms have remained largely elusive. These processes are of critical importance in initiating a series of elementary chemical reactions, leading eventually to organosulfur molecules—among them potential precursors to iron-sulfide grains and to astrobiologically important molecules, such as the amino acid cysteine. Here, we reveal through laboratory experiments, electronic-structure theory, quasi-classical trajectory studies, and astrochemical modeling that the organosulfur chemistry can be initiated in star-forming regions via the elementary gas-phase reaction of methylidyne radicals with hydrogen sulfide, leading to thioformaldehyde (H2CS) and its thiohydroxycarbene isomer (HCSH). The facile route to two of the simplest organosulfur molecules via a single-collision event affords persuasive evidence for a likely source of organosulfur molecules in star-forming regions. These fundamental reaction mechanisms are valuable to facilitate an understanding of the origin and evolution of the molecular universe and, in particular, of sulfur in our Galaxy.
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Ghabbour, Hazem A., Ahmed H. Bakheit, Essam Ezzeldin, and Gamal A. E. Mostafa. "Synthesis Characterization and X-ray Structure of 2-(2,6-Dichlorophenylamino)-2-imidazoline Tetraphenylborate: Computational Study." Applied Sciences 12, no. 7 (2022): 3568. http://dx.doi.org/10.3390/app12073568.
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The title compound tetraphenylborate salt of clonidine (Catapres®), 2-(2,6-dichlorophenylamino)-2-imidazoline tetraphenylborate (3), was prepared in 76 % yield by the reaction of 2-(2,6-dichlorophenylamino)-2-imidazoline hydrochloride (clonidine hydrochloride) (1) with sodium tetraphenylborate (2) in deionized water through anion exchange reaction at ambient temperature. The structure of the title borate salt was characterized by UV, thermal analysis, mass and NMR analyses. White crystals of (3) suitable for an X-ray structural analysis were obtained by slow growing from acetonitrile. The molecular structure of the titled compound (3) was crystallized in the acetonitrile, P21/c, a = 9.151 (3) Å, b = 12.522 (3) Å, c = 25.493 (6) Å, β = 105.161 (13)° V = 2819.5 (13) Å3, Z = 4. A DFT quantum chemistry calculation method was employed to investigate the interaction mechanism of clonidine with tetraphenylborate. The stable configurations of the complexes of clonidine with tetraphenylborate with electrostatic interactions were obtained. Finally, the interaction strength and type of the complexes were studied through the reduced density gradient (RDG) function. This study provides new theoretical insight into the interaction mechanism and a guide for screening and designing the optimal clonidine and tetraphenylborate reacting to form the complex.
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Abplanalp, Matthew J., Samer Gozem, Anna I. Krylov, Christopher N. Shingledecker, Eric Herbst, and Ralf I. Kaiser. "A study of interstellar aldehydes and enols as tracers of a cosmic ray-driven nonequilibrium synthesis of complex organic molecules." Proceedings of the National Academy of Sciences 113, no. 28 (2016): 7727–32. http://dx.doi.org/10.1073/pnas.1604426113.
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Complex organic molecules such as sugars and amides are ubiquitous in star- and planet-forming regions, but their formation mechanisms have remained largely elusive until now. Here we show in a combined experimental, computational, and astrochemical modeling study that interstellar aldehydes and enols like acetaldehyde (CH3CHO) and vinyl alcohol (C2H3OH) act as key tracers of a cosmic-ray-driven nonequilibrium chemistry leading to complex organics even deep within low-temperature interstellar ices at 10 K. Our findings challenge conventional wisdom and define a hitherto poorly characterized reaction class forming complex organic molecules inside interstellar ices before their sublimation in star-forming regions such as SgrB2(N). These processes are of vital importance in initiating a chain of chemical reactions leading eventually to the molecular precursors of biorelevant molecules as planets form in their interstellar nurseries.
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Tymchuk, A. F., O. O. Streltsova, and A. D. Purich. "CONTRIBUTION OF THE ASSOCIATION OF NATURAL HIGH-MOLECULAR COMPOUNDS IN IMPROVING THE EFFICIENCY OF FLOCCULATION PROCESSES." Odesa National University Herald. Chemistry 28, no. 2(85) (2023): 108–15. http://dx.doi.org/10.18524/2304-0947.2023.2(85).286608.
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Natural flocculants as chitosan and sodium alginate has a complex of environmental and physic-chemical properties: biodegradability, playback of the raw material base, reaction and complexing ability. Researches had shown that natural polymers can be used for flocculation of suspensions. Association has a specific role in the flocculation process. Association determined by the nature and charge density of the flocculants. It is necessary to understand the mechanism of processes in these systems in order to select an effective flocculants. The mechanism of action of compositions natural flocculants is different from synthetic. The state of biopolymers depends on the pH of the solution. The aim of our researches was to study the flocculation ability of the compositions natural flocculants. It was studied sedimentation stability of suspensions containing macromolecular substances (flocculants) of different nature. We used an aqueous suspension of kaolin and bentonite. Kaolin and bentonite were dried to constant weight. The concentration of the dispersed phase in suspensions was 1–3%. It was shown that the sedimentation stability defines as flocculants characteristics such as molecular weight, concentration, nature of flocculants, polyelectrolyte’s charge density and nature of the suspensions. It was found that compositions of natural flocculants chitosan and sodium alginate are more effective of individual flocculants. The degree of separation suspensions reaches 90–98%. The findings suggest that the studied natural flocculants have significant potential for use, thanks to a number of advantages: the efficiency of their actions, low reagent consumption, environmental safety.
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Opalade, Adedamola A., Elizabeth N. Grotemeyer, and Timothy A. Jackson. "Mimicking Elementary Reactions of Manganese Lipoxygenase Using Mn-hydroxo and Mn-alkylperoxo Complexes." Molecules 26, no. 23 (2021): 7151. http://dx.doi.org/10.3390/molecules26237151.
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Manganese lipoxygenase (MnLOX) is an enzyme that converts polyunsaturated fatty acids to alkyl hydroperoxides. In proposed mechanisms for this enzyme, the transfer of a hydrogen atom from a substrate C-H bond to an active-site MnIII-hydroxo center initiates substrate oxidation. In some proposed mechanisms, the active-site MnIII-hydroxo complex is regenerated by the reaction of a MnIII-alkylperoxo intermediate with water by a ligand substitution reaction. In a recent study, we described a pair of MnIII-hydroxo and MnIII-alkylperoxo complexes supported by the same amide-containing pentadentate ligand (6Medpaq). In this present work, we describe the reaction of the MnIII-hydroxo unit in C-H and O-H bond oxidation processes, thus mimicking one of the elementary reactions of the MnLOX enzyme. An analysis of kinetic data shows that the MnIII-hydroxo complex [MnIII(OH)(6Medpaq)]+ oxidizes TEMPOH (2,2′-6,6′-tetramethylpiperidine-1-ol) faster than the majority of previously reported MnIII-hydroxo complexes. Using a combination of cyclic voltammetry and electronic structure computations, we demonstrate that the weak MnIII-N(pyridine) bonds lead to a higher MnIII/II reduction potential, increasing the driving force for substrate oxidation reactions and accounting for the faster reaction rate. In addition, we demonstrate that the MnIII-alkylperoxo complex [MnIII(OOtBu)(6Medpaq)]+ reacts with water to obtain the corresponding MnIII-hydroxo species, thus mimicking the ligand substitution step proposed for MnLOX.
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Haufroid, Marie, Manon Mirgaux, Laurence Leherte, and Johan Wouters. "Crystal structures and snapshots along the reaction pathway of human phosphoserine phosphatase." Acta Crystallographica Section D Structural Biology 75, no. 6 (2019): 592–604. http://dx.doi.org/10.1107/s2059798319006867.
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The equilibrium between phosphorylation and dephosphorylation is one of the most important processes that takes place in living cells. Human phosphoserine phosphatase (hPSP) is a key enzyme in the production of serine by the dephosphorylation of phospho-L-serine. It is directly involved in the biosynthesis of other important metabolites such as glycine and D-serine (a neuromodulator). hPSP is involved in the survival mechanism of cancer cells and has recently been found to be an essential biomarker. Here, three new high-resolution crystal structures of hPSP (1.5–2.0 Å) in complexes with phosphoserine and with serine, which are the substrate and the product of the reaction, respectively, and in complex with a noncleavable substrate analogue (homocysteic acid) are presented. New types of interactions take place between the enzyme and its ligands. Moreover, the loop involved in the open/closed state of the enzyme is fully refined in a totally unfolded conformation. This loop is further studied through molecular-dynamics simulations. Finally, all of these analyses allow a more complete reaction mechanism for this enzyme to be proposed which is consistent with previous publications on the subject.
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Bazany, Denis, Hana Greifova, Lucia Zuscikova, et al. "Can Bisphenols Alter the Inflammation Process?" Life 15, no. 5 (2025): 782. https://doi.org/10.3390/life15050782.
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This review’s main purpose is to draw attention to the possible influence of widely used bisphenols on the inflammatory process. Bisphenols are endocrine-disrupting chemicals that are produced worldwide in great quantities. From this point of view, it is very important to clarify their influence on innate immune reactions, which protect the integrity of the body against the action of various pathogens on a daily basis. The inflammation process consists of several key factors that are produced at different levels of this reaction. Each of these levels can be affected by endocrine disruptors, from the point of view of modifying either the immune system cells that intervene in this process or the way in which they produce inflammatory mediators. The development of new recommendations for the use of bisphenols is a complex issue given their influence on inflammatory processes. Because the immune system and immune response are so intricate, bisphenols may pose more risk to humans than is presently recognized. This paper discusses the classification of bisphenols, the fundamental mechanism of inflammation, the characterization of inflammatory mediators, and the current knowledge of the molecular mechanisms behind the impact of bisphenols on the inflammatory response.
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Thanh, Vo Hong. "RSSALib: a library for stochastic simulation of complex biochemical reactions." Bioinformatics 36, no. 18 (2020): 4825–26. http://dx.doi.org/10.1093/bioinformatics/btaa602.
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Abstract Motivation Stochastic chemical kinetics is an essential mathematical framework for investigating the dynamics of biological processes, especially when stochasticity plays a vital role in their development. Simulation is often the only option for the analysis of many practical models due to their analytical intractability. Results We present in this article, the simulation library RSSALib, implementing our recently developed rejection-based stochastic simulation algorithm (RSSA) and a wide range of its improvements, to accelerate the simulation and analysis of biochemical reactions. RSSALib supports reactions with complex kinetics and time delays, necessary to model complexities of reaction mechanisms. Our library provides both an application program interface and a graphic user interface to ease the set-up and visualization of the simulation results. Availability and implementation RSSALib is freely available at: https://github.com/vo-hong-thanh/rssalib. Supplementary information Supplementary data are available at Bioinformatics online.
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Brönstrup, Mark, Detlef Schröder, and Helmut Schwarz. "Oxidative dealkylation of aromatic amines by "bare" FeO+ in the gas phase." Canadian Journal of Chemistry 77, no. 5-6 (1999): 774–80. http://dx.doi.org/10.1139/v99-065.
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The gas-phase oxidations of aniline, N-methylaniline, and N,N-dimethylaniline by FeO+ cation are examined by using mass spectrometric techniques. Although bare FeO+ is capable of hydroxylating aromatic CH bonds, the fate of the oxidation of arylamines is determined by docking of the FeO+ unit at nitrogen. The major reactions of the metastable aniline/FeO+ complex are losses of molecular hydrogen, ammonia, and water, all involving at least one N-H proton. N-alkylation results in a complete shift of the course of the reaction. The unimolecular processes observed can be regarded as initial steps of an oxidative dealkylation of the amines mediated by FeO+. More detailed mechanistic insight is obtained by examining the CH(D) bond activation of N-methyl-N-([D3]-methyl)aniline by bare and ligated FeO+ species. The gas-phase reactions of FeO+ with methylanilines show some similarities to the enzymatic dealkylation of amines by cytochrome P-450. The kinetic isotope effects observed experimentally suggest an electron transfer mechanism for the gas-phase reaction.Key words: mass spectrometry, gas-phase chemistry, iron, dealkylation, N,N-dimethylaniline.
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Shin, Dongyup, and Sang Soo Han. "Design Strategies for Oxygen Evolution Reaction Catalysts: Insights from a Kinetic Perspective via Constrained Ab Initio Molecular Dynamics." ECS Meeting Abstracts MA2024-02, no. 42 (2024): 2848. https://doi.org/10.1149/ma2024-02422848mtgabs.
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Abstract In the pursuit of sustainable energy, the efficient production of green hydrogen through electrochemical water splitting has emerged as a promising strategy.1 Central to this process is the optimization of the Oxygen Evolution Reaction (OER), where the necessity for a high overpotential at the anodic electrode poses a significant barrier. Among the myriad of catalysts studied, iridium oxides (IrOx) have garnered attention for their superior catalytic activity and stability in acidic environments.2 Yet, the quest for unlocking the full potential of IrOx catalysts necessitates a deeper dive into their operational mechanisms under OER conditions, a challenge that traditional Density Functional Theory (DFT) methodologies have struggled to meet due to their limited representation of the dynamic electrochemical environment intrinsic to OER catalysis.3 Addressing these challenges, our research introduces a novel approach by integrating constant Fermi-level ab initio molecular dynamics (AIMD) simulations with slow-growth kinetic analysis. This methodological innovation captures the complex electrochemical environment of OER catalysis, unveiling reaction pathways and energy barriers with close to actual electrochemical reaction. Through this approach, we explore the impact of the oxygen 2p orbital, Ir–O bond strength, and proton affinity on the Lattice Oxygen Mechanism (LOM) and Adsorbate Evolution Mechanism (AEM), establishing new paradigms for catalyst evaluation and design. A focal point of our study is the detailed analysis of the elemental phases of LOM and AEM, which provides a granular understanding of the catalytic actions within these mechanisms. In the case of LOM, our focus is on the dynamics and electronic state of lattice oxygen, which play pivotal roles in defining the energy barriers distinct to each elemental phase. This analysis identifies the electronic structure of lattice oxygen and the robustness of Ir–O bonds as key determinants of LOM activity. Similarly, the phase of AEM process is characterized by the sequential proton transfer of water molecules and surface proton, highlighting the importance of the structural arrangement of surface hydrogen and the proton affinity of lattice oxygen in determining AEM activation stages. Subsequent to the mechanism phase analysis, we present the validation of our theoretical insights through the suggestion and evaluation of E–IrTaO2, a lattice-elongated Ir-Ta bimetallic oxide catalyst designed to enhance LOM selectivity. The design of E–IrTaO2 is informed by kinetic analysis, with its activity evaluation underpinned by kinetic results that consider the thermodynamic energy diagram, including pathways through metastable states. This departure from conventional DFT methodologies signals a paradigm shift towards a kinetic-driven approach, crucial for unraveling the intricate behaviors of IrOx in OER processes and laying the groundwork for the development of sophisticated catalysts. This study not only provides an in-depth understanding of the catalytic mechanisms in OER processes but also introduces a programmable strategy for catalyst design, paving the way for the rational development of high-performance OER catalysts. References Taibi, E., Miranda, R., Carmo, M. & Blanco, H. Green hydrogen cost reduction. (2020). King, L. A. et al. A non-precious metal hydrogen catalyst in a commercial polymer electrolyte membrane electrolyser. Nature nanotechnology 14, 1071-1074 (2019). Mefford, J. T. et al. Water electrolysis on La1− x Sr x CoO3− δ perovskite electrocatalysts. Nature communications 7, 11053 (2016) Figure 1
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Guillamón, Eva, Mónica Oliva, Juan Andrés, et al. "Catalytic hydrogenation of azobenzene in the presence of a cuboidal Mo3S4 cluster via an uncommon sulfur-based H2 activation mechanism." ACS Catalysis 11, no. 2 (2020): 608–14. https://doi.org/10.1021/acscatal.0c05299.
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Azobenzene hydrogenation is catalyzed under moderate conditions by a cuboidal Mo<sub>3</sub>(μ<sub>3</sub>-S)(μ-S)<sub>3</sub> diamino complex via a cluster catalysis mechanism. Dihydrogen activation by the molecular [Mo<sub>3</sub>(μ<sub>3</sub>-S)(μ-S)<sub>3</sub>Cl<sub>3</sub>(dmen)<sub>3</sub>]<sup>+</sup> cluster cation takes place at the μ-S bridging atoms without direct participation of the metals in clear contrast with classical concepts. The reaction occurs with the formation of 1,2-diphenylhydrazine as an intermediate with similar appearance and disappearance rate constants. On the basis of DFT calculations, a mechanism is proposed in which formation of 1,2-diphenylhydrazine and aniline occurs through two interconnected catalytic cycles that share a common reaction step that involves H<sub>2</sub> addition to two of the bridging sulfur atoms of the catalyst to form a dithiolate Mo<sub>3</sub>(μ<sub>3</sub>-S)(μ-SH)<sub>2)</sub>(μ-S) adduct. Both catalytic cycles have similar activation barriers, in agreement with the experimental observation of close rate constant values. Microkinetic modeling of the process leads to computed concentration–time profiles in excellent agreement with the experimental ones providing additional support to the calculated reaction mechanism. Slight modifications on the experimental conditions of the catalytic protocol in combination with theoretical calculations discard a direct participation of the metal on the reaction mechanism. The effect of the ancillary ligands on the catalytic activity of the cluster fully agrees with the present mechanistic proposal. The results herein demonstrate the capability of molybdenum sulfide materials to activate hydrogen through an uncommon sulfur based mechanism opening attractive possibilities toward their applications as catalysts in other hydrogenation processes.
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Gerlits, Oksana, Amit Das, Jianhui Tian, et al. "Insights into the phosphoryl transfer catalyzed by cAMP-dependent protein kinase." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C449. http://dx.doi.org/10.1107/s2053273314095503.
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Protein kinases are involved in a number of cell signaling pathways. They catalyze phosphorylation of proteins and regulate the majority of cellular processes (such as growth, differentiation, lipid metabolism, regulation of sugar, nucleic acid synthesis, etc.). Chemically, protein kinases covalently transfer the gamma-phosphate group of a nucleoside triphosphate (e.g. ATP) to a hydroxyl group of a Ser, Thr or Tyr residue of substrate protein or peptide. The reaction involves moving hydrogen atoms between the enzyme, substrate and nucleoside. The unanswered question is whether the proton transfer from the Ser residue happens before the phosphoryl transfer using the general acid-base catalyst, Asp166, or after the reaction went through the transition state by directly protonating the phosphate group. To address this key question about the phosphoryl transfer, we determined a number of X-ray structures of ternary complexes of catalytic subunit of cAMP-dependent protein kinase (PKAc) with various substrates, nucleotides and cofactors. Importantly, we were able to trap and mimic the initial (Michaelis complex) and final (product complex) stages of the reaction. The results demonstrate that Mg2+, Ca2+, Sr2+, and Ba2+ metal ions bind to the active site and facilitate the reaction to produce ADP and a phosphorylated peptide. The study also revealed that metal-free PKAc can facilitate the phosphoryl transfer reaction; a result that was confirmed with single turnover enzyme kinetics measurements. Comparison of the product and the pseudo-Michaelis complex structures, in conjunction with molecular dynamics simulations, reveals conformational, coordination, and hydrogen bonding changes that help further our understanding of the mechanism, roles of metals, and active site residues involved in PKAc activity.
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Senapathi, Tharindu, Simon Bray, Christopher B. Barnett, Björn Grüning, and Kevin J. Naidoo. "Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)." Bioinformatics 35, no. 18 (2019): 3508–9. http://dx.doi.org/10.1093/bioinformatics/btz107.
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Abstract Motivation The pathway from genomics through proteomics and onto a molecular description of biochemical processes makes the discovery of drugs and biomaterials possible. A research framework common to genomics and proteomics is needed to conduct biomolecular simulations that will connect biological data to the dynamic molecular mechanisms of enzymes and proteins. Novice biomolecular modelers are faced with the daunting task of complex setups and a myriad of possible choices preventing their use of molecular simulations and their ability to conduct reliable and reproducible computations that can be shared with collaborators and verified for procedural accuracy. Results We present the foundations of Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE) developed on the Galaxy platform that makes possible fundamental molecular dynamics of proteins through workflows and pipelines via commonly used packages, such as NAMD, GROMACS and CHARMM. BRIDGE can be used to set up and simulate biological macromolecules, perform conformational analysis from trajectory data and conduct data analytics of large scale protein motions using statistical rigor. We illustrate the basic BRIDGE simulation and analytics capabilities on a previously reported CBH1 protein simulation. Availability and implementation Publicly available at https://github.com/scientificomputing/BRIDGE and https://usegalaxy.eu Supplementary information Supplementary data are available at Bioinformatics online.
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Karvatska, M., H. Lavrenyuk, V. P. Parhomenko, and B. Mykhalichko. "QUANTUM CHEMICAL SIMULATION OF THE INHIBITORY EFFECT OF AQUEOUS SOLUTIONS OF INORGANIC COPPER(II) SALTS ON THE COMBUSTION OF HYDROCARBONS." Bulletin of Lviv State University of Life Safety 23 (June 30, 2021): 33–38. http://dx.doi.org/10.32447/20784643.23.2021.05.
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Introduction. The search for chemicals that would have an effective fire extinguishing effect and the development of new fire extinguishers based on them is an extremely important problem of fire safety. It is known from the literature that new aqueous fire extinguishing agents (AFEAs) based on dissolved inorganic salts of transition metals, in particular, copper(II) chloride salts, have a rather efficient inhibitory effect on the hydrocarbon flame. However, the mechanism of inhibition of hydrocarbon combustion by this class of substances is not completely ascertained. However, it is reliable information about the processes that take place in the flame after the bringing in there of the aerosol of the mentioned AFEA will allow a systematic search for more optimal chemical composition of dissolved inorganic salts of d-metals. Purpose. The purpose of the work is to reveal the peculiarities of the interaction of concentrated aqueous solutions of copper(II) chloride salts with chemically active flame particles.Methods. Quantum chemical calculations of the chemical activity of radicals that appear in the flame and the physicochemical processes that occur in the flame after the bringing on there of AFEA aerosol.Results. The mechanism of a fire-extinguishing effect of aqueous solutions of inorganic copper(II) salts on a hydrocarbon flame is investigated by a calculation method. The sequence of stages of chemical processes that occur in the flame during the inhibiting combustion of hydrocarbons by AFEAs—concentrated solutions of CuCl2 and K2[CuCl4]—and the thermal effects of all reactions that accompany each of these stepwise transformations were ascertained. The stages of the interaction of gaseous Cu2Cl4 molecules with ×OH and ×H radicals in flame with the formation of first a radical-molecular complex and then a molecular complex are decisive in the process of inhibition and display the processes of interruption of chain reactions, i.e. deactivation of radicals in a flame.Conclusion. Thus, using the method of quantum chemical calculations the mechanism of inhibition of hydrocarbon combustion by copper(II) salts was offered. The mechanism of this process is considered to be associative, the decisive elementary act of which is carried out according to the scheme of addition of active radicals of a flame (×OH particles) to gaseous molecules Cu2Cl4 with the formation of radical-molecular complex [{Cu(×OH)Cl2}2] and with its subsequent deactivation by ×H particles.
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Stolarczyk, Elżbieta U., Weronika Strzempek, Marta Łaszcz, et al. "Anti-Cancer and Electrochemical Properties of Thiogenistein—New Biologically Active Compound." International Journal of Molecular Sciences 22, no. 16 (2021): 8783. http://dx.doi.org/10.3390/ijms22168783.
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Pharmacological and nutraceutical effects of isoflavones, which include genistein (GE), are attributed to their antioxidant activity protecting cells against carcinogenesis. The knowledge of the oxidation mechanisms of an active substance is crucial to determine its pharmacological properties. The aim of the present work was to explain complex oxidation processes that have been simulated during voltammetric experiments for our new thiolated genistein analog (TGE) that formed the self-assembled monolayer (SAM) on the gold electrode. The thiol linker assured a strong interaction of sulfur nucleophiles with the gold surface. The research comprised of the study of TGE oxidative properties, IR-ATR, and MALDI-TOF measurements of SAM before and after electrochemical oxidation. TGE has been shown to be electrochemically active. It undergoes one irreversible oxidation reaction and one quasi-reversible oxidation reaction in PBS buffer at pH 7.4. The oxidation of TGE results in electroactive products composed likely from TGE conjugates (e.g., trimers) as part of polymer. The electroactive centers of TGE and its oxidation mechanism were discussed using IR supported by quantum chemical and molecular mechanics calculations. Preliminary in-vitro studies indicate that TGE exhibits higher cytotoxic activity towards DU145 human prostate cancer cells and is safer for normal prostate epithelial cells (PNT2) than genistein itself.
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Xu, Zheng, So Fun Chau, Kwok Ho Lam, Ho Yin Chan, Tzi Bun Ng, and Shannon W. N. Au. "Crystal structure of the SENP1 mutant C603S–SUMO complex reveals the hydrolytic mechanism of SUMO-specific protease." Biochemical Journal 398, no. 3 (2006): 345–52. http://dx.doi.org/10.1042/bj20060526.
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SUMO (small ubiquitin-related modifier)-specific proteases catalyse the maturation and de-conjugation processes of the sumoylation pathway and modulate various cellular responses including nuclear metabolism and cell cycle progression. The active-site cysteine residue is conserved among all known SUMO-specific proteases and is not substitutable by serine in the hydrolysis reactions demonstrated previously in yeast. We report here that the catalytic domain of human protease SENP1 (SUMO-specific protease 1) mutant SENP1CC603S carrying a mutation of cysteine to serine at the active site is inactive in maturation and de-conjugation reactions. To further understand the hydrolytic mechanism catalysed by SENP1, we have determined, at 2.8 Å resolution (1 Å=0.1 nm), the X-ray structure of SENP1CC603S–SUMO-1 complex. A comparison of the structure of SENP2–SUMO-1 suggests strongly that SUMO-specific proteases require a self-conformational change prior to cleavage of peptide or isopeptide bond in the maturation and de-conjugation processes respectively. Moreover, analysis of the interface of SENP1 and SUMO-1 has led to the identification of four unique amino acids in SENP1 that facilitate the binding of SUMO-1. By means of an in vitro assay, we further demonstrate a novel function of SENP1 in hydrolysing the thioester linkage in E1-SUMO and E2-SUMO complexes. The results disclose a new mechanism of regulation of the sumoylation pathway by the SUMO-specific proteases.
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Davidson, Amy L., Elie Dassa, Cedric Orelle, and Jue Chen. "Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems." Microbiology and Molecular Biology Reviews 72, no. 2 (2008): 317–64. http://dx.doi.org/10.1128/mmbr.00031-07.
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SUMMARY ATP-binding cassette (ABC) systems are universally distributed among living organisms and function in many different aspects of bacterial physiology. ABC transporters are best known for their role in the import of essential nutrients and the export of toxic molecules, but they can also mediate the transport of many other physiological substrates. In a classical transport reaction, two highly conserved ATP-binding domains or subunits couple the binding/hydrolysis of ATP to the translocation of particular substrates across the membrane, through interactions with membrane-spanning domains of the transporter. Variations on this basic theme involve soluble ABC ATP-binding proteins that couple ATP hydrolysis to nontransport processes, such as DNA repair and gene expression regulation. Insights into the structure, function, and mechanism of action of bacterial ABC proteins are reported, based on phylogenetic comparisons as well as classic biochemical and genetic approaches. The availability of an increasing number of high-resolution structures has provided a valuable framework for interpretation of recent studies, and realistic models have been proposed to explain how these fascinating molecular machines use complex dynamic processes to fulfill their numerous biological functions. These advances are also important for elucidating the mechanism of action of eukaryotic ABC proteins, because functional defects in many of them are responsible for severe human inherited diseases.
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Hu, Zhong, and Lin Wei. "Review on Characterization of Biochar Derived from Biomass Pyrolysis via Reactive Molecular Dynamics Simulations." Journal of Composites Science 7, no. 9 (2023): 354. http://dx.doi.org/10.3390/jcs7090354.
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Biochar is a carbon-rich solid produced during the thermochemical processes of various biomass feedstocks. As a low-cost and environmentally friendly material, biochar has multiple significant advantages and potentials, and it can replace more expensive synthetic carbon materials for many applications in nanocomposites, energy storage, sensors, and biosensors. Due to biomass feedstock species, reactor types, operating conditions, and the interaction between different factors, the compositions, structure and function, and physicochemical properties of the biochar may vary greatly, traditional trial-and-error experimental approaches are time consuming, expensive, and sometimes impossible. Computer simulations, such as molecular dynamics (MD) simulations, are an alternative and powerful method for characterizing materials. Biomass pyrolysis is one of the most common processes to produce biochar. Since pyrolysis of decomposing biomass into biochar is based on the bond-order chemical reactions (the breakage and formation of bonds during carbonization reactions), an advanced reactive force field (ReaxFF)-based MD method is especially effective in simulating and/or analyzing the biomass pyrolysis process. This paper reviewed the fundamentals of the ReaxFF method and previous research on the characterization of biochar physicochemical properties and the biomass pyrolysis process via MD simulations based on ReaxFF. ReaxFF implicitly describes chemical bonds without requiring quantum mechanics calculations to disclose the complex reaction mechanisms at the nano/micro scale, thereby gaining insight into the carbonization reactions during the biomass pyrolysis process. The biomass pyrolysis and its carbonization reactions, including the reactivity of the major components of biomass, such as cellulose, lignin, and hemicellulose, were discussed. Potential applications of ReaxFF MD were also briefly discussed. MD simulations based on ReaxFF can be an effective method to understand the mechanisms of chemical reactions and to predict and/or improve the structure, functionality, and physicochemical properties of the products.
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Jiang, Chunqiang, Guohe Xu, and Jianping Gao. "Stimuli-Responsive Macromolecular Self-Assembly." Sustainability 14, no. 18 (2022): 11738. http://dx.doi.org/10.3390/su141811738.
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Macromolecular self-assembly has great potential for application in the field of the design of molecular machines, in molecular regulation, for biological tissue, and in biomedicine for the optical, electrical, and biological characteristics that the assembly unit does not possess. In this paper, the progress in macromolecular self-assembly is systematically reviewed, including its conception, processes and mechanisms, with a focus on macromolecular self-assembly by stimuli. According to the difference in stimuli, macromolecular self-assembly can be classified into temperature-responsive self-assembly, light-responsive self-assembly, pH-responsive self-assembly, redox-responsive self-assembly, and multi-responsive self-assembly. A preliminary study on constructing dynamic macromolecular self-assembly based on a chemical self-oscillating reaction is described. Furthermore, the problems of macromolecular self-assembly research, such as the extremely simple structure of artificial self-assembly and the low degree of overlap between macromolecular self-assembly and life sciences, are analyzed. The future development of stimuli-responsive macromolecular self-assembly should imitate the complex structures, processes and functions in nature and incorporate the chemical-oscillation reaction to realize dynamic self-assembly.
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Warneke, Jonas, Martin Mayer, Markus Rohdenburg, et al. "Direct functionalization of C−H bonds by electrophilic anions." Proceedings of the National Academy of Sciences 117, no. 38 (2020): 23374–79. http://dx.doi.org/10.1073/pnas.2004432117.
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Alkanes and [B12X12]2−(X = Cl, Br) are both stable compounds which are difficult to functionalize. Here we demonstrate the formation of a boron−carbon bond between these substances in a two-step process. Fragmentation of [B12X12]2−in the gas phase generates highly reactive [B12X11]−ions which spontaneously react with alkanes. The reaction mechanism was investigated using tandem mass spectrometry and gas-phase vibrational spectroscopy combined with electronic structure calculations. [B12X11]−reacts by an electrophilic substitution of a proton in an alkane resulting in a B−C bond formation. The product is a dianionic [B12X11CnH2n+1]2−species, to which H+is electrostatically bound. High-flux ion soft landing was performed to codeposit [B12X11]−and complex organic molecules (phthalates) in thin layers on surfaces. Molecular structure analysis of the product films revealed that C−H functionalization by [B12X11]−occurred in the presence of other more reactive functional groups. This observation demonstrates the utility of highly reactive fragment ions for selective bond formation processes and may pave the way for the use of gas-phase ion chemistry for the generation of complex molecular structures in the condensed phase.
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Ramzy, Esraa, Mohamed M. Ibrahim, Ibrahim M. El-Mehasseb, et al. "Synthesis, Biophysical Interaction of DNA/BSA, Equilibrium and Stopped-Flow Kinetic Studies, and Biological Evaluation of bis(2-Picolyl)amine-Based Nickel(II) Complex." Biomimetics 7, no. 4 (2022): 172. http://dx.doi.org/10.3390/biomimetics7040172.
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Reaction of bis(2-picolyl)amine (BPA) with Ni(II) salt yielded [(BPA)NiCl2(H2O)] (NiBPA). The Ni(II) in NiBPA bound to a BPA ligand, two chloride, and one aqua ligands. Because most medications inhibit biological processes by binding to a specific protein, the stopped-flow technique was used to investigate DNA/protein binding in-vitro, and a mechanism was proposed. NiBPA binds to DNA/protein more strongly than BPA via a static quenching mechanism. Using the stopped-flow technique, a mechanism was proposed. BSA interacts with BPA via a fast reversible step followed by a slow irreversible step, whereas NiBPA interacts via two reversible steps. DNA, on the other hand, binds to BPA and NiBPA via the same mechanism through two reversible steps. Although BSA interacts with NiBPA much faster, NiBPA has a much higher affinity for DNA (2077 M) than BSA (30.3 M). Compared to NiBPA, BPA was found to form a more stable BSA complex. When BPA and NiBPA bind to DNA, the Ni(II) center was found to influence the rate but not the mechanism, whereas, for BSA, the Ni(II) center was found to change both the mechanism and the rate. Additionally, NiBPA exhibited significant cytotoxicity and antibacterial activity, which is consistent with the binding constants but not the kinetic stability. This shows that in our situation, biological activity is significantly more influenced by binding constants than by kinetic stability. Due to its selectivity and cytotoxic activity, complex NiBPA is anticipated to be used in medicine.
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Lu, Haiyan, Hua Zhang, Shuling Xu, and Lingjun Li. "Review of Recent Advances in Lipid Analysis of Biological Samples via Ambient Ionization Mass Spectrometry." Metabolites 11, no. 11 (2021): 781. http://dx.doi.org/10.3390/metabo11110781.
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The rapid and direct structural characterization of lipids proves to be critical for studying the functional roles of lipids in many biological processes. Among numerous analytical techniques, ambient ionization mass spectrometry (AIMS) allows for a direct molecular characterization of lipids from various complex biological samples with no/minimal sample pretreatment. Over the recent years, researchers have expanded the applications of the AIMS techniques to lipid structural elucidation via a combination with a series of derivatization strategies (e.g., the Paternò–Büchi (PB) reaction, ozone-induced dissociation (OzID), and epoxidation reaction), including carbon–carbon double bond (C=C) locations and sn-positions isomers. Herein, this review summarizes the reaction mechanisms of various derivatization strategies for C=C bond analysis, typical instrumental setup, and applications of AIMS in the structural elucidation of lipids from various biological samples (e.g., tissues, cells, and biofluids). In addition, future directions of AIMS for lipid structural elucidation are discussed.
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Boamah, Mavis D., Kristal K. Sullivan, Katie E. Shulenberger, et al. "Low-energy electron-induced chemistry of condensed methanol: implications for the interstellar synthesis of prebiotic molecules." Faraday Discuss. 168 (2014): 249–66. http://dx.doi.org/10.1039/c3fd00158j.
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In the interstellar medium, UV photolysis of condensed methanol (CH<sub>3</sub>OH), contained in ice mantles surrounding dust grains, is thought to be the mechanism that drives the formation of “complex” molecules, such as methyl formate (HCOOCH<sub>3</sub>), dimethyl ether (CH<sub>3</sub>OCH<sub>3</sub>), acetic acid (CH<sub>3</sub>COOH), and glycolaldehyde (HOCH<sub>2</sub>CHO). The source of this reaction-initiating UV light is assumed to be local because externally sourced UV radiation cannot penetrate the ice-containing dark, dense molecular clouds. Specifically, exceedingly penetrative high-energy cosmic rays generate secondary electrons within the clouds through molecular ionizations. Hydrogen molecules, present within these dense molecular clouds, are excited in collisions with these secondary electrons. It is the UV light, emitted by these electronically excited hydrogen molecules, that is generally thought to photoprocess interstellar icy grain mantles to generate “complex” molecules. In addition to producing UV light, the large numbers of low-energy (<20 eV) secondary electrons, produced by cosmic rays, can also directly initiate radiolysis reactions in the condensed phase. The goal of our studies is to understand the low-energy, electron-induced processes that occur when high-energy cosmic rays interact with interstellar ices, in which methanol, a precursor of several prebiotic species, is the most abundant organic species. Using post-irradiation temperature-programmed desorption, we have investigated the radiolysis initiated by low-energy (7 eV and 20 eV) electrons in condensed methanol at ∼ 85 K under ultrahigh vacuum (5 × 10<sup>−10</sup> Torr) conditions. We have identified eleven electron-induced methanol radiolysis products, which include many that have been previously identified as being formed by methanol UV photolysis in the interstellar medium. These experimental results suggest that low-energy, electron-induced condensed phase reactions may contribute to the interstellar synthesis of “complex” molecules previously thought to form exclusively via UV photons.
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Tang, Liang, Haiyan Zhao, Theodore Christensen, Zihan Lin, and Annie Lynn. "Visualizing ATP hydrolysis in a viral DNA-packaging molecular motor." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1604. http://dx.doi.org/10.1107/s2053273314083958.
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Many DNA viruses encode powerful molecular machines to package viral genome into preformed protein shells. These DNA-packaging motors contain an ATPase module that converts the chemical reaction of ATP hydrolysis to physical motion of DNA. We previously determined the structures of the DNA-packaging motor gp2 of Shigella phage Sf6 in the apo form and in complex with ADP and ATP-gamma-S (Zhao et al, 2013, PNAS, 110, 8075). Here we report the structure of gp2 in complex with its substrate ATP at 2.0 Angstrom resolution. To our knowledge, this is the first time to capture, at high resolution, a precatalytic state for ASCE-superfamily ATPases, which include a large group of nucleic acid helicases and translocases involved in a broad range of cellular and viral processes. The structure reveals the precise architecture of the ATP-bound state of the motor immediately prior to catalysis. Comparison with structures of the apo and ADP-complexed forms unveils motions of the Walker A motif coupled with ATP and Mg2+ binding and ATP hydrolysis. In the Walker B motif, residue E118 undergoes a side chain conformational switching coupled with the ATP hydrolysis, whereas residue E119 locks residue R51 side chain to a conformation that is readily reachable to residue E118 side chain. Residue E121 in the Walker B motif deprotonates a water molecule, which acts as a nucleophile to attack the gamma-phosphorous, leading to ATP hydrolysis. The alpha-helix (residue G182-R194) in the linker domain undergoes a translational motion against the ATPase domain triggered by ATP hydrolysis, serving as a mechanism for translating the energy from the chemical reaction into physical movement of DNA. We further observed the time course of ATP hydrolysis by gp2 by determining structures of gp2:ATP complexes captured at various incubation time. These structures have made it possible to delineate, at atomic detail, the complete cycle of ATP hydrolysis of this viral DNA-packaging molecular motor.
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Perazzolli, Michele, Noemí Herrero, Lieven Sterck, et al. "Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat." BMC Genomics 17, no. 1 (2016): 838. https://doi.org/10.1186/s12864-016-3174-4.
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<strong>Background: </strong>Soil microorganisms are key determinants of soil fertility and plant health. Soil phytopathogenic fungi are one of the most important causes of crop losses worldwide. Microbial biocontrol agents have been extensively studied as alternatives for controlling phytopathogenic soil microorganisms, but molecular interactions between them have mainly been characterised in dual cultures, without taking into account the soil microbial community. We used an RNA sequencing approach to elucidate the molecular interplay of a soil microbial community in response to a plant pathogen and its biocontrol agent, in order to examine the molecular patterns activated by the microorganisms.<strong>Results: </strong>A simplified soil microcosm containing 11 soil microorganisms was incubated with a plant root pathogen (<i>Armillaria mellea</i>) and its biocontrol agent (<i>Trichoderma atroviride</i>) for 24 h under controlled conditions. More than 46 million paired-end reads were obtained for each replicate and 28,309 differentially expressed genes were identified in total. Pathway analysis revealed complex adaptations of soil microorganisms to the harsh conditions of the soil matrix and to reciprocal microbial competition/cooperation relationships. Both the phytopathogen and its biocontrol agent were specifically recognised by the simplified soil microcosm: defence reaction mechanisms and neutral adaptation processes were activated in response to competitive (<i>T. atroviride</i>) or non-competitive (<i>A. mellea</i>) microorganisms, respectively. Moreover, activation of resistance mechanisms dominated in the simplified soil microcosm in the presence of both <i>A. mellea</i> and <i>T. atroviride</i>. Biocontrol processes of <i>T. atroviride</i> were already activated during incubation in the simplified soil microcosm, possibly to occupy niches in a competitive ecosystem, and they were not further enhanced by the introduction of <i>A. mellea</i>.<strong>Conclusions: </strong>This work represents an additional step towards understanding molecular interactions between plant pathogens and biocontrol agents within a soil ecosystem. Global transcriptional analysis of the simplified soil microcosm revealed complex metabolic adaptation in the soil environment and specific responses to antagonistic or neutral intruders.
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Liu, Baojie, Lu Liu, Xin Qin, et al. "Effect of Substituents on Molecular Reactivity during Lignin Oxidation by Chlorine Dioxide: A Density Functional Theory Study." International Journal of Molecular Sciences 24, no. 14 (2023): 11809. http://dx.doi.org/10.3390/ijms241411809.
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Lignin is a polymer with a complex structure. It is widely present in lignocellulosic biomass, and it has a variety of functional group substituents and linkage forms. Especially during the oxidation reaction, the positioning effect of the different substituents of the benzene ring leads to differences in lignin reactivity. The position of the benzene ring branched chain with respect to methoxy is important. The study of the effect of benzene substituents on the oxidation reaction’s activity is still an unfinished task. In this study, density functional theory (DFT) and the m062x/6-311+g (d) basis set were used. Differences in the processes of phenolic oxygen intermediates formed by phenolic lignin structures (with different substituents) with chlorine dioxide during the chlorine dioxide reaction were investigated. Six phenolic lignin model species with different structures were selected. Bond energies, electrostatic potentials, atomic charges, Fukui functions and double descriptors of lignin model substances and reaction energy barriers are compared. The effects of benzene ring branched chains and methoxy on the mechanism of chlorine dioxide oxidation of lignin were revealed systematically. The results showed that the substituents with shorter branched chains and strong electron-absorbing ability were more stable. Lignin is not easily susceptible to the effects of chlorine dioxide. The substituents with longer branched chains have a significant effect on the flow of electron clouds. The results demonstrate that chlorine dioxide can affect the electron arrangement around the molecule, which directly affects the electrophilic activity of the molecule. The electron-absorbing effect of methoxy leads to a low dissociation energy of the phenolic hydroxyl group. Electrophilic reagents are more likely to attack this reaction site. In addition, the stabilizing effect of methoxy on the molecular structure of lignin was also found.
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Garrod, Robin T., Mihwa Jin, Kayla A. Matis, Dylan Jones, Eric R. Willis, and Eric Herbst. "Formation of Complex Organic Molecules in Hot Molecular Cores through Nondiffusive Grain-surface and Ice-mantle Chemistry." Astrophysical Journal Supplement Series 259, no. 1 (2022): 1. http://dx.doi.org/10.3847/1538-4365/ac3131.
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Abstract A new, more comprehensive model of gas–grain chemistry in hot molecular cores is presented, in which nondiffusive reaction processes on dust-grain surfaces and in ice mantles are implemented alongside traditional diffusive surface/bulk-ice chemistry. We build on our nondiffusive treatments used for chemistry in cold sources, adopting a standard collapse/warm-up physical model for hot cores. A number of other new chemical model inputs and treatments are also explored in depth, culminating in a final model that demonstrates excellent agreement with gas-phase observational abundances for many molecules, including some (e.g., methoxymethanol) that could not be reproduced by conventional diffusive mechanisms. The observed ratios of structural isomers methyl formate, glycolaldehyde, and acetic acid are well reproduced by the models. The main temperature regimes in which various complex organic molecules (COMs) are formed are identified. Nondiffusive chemistry advances the production of many COMs to much earlier times and lower temperatures than in previous model implementations. Those species may form either as by-products of simple-ice production, or via early photochemistry within the ices while external UV photons can still penetrate. Cosmic ray-induced photochemistry is less important than in past models, although it affects some species strongly over long timescales. Another production regime occurs during the high-temperature desorption of solid water, whereby radicals trapped in the ice are released onto the grain/ice surface, where they rapidly react. Several recently proposed gas-phase COM-production mechanisms are also introduced, but they rarely dominate. New surface/ice reactions involving CH and CH2 are found to contribute substantially to the formation of certain COMs.
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Alferova, Vera A., Anna A. Baranova, Olga A. Belozerova, et al. "Molecular Decoration and Unconventional Double Bond Migration in Irumamycin Biosynthesis." Antibiotics 13, no. 12 (2024): 1167. https://doi.org/10.3390/antibiotics13121167.
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Irumamycin (Iru) is a complex polyketide with pronounced antifungal activity produced by a type I polyketide (PKS) synthase. Iru features a unique hemiketal ring and an epoxide group, making its biosynthesis and the structural diversity of related compounds particularly intriguing. In this study, we performed a detailed analysis of the iru biosynthetic gene cluster (BGC) to uncover the mechanisms underlying Iru formation. We examined the iru PKS, including the domain architecture of individual modules and the overall spatial structure of the PKS, and uncovered discrepancies in substrate specificity and iterative chain elongation. Two potential pathways for the formation of the hemiketal ring, involving either an olefin shift or electrocyclization, were proposed and assessed using 18O-labeling experiments and reaction activation energy calculations. Based on our findings, the hemiketal ring is likely formed by PKS-assisted double bond migration and TE domain-mediated cyclization. Furthermore, putative tailoring enzymes mediating epoxide formation specific to Iru were identified. The revealed Iru biosynthetic machinery provides insight into the complex enzymatic processes involved in Iru production, including macrocycle sculpting and decoration. These mechanistic details open new avenues for a targeted architecture of novel macrolide analogs through synthetic biology and biosynthetic engineering.
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Nijakowski, Kacper, Martyna Ortarzewska, Jakub Jankowski, Anna Lehmann, and Anna Surdacka. "The Role of Cellular Metabolism in Maintaining the Function of the Dentine-Pulp Complex: A Narrative Review." Metabolites 13, no. 4 (2023): 520. http://dx.doi.org/10.3390/metabo13040520.
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The cellular metabolic processes ensure the physiological integrity of the dentine-pulp complex. Odontoblasts and odontoblast-like cells are responsible for the defence mechanisms in the form of tertiary dentine formation. In turn, the main defence reaction of the pulp is the development of inflammation, during which the metabolic and signalling pathways of the cells are significantly altered. The selected dental procedures, such as orthodontic treatment, resin infiltration, resin restorations or dental bleaching, can impact the cellular metabolism in the dental pulp. Among systemic metabolic diseases, diabetes mellitus causes the most consequences for the cellular metabolism of the dentine-pulp complex. Similarly, ageing processes present a proven effect on the metabolic functioning of the odontoblasts and the pulp cells. In the literature, several potential metabolic mediators demonstrating anti-inflammatory properties on inflamed dental pulp are mentioned. Moreover, the pulp stem cells exhibit the regenerative potential essential for maintaining the function of the dentine-pulp complex.
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Meinhardt, Hans. "Biological Pattern Formation as a Complex Dynamic Phenomenon." International Journal of Bifurcation and Chaos 07, no. 01 (1997): 1–26. http://dx.doi.org/10.1142/s0218127497000029.
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Self-enhancement coupled with one or more antagonistic reactions is the crucial element in pattern forming reactions. Depending on the parameter, this can lead to patterns in space and/or in time which can be either extremely robust and reproducible or highly variable. Complex patterns result from a linkage of many pattern forming reactions, one pattern generates the prerequisites for the next. The support these models have obtained recently by molecular-genetic observations give rise to the hope that in the future an interplay between theory and experiment will lead to a still better understanding of this central issue. Free from functional constraints, the diversity of patterns on the shells of mollusks provide a rich source to study the properties of dynamic systems in general. Everyday, we are confronted by systems that have an inherent tendency to change. The weather, the stock market, or the economic situation are examples in which self-enhancing and antagonistic processes also play a decisive role. The shell patterns are sufficiently complex to be a challenge but also sufficiently simple to be accessible to modeling. Their one-dimensional character and the preservation of the history of their formation provide unusual help for deciphering these patterns. They illustrate the range of behavior that can be generated by modifications of a basic mechanism. They can be regarded as a natural exercise book to study dynamic systems.
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Imanishi, Akihito. "(Invited) Surface Local Structure Dependence of Photoinduced Reaction Process on TiO2 Single Crystal Electrode in Aqueous Solution." ECS Meeting Abstracts MA2024-02, no. 59 (2024): 3988. https://doi.org/10.1149/ma2024-02593988mtgabs.
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Metal oxides such as TiO2 are widely used as electrocatalysts and photo-responsive electrodes in various electrochemical devices, and many researchers have studied them. However, the reaction processes at their interfaces are generally complex, and there are many aspects that remain to be elucidated. Even for TiO2 electrodes, which have been the most widely studied, the mechanism of interfacial reactions still remains unclear, especially the effects of crystal faces and atomic- to nano-level surface structures on electrode reactions. Our group has been investigated how the atomic- to nano-level structure of the TiO2 electrode surface affects the reaction at the TiO2 electrode interface. In our previous study, we revealed that the water photooxidation reaction (i.e. oxygen evolution reaction) on TiO2 surface accompanies with other three kinds of side reactions (photoluminescence (PL), surface roughening and non-radiative recombination) [1]. These reactions are competitive with each other and the ratio of their quantum efficiencies strongly depends on the atomic-scale surface local structure. Thus, we investigated the surface local structure dependence of those competitive reactions on TiO2 surface using atomically flat TiO2 (rutile) single crystal electrode those step-terrace structure was strictly controlled. It was revealed that the ratio of the quantum efficiency of four kinds of reactions strongly depends on the surface local structure such as step-terrace structure. On the other hand, the surface roughening process, which is one of the four competitive reactions, induced the drastic change of the surface local structure and also induced the change in the ratio of quantum efficiency of four kinds of competitive reactions, leading to the increase of the photocatalytic activity for oxygen photoevolution [2]. Such an investigation would be very important because some recent studies indicate that the surface local structure changes during the photooxidation process even in the case of practical catalyst. We also investigated the influence of nanostructure formed on the TiO2 electrode on the branch ratio of 4 competitive photooxidation reactions. We found that the overvoltage for O2 evolution on nanostructured electrode was decreased comparing with that on atomically flat (100) surface. We can explain these results by the spatial configuration of edge and facet sites which depends on the surface nanostructure. The organic synthesis by using of photooxidation reaction on photocatalysis has been investigated by many researchers. Although the formation of phenol from benzene on TiO2 surface by photo-induced oxidation reaction is one of the representative reactions, its molecular mechanism is still unclear. We can assumed that the quantum efficiencies of phenol generation depends on the atomic-scale surface local structure. We investigated the atomic leveled surface local structure dependence of the efficiency of photooxidation reaction of benzene (in HClO4aq solution) on Nb-doped rutile TiO2(110) single crystal electrode. It was found that the efficiency of the photooxidation reaction of benzene is largely affected by the step structure on the TiO2 surface [3]. Detailed analysis of the dependence on surface structure revealed that the photooxidation reaction of benzene and the photoinduced decomposition of water (Oxygen evolution reaction) proceed competitively via the same intermediate, and that the ratio of their efficiencies is strongly affected by the step direction and step density. [1] A. Imanishi, T. Okamura, N. Ohashi, R. Nakamura, Y. Nakato, J. Am. Chem. Soc., 129, 11569(2007)., A. Imanishi, K. Fukui, J. Phys. Chem. Lett. 5, 2108(2014) [2] E. Tsuji, K. Fukui, A. Imanishi, J. Phys. Chem. C, 118, 5406(2014). [3] S. Nagaoka, S. Kadono, K. Fukui, A. Imanishi, Abstract of the 87th ECSJ Spring Meeting (2020).
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Bobadilla, Luis F., Lola Azancot, Ligia A. Luque-Álvarez, et al. "Development of Power-to-X Catalytic Processes for CO2 Valorisation: From the Molecular Level to the Reactor Architecture." Chemistry 4, no. 4 (2022): 1250–80. http://dx.doi.org/10.3390/chemistry4040083.
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Nowadays, global climate change is likely the most compelling problem mankind is facing. In this scenario, decarbonisation of the chemical industry is one of the global challenges that the scientific community needs to address in the immediate future. Catalysis and catalytic processes are called to play a decisive role in the transition to a more sustainable and low-carbon future. This critical review analyses the unique advantages of structured reactors (isothermicity, a wide range of residence times availability, complex geometries) with the multifunctional design of efficient catalysts to synthesise chemicals using CO2 and renewable H2 in a Power-to-X (PTX) strategy. Fine-chemistry synthetic methods and advanced in situ/operando techniques are essential to elucidate the changes of the catalysts during the studied reaction, thus gathering fundamental information about the active species and reaction mechanisms. Such information becomes crucial to refine the catalyst’s formulation and boost the reaction’s performance. On the other hand, reactors architecture allows flow pattern and temperature control, the management of strong thermal effects and the incorporation of specifically designed materials as catalytically active phases are expected to significantly contribute to the advance in the valorisation of CO2 in the form of high added-value products. From a general perspective, this paper aims to update the state of the art in Carbon Capture and Utilisation (CCU) and PTX concepts with emphasis on processes involving the transformation of CO2 into targeted fuels and platform chemicals, combining innovation from the point of view of both structured reactor design and multifunctional catalysts development.
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Arbatskiy, Mikhail, Dmitriy Balandin, Ilya Akberdin, and Alexey Churov. "A Systems Biology Approach Towards a Comprehensive Understanding of Ferroptosis." International Journal of Molecular Sciences 25, no. 21 (2024): 11782. http://dx.doi.org/10.3390/ijms252111782.
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Ferroptosis is a regulated cell death process characterized by iron ion catalysis and reactive oxygen species, leading to lipid peroxidation. This mechanism plays a crucial role in age-related diseases, including cancer and cardiovascular and neurological disorders. To better mimic iron-induced cell death, predict the effects of various elements, and identify drugs capable of regulating ferroptosis, it is essential to develop precise models of this process. Such drugs can be tested on cellular models. Systems biology offers a powerful approach to studying biological processes through modeling, which involves accumulating and analyzing comprehensive research data. Once a model is created, it allows for examining the system’s response to various stimuli. Our goal is to develop a modular framework for ferroptosis, enabling the prediction and screening of compounds with geroprotective and antiferroptotic effects. For modeling and analysis, we utilized BioUML (Biological Universal Modeling Language), which supports key standards in systems biology, modular and visual modeling, rapid simulation, parameter estimation, and a variety of numerical methods. This combination fulfills the requirements for modeling complex biological systems. The integrated modular model was validated on diverse datasets, including original experimental data. This framework encompasses essential molecular genetic processes such as the Fenton reaction, iron metabolism, lipid synthesis, and the antioxidant system. We identified structural relationships between molecular agents within each module and compared them to our proposed system for regulating the initiation and progression of ferroptosis. Our research highlights that no current models comprehensively cover all regulatory mechanisms of ferroptosis. By integrating data on ferroptosis modules into an integrated modular model, we can enhance our understanding of its mechanisms and assist in the discovery of new treatment targets for age-related diseases. A computational model of ferroptosis was developed based on a modular modeling approach and included 73 differential equations and 93 species.
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Johnson, Matthew S., Charles J. McGill, and William H. Green. "Transitory sensitivity in automatic chemical kinetic mechanism analysis." International Journal of Chemical Kinetics, October 21, 2024. http://dx.doi.org/10.1002/kin.21766.
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AbstractDetailed chemical kinetic mechanisms are necessary for resolving many important chemical processes. As the chemistry of smaller molecules has become better grounded and quantum chemistry calculations have become cheaper, kineticists have become interested in constructing progressively larger kinetic mechanisms to model increasingly complex chemical processes. These large kinetic mechanisms prove incredibly difficult to refine and time‐consuming to interpret. Traditional sensitivity analysis on a large mechanism can range from inconvenient to practically impossible without special techniques to reduce the computational cost. We first present a new time‐local sensitivity analysis we term transitory sensitivity analysis. Transitory sensitivity analysis is demonstrated in an example to accurately identify traditionally sensitive reactions at an 18,000x speed up over traditional sensitivities. By fusing transitory sensitivity analysis with more traditional time‐local branching, pathway, and cluster analyses, we develop an algorithm for efficient automatic mechanism analysis. This automatic mechanism analysis at a time point is able to identify the reactions a target is most sensitive to using transitory sensitivity analysis and then propose hypotheses why the reaction might be sensitive using branching, pathway, and cluster analyses. We implement these algorithms within the reaction mechanism simulator (RMS) package, which enables us to report the automatic mechanism analysis results in highly readable text formats and in molecular flux diagrams.
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LI, Yuhai, Qingshun Bai, Yuheng Guan, et al. "The mechanism study of low-pressure air plasma cleaning on large-aperture optical surface unraveled by experiment and reactive molecular dynamics simulation." Plasma Science and Technology, April 22, 2022. http://dx.doi.org/10.1088/2058-6272/ac69b6.
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Abstract The low-pressure air plasma cleaning is an effective method for removing the organic contaminants on large-aperture optical components in-situ in the inertial confinement fusion facility. Chemical reactions play a significant role in plasma cleaning, which is a complex process involving abundant bonds cleavage and species generation. In this work, experiments and reactive molecular dynamics simulations were carried out to unravel the reaction mechanism between the benchmark organic contaminants of dibutyl phthalate and air plasma. The optical emission spectroscopy was used to study the overall evolution behaviors of excited molecular species and radical signals from air plasma as a reference to simulations. Detailed reaction pathways were revealed and characterized, and specific intermediate radicals and products were analyzed during experiments and simulation. The reactive species in the air plasma, such as O, HO2 and O3 radicals, played a crucial role in cleaving organic molecular structures. Together, our findings provide an atomic-level understanding of complex reaction processes of low-pressure air plasma cleaning mechanisms and are essential for its application in industrial plasma cleaning.
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Furushima, Yoshitomo, Takayuki Hirano, Keiji Naka, et al. "Effect of Silica Fillers on Epoxy–Imidazole Curing Reaction." Journal of Applied Polymer Science, February 20, 2025. https://doi.org/10.1002/app.56895.
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ABSTRACT(Epoxy–imidazole thermosetting resins exhibit a complex reaction mechanism involving two concurrent processes when heated: exothermic addition polymerization and endothermic reactions, during which the catalyst, imidazole, is regenerated. Thus, the relationship between conversion (defined by enthalpy change) and glass transition temperature varies with curing conditions. Herein, we investigate the effects of fillers on the properties of complex epoxy–imidazole systems. Fast scanning calorimetry reveals that the reaction rate in the samples with filler is delayed. Molecular dynamics simulations show that epoxy groups localize near the OH groups on the filler surface, supporting the interpretation that the addition reaction is suppressed by the formation of epoxy‐imidazole intermediate adducts. Matrix‐assisted laser desorption/ionization–mass spectrometry reveals the formation of short‐length linear chain structures in the early stages of the curing reaction for the filler‐containing sample. This behavior is similar to that observed in the non‐filler system, as reported in a previous study, indicating that the reaction mechanism is preserved in the filler‐containing system. This study provides valuable insights into the epoxy–imidazole reaction mechanism, thereby paving the way for further development of the material and promoting its industrial applications).