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1
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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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.
3
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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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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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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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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Kubař, Tomáš, and Marcus Elstner. "A hybrid approach to simulation of electron transfer in complex molecular systems." Journal of The Royal Society Interface 10, no. 87 (2013): 20130415. http://dx.doi.org/10.1098/rsif.2013.0415.
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Electron transfer (ET) reactions in biomolecular systems represent an important class of processes at the interface of physics, chemistry and biology. The theoretical description of these reactions constitutes a huge challenge because extensive systems require a quantum-mechanical treatment and a broad range of time scales are involved. Thus, only small model systems may be investigated with the modern density functional theory techniques combined with non-adiabatic dynamics algorithms. On the other hand, model calculations based on Marcus's seminal theory describe the ET involving several assumptions that may not always be met. We review a multi-scale method that combines a non-adiabatic propagation scheme and a linear scaling quantum-chemical method with a molecular mechanics force field in such a way that an unbiased description of the dynamics of excess electron is achieved and the number of degrees of freedom is reduced effectively at the same time. ET reactions taking nanoseconds in systems with hundreds of quantum atoms can be simulated, bridging the gap between non-adiabatic ab initio simulations and model approaches such as the Marcus theory. A major recent application is hole transfer in DNA, which represents an archetypal ET reaction in a polarizable medium. Ongoing work focuses on hole transfer in proteins, peptides and organic semi-conductors.
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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Chen, Chien-Hung, Vladimir Kiyan, Assylbek A. Zhylkibayev, et al. "Autoregulation of the Mechanistic Target of Rapamycin (mTOR) Complex 2 Integrity Is Controlled by an ATP-dependent Mechanism." Journal of Biological Chemistry 288, no. 38 (2013): 27019–30. http://dx.doi.org/10.1074/jbc.m113.498055.
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Nutrients are essential for living organisms because they fuel biological processes in cells. Cells monitor nutrient abundance and coordinate a ratio of anabolic and catabolic reactions. Mechanistic target of rapamycin (mTOR) signaling is the essential nutrient-sensing pathway that controls anabolic processes in cells. The central component of this pathway is mTOR, a highly conserved and essential protein kinase that exists in two distinct functional complexes. The nutrient-sensitive mTOR complex 1 (mTORC1) controls cell growth and cell size by phosphorylation of the regulators of protein synthesis S6K1 and 4EBP1, whereas its second complex, mTORC2, regulates cell proliferation by functioning as the regulatory kinase of Akt and other members of the AGC kinase family. The regulation of mTORC2 remains poorly characterized. Our study shows that the cellular ATP balance controls a basal kinase activity of mTORC2 that maintains the integrity of mTORC2 and phosphorylation of Akt on the turn motif Thr-450 site. We found that mTOR stabilizes SIN1 by phosphorylation of its hydrophobic and conserved Ser-260 site to maintain the integrity of mTORC2. The optimal kinase activity of mTORC2 requires a concentration of ATP above 1.2 mm and makes this kinase complex highly sensitive to ATP depletion. We found that not amino acid but glucose deprivation of cells or acute ATP depletion prevented the mTOR-dependent phosphorylation of SIN1 on Ser-260 and Akt on Thr-450. In a low glucose medium, the cells carrying a substitution of SIN1 with its phosphomimetic mutant show an increased rate of cell proliferation related to a higher abundance of mTORC2 and phosphorylation of Akt. Thus, the homeostatic ATP sensor mTOR controls the integrity of mTORC2 and phosphorylation of Akt on the turn motif site.
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Tursunova, N. V., M. G. Klinnikova, O. A. Babenko, and E. L. Lushnikova. "Molecular mechanisms of the cardiotoxic action of anthracycline antibiotics and statin-induced cytoprotective reactions of cardiomyocytes." Biomeditsinskaya Khimiya 66, no. 5 (2020): 357–71. http://dx.doi.org/10.18097/pbmc20206605357.
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The manifestation of the side cardiotoxic effect of anthracycline antibiotics limits their use in the treatment of malignant processes in some patients. The review analyzes the main causes of the susceptibility of cardiomyocytes to the damaging effect of anthracyclines, primarily associated with an increase in the processes of free radical oxidation. Currently, research is widely carried out to find ways to reduce anthracycline cardiotoxicity, in particular, the use of cardioprotective agents in the complex treatment of tumors. Hydroxymethylglutaryl coenzyme A reductase inhibitors (statins) have been shown to improve the function and metabolism of the cardiovascular system under various pathological impacts, therefore, it is proposed to use them to reduce cardiotoxic complications of chemotherapy. Statins exhibit direct (hypolipidemic) and pleiotropic effects due to the blockade of mevalonic acid synthesis and downward biochemical cascades that determine their cardioprotective properties. The main point of intersection of the pharmacological activity of anthracyclines and statins is the ability of both to regulate the functioning of small GTPase from the Rho family, and their effect in this regard is the opposite. The influence of statins on the modification and membrane dislocation of Rho proteins mediates the indirect antioxidant, anti-inflammatory, endothelioprotective, antiapoptotic effect. The mechanism of statin inhibition of doxorubicin blockade of the DNA-topoisomerase complex, which may be important in preventing cardiotoxic damage during chemotherapy, is discussed. At the same time, it should be noted that the use of statins can be accompanied by adverse side effects: a provocation of increased insulin resistance and glucose tolerance, which often causes them to be canceled in patients with impaired carbohydrate metabolism, so further studies are needed here. The review also analyzes data on the antitumor effect of statins, their ability to sensitize the tumor to treatment with cytostatic drug. It has been shown that the relationship between anthracycline antibiotics and statins is characterized not only by antagonism, but also in some cases by synergism. Despite some adverse effects, statins are one of the most promising cardio- and vasoprotectors for use in anthracycline cardiomyopathy.
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Wrotek, Sylwia, Justyna Sobocińska, Henryk M. Kozłowski, Małgorzata Pawlikowska, Tomasz Jędrzejewski, and Artur Dzialuk. "New Insights into the Role of Glutathione in the Mechanism of Fever." International Journal of Molecular Sciences 21, no. 4 (2020): 1393. http://dx.doi.org/10.3390/ijms21041393.
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Glutathione is one of the most important and potent antioxidants. The development of pharmacological compounds that can either increase or decrease glutathione concentrations has allowed investigation into the role of glutathione in various biological processes, including immune responses. Recent findings have shown that glutathione not only affects certain factors involved in immunological processes but also modifies complex immune reactions such as fever. Until recently, it was not known why some patients do not develop fever during infection. Data suggest that fever induction is associated with oxidative stress; therefore, antioxidants such as glutathione can reduce pyrexia. Surprisingly, new studies have shown that low glutathione levels can also inhibit fever. In this review, we focus on recent advances in this area, with an emphasis on the role of glutathione in immune responses accompanied by fever. We describe evidence showing that disturbed glutathione homeostasis may be responsible for the lack of fever during infections. We also discuss the biological significance of the antipyretic effects produced by pharmacological glutathione modulators.
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Gaffke, Lidia, Karolina Pierzynowska, Magdalena Podlacha, et al. "Underestimated Aspect of Mucopolysaccharidosis Pathogenesis: Global Changes in Cellular Processes Revealed by Transcriptomic Studies." International Journal of Molecular Sciences 21, no. 4 (2020): 1204. http://dx.doi.org/10.3390/ijms21041204.
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Mucopolysaccharidoses (MPS), a group of inherited metabolic disorders caused by deficiency in enzymes involved in degradation of glycosaminoglycans (GAGs), are examples (and models) of monogenic diseases. Accumulation of undegraded GAGs in lysosomes was supposed to be the major cause of MPS symptoms; however, their complexity and variability between particular types of the disease can be hardly explained by such a simple storage mechanism. Here we show that transcriptomic (RNA-seq) analysis of the material derived from fibroblasts of patients suffering from all types and subtypes of MPS, supported by RT-qPCR results, revealed surprisingly large changes in expression of genes involved in various cellular processes, indicating complex mechanisms of MPS. Although each MPS type and subtype was characterized by specific changes in gene expression profile, there were genes with significantly changed expression relative to wild-type cells that could be classified as common for various MPS types, suggesting similar disturbances in cellular processes. Therefore, both common features of all MPS types, and differences between them, might be potentially explained on the basis of changes in certain cellular processes arising from disturbed regulations of genes’ expression. These results may shed a new light on the mechanisms of genetic diseases, indicating how a single mutation can result in complex pathomechanism, due to perturbations in the network of cellular reactions. Moreover, they should be considered in studies on development of novel therapies, suggesting also why currently available treatment methods fail to correct all/most symptoms of MPS. We propose a hypothesis that disturbances in some cellular processes cannot be corrected by simple reduction of GAG levels; thus, combined therapies are necessary which may require improvement of these processes.
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Feskov, Sergey. "The Green’s Function Method for Evaluating the Transient Spectra of Non-Equilibrium Molecular Systems." Mathematical Physics and Computer Simulation, no. 4 (December 2022): 95–106. http://dx.doi.org/10.15688/mpcm.jvolsu.2022.4.8.
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Interest in ultrafast photochemical processes is due to their role in wildlife and the possibility of using them in solar energy conversion devices. Significant part of experimental research in this area is carried out using different spectroscopic techniques, for example, based on recording the dynamic response of the system to optical excitation by a short laser pulse. This method is basic for photochemistry and is used for studying both small inorganic molecules in liquids or mixtures, and complex biological objects, such as photosynthetic reaction centers of bacteria and plants. Time-resolved luminescence/absorption spectra contain information about the processes of population of the electronic and vibrational states of the system, and therefore make it possible to study the mechanisms of photoreactions. At the same time, the question of the correct interpretation of experimental data in the case of ultrafast reactions at picosecond timescales is still relevant. The traditional approach is based on the decomposition of transient spectra into the dynamic components, associated with different electronic states. This state-associated analysis turns out to be much less accurate in ultrafast nonequilibrium reactions. The spectral dynamics of the system in this case depends not only on chemical transformations (that is, changes in state populations), but also on the evolution of the spectral response for each of the states. Particularly, relaxation of high-frequency intramolecular vibrations in ultrafast reactions was shown to cause not only a shift in the luminescence spectrum, but also significant changes in spectral profiles themselves. An assumption about the invariable shape of individual spectral components cannot be justified here. Relevant analysis of spectral dynamics in such systems thus requires taking into account the nonequilibrium state of intramolecular degrees of freedom and the environment. Development of theoretical models of nonequilibrium processes, as well as software tools for numerical simulation of spectral dynamics and the fitting techniques for experimental results data, allows us to improve the relevance of the analysis. This study is devoted to the development of a mathematical model of spectral dynamics of macromolecular systems, in which photoexcitation triggers a series of ultrafast electron transfer reactions involving several redox centers. The main attention is paid to accounting for nonequilibrium states of the medium and intramolecular degrees of freedom formed both at the stage of photoexcitation and in the course of a multistage reaction. This allows us to expand the range of phenomena under study and apply the model for interpretation of experimental data on multistage charge transfer in biological objects. The model is based on the semiclassical theory of multistage electron transfer in a multicomponent non-Debye solvent, as well as the Green’s function method for the classical (polarization) and quantum (intramolecular) coordinates of the system.
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Pivovarova, Nadezhda Anatolievna. "Characteristics of molecular interaction in oil dispersed systems." Oil and gas technologies and environmental safety 2023, no. 2 (2023): 23–33. http://dx.doi.org/10.24143/1812-9498-2023-2-23-33.
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Oil, gas condensates, oil products present a complex colloidal-dispersed system which often demonstrates the abnormally changing properties when external conditions change. Mixing the petroleum products can be accompanied by a non-linear behavior accompanied by synergistic and antagonistic effects. Understanding of the oil and oil products as oil dispersed systems, the specific features of intermolecular interaction largely clarify their behavior, changes in properties, chemistry and mechanism of reactions occurring in them. Petroleum systems are polydisperse, in which the components can coexist in different aggregate states, and the size of the dispersed phase can vary over a wide range. They consist of diverse compounds that differ in properties, structure, shapes and sizes of molecules. Due to the variety of components that make up oil disperse systems the intermolecular interactions determine such a feature of the behavior of oil systems as the phenomenon of self-organization and structuring, which manifest themselves when external influences change and are sensitive to them. They are characterized by the absence of charge and a minimum of charge-polarization interactions of molecules, and intermolecular interactions are largely determined by the presence of paramagnetic molecules. The uncompensated spin of macromolecular compounds due to the steric obstacles, a homolytic dissociation, and the presence of microelement compounds ensure the paramagnetism of petroleum dispersed systems. This leads to developing the stable associative combinations and the formation of complex structural units capable of redistributing components and layers between phases under the influence of external effects. Comprehensive analysis and unanimity of views on the physical and chemical interactions of the components of oil systems leading to a change in their structure, open up fundamentally new opportunities for intensifying processes in the practice of production, transportation and processing of hydrocarbon raw materials and the use of petroleum products, and also allow predicting the behavior of oil systems in processes which they are participating.
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Luo, Yan, Si-ting Gao, Jun-xiong Cheng, Wei-jian Xiong, and Wen-Fu Cao. "Elucidation of the Mechanisms and Molecular Targets of Lianhuaqingwen for Treatment of COVID-19 Based on Network Pharmacology." Asian Journal of Complementary and Alternative Medicine 9, no. 4 (2021): 111–22. http://dx.doi.org/10.53043/2347-3894.acam90020.
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Lianhuaqingwen (LH) is the widely used in the treatment of Coronavirus disease 2019 (COVID-19). However, its mechanisms of action and molecular targets for treatment of COVID-19 are not clear. The active compounds of LH were collected and their targets were identified through the network pharmacology. The mechanism of compound multi components and multi targets and its relationship with disease are analyzed. COVID-19 targets were obtained by analyzing with TCMSP. In total, 282 active ingredients and 510 targets of LH were identified. Twenty-one target genes associated with LH and COVID-19. Protein-protein interaction (PPI) data were then obtained and PPI networks of LH putative targets and COVID-19-related targets were visualized and merged to identify the candidate targets for LH against COVID-19. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis were carried out. The gene-pathway network was constructed to screen the crucial target genes. The functional annotations of target genes were found to be related to immune regulation, host defense, inflammatory reaction and autoimmune diseases and so on. Twenty pathways including immunology, cancer, and cell processing were significantly enriched. Quercetin and luteolin might be the crucial ingredients. IL6 was the core gene and other several genes including IL1B, STAT1, IFNGR1, and NCF1 were the key genes in the gene-pathway network of LH for treatment of COVID-19. The results indicated that LH’s effects against COVID-19 might relate to regulation of immunological function through the specific biological processes and the related pathways. This study demonstrates the application of network pharmacology in evaluating mechanisms of action and molecular targets of complex herbal formulations.
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Chang, Ze, Li-Juan He, Dang-Feng Tian, et al. "Therapeutic Targets and Mechanism of Xingpi Jieyu Decoction in Depression: A Network Pharmacology Study." Evidence-Based Complementary and Alternative Medicine 2021 (June 23, 2021): 1–15. http://dx.doi.org/10.1155/2021/5516525.
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Background. Depression is a common mental disease that lacks effective therapeutic drugs with good curative effects and few adverse reactions. Traditional Chinese medicine (TCM) has the advantages of multiple components, multiple channels, and fewer adverse reactions in the treatment of depression. Although Xingpi Jieyu Decoction (XPJYD) demonstrates a good therapeutic effect on depression, the pharmacological mechanism underlying its antidepressant effect is still unclear. Methods. We used a network pharmacology strategy, including the construction and analysis of a complex drug-disease network, to explore the complex mechanism of XPJYD treatment of depression. In addition, molecular docking technology was used to preliminarily study the binding ability of the potential active components and core therapeutic targets of XPJYD. Results. The network pharmacology results showed 42 targets of XPJYD that are involved in depression. PPI network analysis demonstrated that the top 10 core targets were AKT1, VEGFA, MAPK8, FOS, ESR1, NR3C1, IL6, HIF1A, NOS3, and AR. The molecular docking results showed that the binding energies of beta sitosterol with AR, FOS, AKT1, VEGFA, NR3C1, and NOS3 were less than −7.0 kcal·mol−1, indicating a good docking effect. The GO enrichment analysis results showed that the XPJYD antidepression mechanism mainly involves the following biological processes such as apoptotic signaling pathway, cellular response to lipid, inflammatory response, and others. The KEGG analysis results indicated that XPJYD may regulate 13 pathways such as PI3K-Akt signaling pathway and estrogen signaling pathway in the treatment of depression. Conclusions. This study reflects the characteristics of the mechanism of action by which XPJYD treats depression, which includes multiple components, multiple targets, and multiple pathways, and provides a biological basis for further verification and a novel perspective for drug discovery in depression.
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Prodanchuk, M. G., G. M. Balan, N. V. Kurdil, A. V. Basanets, P. G. Zhminko, and O. P. Kravchuk. "Chlorine gas: molecular mechanisms of toxicity, clinical manifestations, diagnostic biomarkers and modern treatment strategy." Ukrainian Journal of Modern Toxicological Aspects 92, no. 1 (2022): 7–34. http://dx.doi.org/10.33273/2663-4570-2022-92-1-7-34.
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The hostilities on the territory of our state are accompanied by the destruction of the infrastructure of cities and industrial enterprises, which critically increased the risk of toxic gas emissions (including chlorine) and the occurrence of mass poisoning. Aim. To summarize modern knowledge about the molecular mechanisms of chlorine gas toxicity, clinical biomarkers of the toxic process, and modern treatment strategy. Material and Methods. Information data of the Ministry of Health of Ukraine, the State Emergency Service of Ukraine (SES of Ukraine), the American Health Service (CDC), the American Association of Poison Control Centers (AAPCC), materials of scientific libraries PubMed, Medline, Elsevier. Content analysis, systematic and comparative analysis were used. Results and their Discussion. Chemical accidents with the release of chlorine and the occurrence of mass poisonings are registered in various countries. Until now, the mechanisms of the toxic action of chlorine remain completely unstudied, especially at the level of intracellular structures. The results of recent studies demonstrate that irritant and irritant-necrotic effects are not directly caused by chlorine molecules, but by their hydration products – hydrochloric and hypochlorous acids. These acids directly provide a high production of reactive superoxides and nitrogen oxidants, which form oxidative stress in the epithelial cells of the mucous membrane of the bronchopulmonary structure in deeper tissues. The destruction of the cells of the ciliated epithelium occurs, the functioning of ion channels is disturbed and the permeability of cell membranes increases, inflammatory reactions develop: hyperemia, edema, bronchospasm, and surfactant destruction. These processes are facilitated by a massive release of biologically active substances – proinflammatory cytokines – IL-1β, IL-6, IL-18, nuclear factor (NF-KB), 8-isoprostane and tumor necrosis factor (TNF-β) – one of the main biomarkers of oxidative stress. These processes cause: damage to intracellular structures – mitochondria; imbalance in the functioning of the signaling molecule cAMP and disruption of autophagy processes; a decrease in the energy potential of cells with the development of endothelial dysfunction, a violation of the vascular mechanisms of NO homeostasis, both in the cells of the respiratory tract and outside the lungs, which contributes to anatomical damage and impaired function of the organs of the cardiovascular system and kidneys. Conclusion. The mechanism of the toxic action of chlorine at the level of intracellular structures undoubtedly requires further study. Another relevant direction of research may be the search for new sensitive biomarkers of the toxic process, which will allow us to objectively assess the severity of poisoning and increase the effectiveness of the rather complex process of treating patients, in the absence of antidotes. Key Words: chlorine gas, toxicity, mechanism of action, acute poisoning, treatment of poisoning.
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Lunz, Davin, Gregory Batt, Jakob Ruess, and J. Frédéric Bonnans. "Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes." PLOS Computational Biology 17, no. 7 (2021): e1009214. http://dx.doi.org/10.1371/journal.pcbi.1009214.
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The chemical master equation and its continuum approximations are indispensable tools in the modeling of chemical reaction networks. These are routinely used to capture complex nonlinear phenomena such as multimodality as well as transient events such as first-passage times, that accurately characterise a plethora of biological and chemical processes. However, some mechanisms, such as heterogeneous cellular growth or phenotypic selection at the population level, cannot be represented by the master equation and thus have been tackled separately. In this work, we propose a unifying framework that augments the chemical master equation to capture such auxiliary dynamics, and we develop and analyse a numerical solver that accurately simulates the system dynamics. We showcase these contributions by casting a diverse array of examples from the literature within this framework and applying the solver to both match and extend previous studies. Analytical calculations performed for each example validate our numerical results and benchmark the solver implementation.
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Makolinets, Vasyl, Tamara Grashenkova, Volodymyr Moseichuk, Kyrylo Makolinets, and Vladyslav Moseichuk. "Molecular hydrogen as a possible therapeutic factor in complex rehabilitation therapy in patients with muscular skeletal disorders (literature review)." ORTHOPAEDICS, TRAUMATOLOGY and PROSTHETICS, no. 1 (October 5, 2021): 92–97. http://dx.doi.org/10.15674/0030-59872021192-97.
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The paper presents an analysis of foreign scientific and medical data on the therapeutic factor — molecular hydrogen. The effectiveness of its application in the complex therapy of many diseases is revealed. The effect is achieved due to the small size of the molecule, which passes through biological membranes and inhibits dangerous free radicals in the mitochondria, as well as in the nucleus, which reduces the possibility of DNA damaging. Molecular hydrogen neutralizes oxidants in the brain due to its ability to cross the blood-brain barrier. It normalizes the functions and metabolic processes in the body and, as an antioxidant, is selective: it does not affect the useful free radicals involved in important metabolic processes and selectively eliminates only the most dangerous oxidants — hydroxyl radicals. Interacting with them, hydrogen converts them into water molecules without the formation of by-products and chain reactions. Unlike other known antioxidants, molecular hydrogen does not disrupt normal metabolism, does not cause negative changes in cells, activates the body’s own antioxidant systems. The possibility and expediency of the use of molecular hydrogen in the case of pathology of the musculoskeletal system has been confirmed. The peculiarities of its effect on bone and cartilage tissue in the experiment are shown. It has been determined that the use of molecular hydrogen is a new pharmacological strategy aimed at the selective removal of ONOO—, and can be an effective method in the treatment of joint diseases. Because cartilage receives nutrients through a diffusion-loading mechanism, and molecular hydrogen penetrates rapidly into tissues, it can be useful for the prevention of diseases of joints of degenerative origin. It reduces oxidative stress and slows down the reduction of matrix proteins and inhibition of proteinase degradation. Its effectiveness has been proven after injuries to the spinal cord, muscles and tendons, comorbid diseases such as hypertension, coronary heart disease, diabetes and metabolic syndrome. Key words. Molecular hydrogen, hydrogen water, hydrogen inhalations, joint diseases, consequences of musculoskeletal injuries, comorbid pathology.
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Yin, Qiushi, Zihao Xu, Tianquan Lian, Djamaladdin G. Musaev, Craig L. Hill, and Yurii V. Geletii. "Tafel Slope Analyses for Homogeneous Catalytic Reactions." Catalysts 11, no. 1 (2021): 87. http://dx.doi.org/10.3390/catal11010087.
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Tafel analysis of electrocatalysts is essential in their characterization. This paper analyzes the application of Tafel-like analysis to the four-electron nonelectrochemical oxidation of water by the stoichiometric homogeneous 1-electron oxidant [Ru(bpy)3]3+ to dioxygen catalyzed by homogeneous catalysts, [Ru4O4(OH)2(H2O)4(γ-SiW10O36)2]10− (Ru4POM) and [Co4(H2O)2(PW9O34)2]10– (Co4POM). These complexes have slow electron exchange rates with electrodes due to the Frumkin effect, which precludes the use of known electrochemical methods to obtain Tafel plots at ionic strengths lower than 0.5 M. The application of an electron transfer catalyst, [Ru(bpy)3]3+/2+, increases the rates between the Ru4POM and electrode, but a traditional Tafel analysis of such a complex system is precluded due to a lack of appropriate theoretical models for 4-electron processes. Here, we develop a theoretical framework and experimental procedures for a Tafel-like analysis of Ru4POM and Co4POM, using a stoichiometric molecular oxidant [Ru(bpy)3]3+. The dependence of turnover frequency (TOF) as a function of electrochemical solution potential created by the [Ru(bpy)3]3+/[Ru(bpy)3]2+ redox couple (an analog of the Tafel plot) was obtained from kinetics data and interpreted based on the suggested reaction mechanism.
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Yin, Qiushi, Zihao Xu, Tianquan Lian, Djamaladdin G. Musaev, Craig L. Hill, and Yurii V. Geletii. "Tafel Slope Analyses for Homogeneous Catalytic Reactions." Catalysts 11, no. 1 (2021): 87. http://dx.doi.org/10.3390/catal11010087.
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Tafel analysis of electrocatalysts is essential in their characterization. This paper analyzes the application of Tafel-like analysis to the four-electron nonelectrochemical oxidation of water by the stoichiometric homogeneous 1-electron oxidant [Ru(bpy)3]3+ to dioxygen catalyzed by homogeneous catalysts, [Ru4O4(OH)2(H2O)4(γ-SiW10O36)2]10− (Ru4POM) and [Co4(H2O)2(PW9O34)2]10– (Co4POM). These complexes have slow electron exchange rates with electrodes due to the Frumkin effect, which precludes the use of known electrochemical methods to obtain Tafel plots at ionic strengths lower than 0.5 M. The application of an electron transfer catalyst, [Ru(bpy)3]3+/2+, increases the rates between the Ru4POM and electrode, but a traditional Tafel analysis of such a complex system is precluded due to a lack of appropriate theoretical models for 4-electron processes. Here, we develop a theoretical framework and experimental procedures for a Tafel-like analysis of Ru4POM and Co4POM, using a stoichiometric molecular oxidant [Ru(bpy)3]3+. The dependence of turnover frequency (TOF) as a function of electrochemical solution potential created by the [Ru(bpy)3]3+/[Ru(bpy)3]2+ redox couple (an analog of the Tafel plot) was obtained from kinetics data and interpreted based on the suggested reaction mechanism.
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Ankora, Maxine, Mesfin Haile Mamme, Koen Lammers, et al. "(Digital Presentation) Fundamental Insights into Electrodeposition of Mixed Chromium Metal-Carbide-Oxides from Trivalent Chromium – Formate Electrolytes." ECS Meeting Abstracts MA2022-02, no. 23 (2022): 976. http://dx.doi.org/10.1149/ma2022-0223976mtgabs.
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Recent restrictions on industrial usage of hexavalent chromium under new REACH legislation have further sparked the development of hexavalent chromium-free chromium plating processes. An industrially important development in this field is Trivalent Chromium Coating Technology (TCCT®), a chromium electroplating technology for packaging steel developed at Tata Steel. In this process, aqueous trivalent chromium electrolytes rather than hexavalent chromium electrolytes are employed for the electrodeposition of metallic chromium. However, to deposit metallic chromium from a trivalent chromium electrolyte, it is necessary to incorporate a complexing agent given the kinetic inertness of aqueous trivalent chromium complexes. Formate plays this role in the TCCT® process yielding coatings comparable to the conventional hexavalent chromium-based process [1-4]. However, understanding the mechanism and kinetics of chromium electrodeposition from this system is quite limited. Fundamental knowledge of the deposition process is key for industrial process optimization. Essential to determining the reaction mechanism and kinetics is the identification of the chemical species involved in the reaction. Using a hybrid multiscale experimental and computational approach, insights into chromium complexation in the bulk electrolytes and how this speciation influences the composition of the deposit have been gained. Samples electroplated in electrolytes of varied formate concentrations were characterized using X-ray Fluorescence (XRF) spectroscopy and X-ray Photoelectron Spectroscopy (XPS). Results from these analyses show that metallic chromium is only deposited when the electrolyte contains formate ions. In the absence of formate, only oxide and carbide species are deposited. The characterization results also show a current efficiency of the TCCT process of ~ 40%. From observations from surface characterization as well as spectroscopic analysis and density functional theory (DFT) and ab initio molecular dynamics studies (AIMD) of the bulk electrolyte, the coordination and complexation of formate ion in the chromium complex responsible for metallic chromium deposition have also been identified. Voltammetric studies coupled with ex-situ XPS and scanning electron microscopy (SEM) surface characterization also lead to a clear definition of the reaction mechanism of metallic chromium deposition that the incorporation of formate in trivalent chromium electrolytes makes possible.
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Jones, Jeff. "Characteristics of Pattern Formation and Evolution in Approximations of Physarum Transport Networks." Artificial Life 16, no. 2 (2010): 127–53. http://dx.doi.org/10.1162/artl.2010.16.2.16202.
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Most studies of pattern formation place particular emphasis on its role in the development of complex multicellular body plans. In simpler organisms, however, pattern formation is intrinsic to growth and behavior. Inspired by one such organism, the true slime mold Physarum polycephalum, we present examples of complex emergent pattern formation and evolution formed by a population of simple particle-like agents. Using simple local behaviors based on chemotaxis, the mobile agent population spontaneously forms complex and dynamic transport networks. By adjusting simple model parameters, maps of characteristic patterning are obtained. Certain areas of the parameter mapping yield particularly complex long term behaviors, including the circular contraction of network lacunae and bifurcation of network paths to maintain network connectivity. We demonstrate the formation of irregular spots and labyrinthine and reticulated patterns by chemoattraction. Other Turing-like patterning schemes were obtained by using chemorepulsion behaviors, including the self-organization of regular periodic arrays of spots, and striped patterns. We show that complex pattern types can be produced without resorting to the hierarchical coupling of reaction-diffusion mechanisms. We also present network behaviors arising from simple pre-patterning cues, giving simple examples of how the emergent pattern formation processes evolve into networks with functional and quasi-physical properties including tensionlike effects, network minimization behavior, and repair to network damage. The results are interpreted in relation to classical theories of biological pattern formation in natural systems, and we suggest mechanisms by which emergent pattern formation processes may be used as a method for spatially represented unconventional computation.