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Journal articles on the topic 'Complex Reaction Mechanism - Molecular Processes'

Author: Grafiati

Published: 7 September 2023

Last updated: 31 July 2025

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1

Saidqulov, Sanjar H. "MECHANISM OF PROPANE-BUTANE FRACTION DECOMPOSITION PROCESS INTO LOW MOLECULAR SATURATED AND UNSATURATED HYDROCARBONS." International Journal of Advance Scientific Research 05, no. 12 (2024): 336–48. https://doi.org/10.37547/ijasr-04-12-52.

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The decomposition of propane-butane fractions into low molecular weight saturated and unsaturated hydrocarbons is a key process in petrochemical production. This study explores the kinetic parameters and reaction mechanisms using reactors designed for impulse and continuous flow operations. The results indicate that the decomposition reactions follow first-order kinetics under specific experimental conditions. Conducted at temperatures ranging from 400°C to 700°C with catalysts, the experiments reveal that the process occurs at two distinct active catalytic sites (Z and Z). The mechanism invol

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2

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 rea

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Sakamoto, Naonari, Keita Sekizawa, Soichi Shirai, et al. "(Digital Presentation) Investigate the Reaction Mechanism in the C3H7OH Electrochemical Reduction Reaction from CO₂ Using Dinuclear Cuprous Molecular Catalyst." ECS Meeting Abstracts MA2024-02, no. 62 (2024): 4256. https://doi.org/10.1149/ma2024-02624256mtgabs.

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The urgent global challenge of climate change and the depletion of energy resources have spotlighted the technology of converting carbon dioxide (CO2) into valuable carbon-based products. The CO2 reduction reaction (CO2RR) via metal complex molecules is expected to improve and enhance the electronic/chemical environment of the catalytic active sites through control with freely modulable organic ligands. The selectivity for the formation of formic acid and carbon monoxide from CO2 in organic solvents has been successfully controlled in some molecular catalysts by small structural differences in

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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 elementar

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Dinolfo, Peter Henry, Andrea L. Mitchell, Charles A. McCabe, and Peter J. Bonitatibus. "(Invited) Utilizing Redox-Coupled Spin-Crossover to Enhance Molecular Bistability." ECS Meeting Abstracts MA2025-01, no. 56 (2025): 2705. https://doi.org/10.1149/ma2025-01562705mtgabs.

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Spin crossover (SCO) is one of the most widely studied phenomena in transition metal complexes, in part due to the possible technological applications of such species in molecular electronics, memory storage, electrochromics, and display devices. Any transition metal complex with a d4–d7 electron configuration, such as 2+ and 3+ ions of Cr, Mn, Fe, and Co, can theoretically exhibit SCO effects which depend highly on the coordination environment and ligand field strength. Redox-coupled SCO processes provide a mechanism to enhance the molecular bistability and trigger transitions between low- an

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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 pr

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Zedler, Linda, Sven Krieck, Stephan Kupfer, and Benjamin Dietzek. "Resonance Raman Spectro-Electrochemistry to Illuminate Photo-Induced Molecular Reaction Pathways." Molecules 24, no. 2 (2019): 245. http://dx.doi.org/10.3390/molecules24020245.

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Electron transfer reactions play a key role for artificial solar energy conversion, however, the underlying reaction mechanisms and the interplay with the molecular structure are still poorly understood due to the complexity of the reaction pathways and ultrafast timescales. In order to investigate such light-induced reaction pathways, a new spectroscopic tool has been applied, which combines UV-vis and resonance Raman spectroscopy at multiple excitation wavelengths with electrochemistry in a thin-layer electrochemical cell to study [RuII(tbtpy)2]2+ (tbtpy = tri-tert-butyl-2,2′:6′,2′′-terpyrid

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Kondyli, Aikaterini, and Wolfgang Schrader. "Investigation of the Behavior of Hydrocarbons during Crude Oil Fouling by High-Resolution Electrospray Ionization Mass Spectrometry." Energies 17, no. 6 (2024): 1299. http://dx.doi.org/10.3390/en17061299.

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Crude oil is probably the most complex natural chemical mixture processed in various ways to make fuel and fine chemicals among a wide range of products in industrial processing. The conditions of those industrial processes often include high temperatures, which often cause undesired chemical reactions. One of those reaction sequences is crude oil fouling, which finally results in the formation of undesired solid deposits of carbon material, a calamity that costs millions of dollars worldwide each year and produces toxic waste. However, the compounds involved in fouling, let alone the underlyi

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9

Zhang, Enhao, Xiumin Chen, Jie Zhou, et al. "Modeling the Carbothermal Chlorination Mechanism of Titanium Dioxide in Molten Salt Using a Deep Neural Network Potential." Materials 18, no. 3 (2025): 659. https://doi.org/10.3390/ma18030659.

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The molten salt chlorination method is one of the two main methods for producing titanium tetrachloride, an important intermediate product in the titanium industry. To effectively improve chlorination efficiency and reduce unnecessary waste salt generation, it is necessary to understand the mechanism of the molten salt chlorination reaction, and consequently this paper conducted studies on the carbon chlorination reaction mechanism in molten salts by combining ab initio molecular dynamics (AIMD) and deep potential molecular dynamics (DeePMD) methods. The use of DeePMD allowed for simulations o

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10

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 cu

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11

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 mot

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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) t

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Todorova, Mira, Jing Yang, Zhenyu Wang, et al. "(Invited) Reaction Mechanisms, Reaction Barriers and Free Energy Surfaces at Electrochemical Solid/Liquid Interfaces from (ab initio) Molecular Dynamics Calculations." ECS Meeting Abstracts MA2025-01, no. 46 (2025): 2442. https://doi.org/10.1149/ma2025-01462442mtgabs.

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Our quest for a sustainable and greener future is closely linked to the processes that occur at electrified solid/liquid interfaces. The rational design and targeted optimization of processes such as hydrogen evolution, oxygen evolution, material dissolution and others will benefit from our understanding of the mechanisms driving electrochemical reactions and how these are affected by environmental changes. Such electrochemical reactions are the result of a complex interplay between fluctuations in the aqueous environment, ionic motion and electronic charge exchange. Molecular dynamics simulat

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Tolasa, Diriba. "Molecular Dynamics Simulations: Unraveling the Complexities of Chemical Reactions at the Atomic Level." American Journal of Physics and Applications 13, no. 3 (2025): 46–58. https://doi.org/10.11648/j.ajpa.20251303.11.

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Molecular dynamics (MD) simulations have emerged as a cornerstone computational technique within the realms of chemistry and materials science, offering profound insights into the intricate behaviors of molecular systems at the atomic scale. By leveraging the principles of classical mechanics and statistical physics, MD simulations afford researchers a detailed, time-resolved perspective on the dynamical behavior of molecules, thereby facilitating the exploration of reaction mechanisms that often elude conventional experimental methodologies. This paper provides a comprehensive overview of the

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15

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

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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

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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 chemi

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18

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 mole

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19

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 re

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Tymchuk, A. F., O. O. Streltsova, and A. D. Purich. "CONTRIBUTION OF THE ASSOCIATION OF NATURAL HIGH-MOLECULAR COMPOUNDS IN IMPROVING THE EFFICIENCY OF FLOCCULATION PROCESSES." Odesa National University Herald. Chemistry 28, no. 2(85) (2023): 108–15. http://dx.doi.org/10.18524/2304-0947.2023.2(85).286608.

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Natural flocculants as chitosan and sodium alginate has a complex of environmental and physic-chemical properties: biodegradability, playback of the raw material base, reaction and complexing ability. Researches had shown that natural polymers can be used for flocculation of suspensions. Association has a specific role in the flocculation process. Association determined by the nature and charge density of the flocculants. It is necessary to understand the mechanism of processes in these systems in order to select an effective flocculants. The mechanism of action of compositions natural floccul

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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 l

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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 phosph

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23

Bazany, Denis, Hana Greifova, Lucia Zuscikova, et al. "Can Bisphenols Alter the Inflammation Process?" Life 15, no. 5 (2025): 782. https://doi.org/10.3390/life15050782.

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This review’s main purpose is to draw attention to the possible influence of widely used bisphenols on the inflammatory process. Bisphenols are endocrine-disrupting chemicals that are produced worldwide in great quantities. From this point of view, it is very important to clarify their influence on innate immune reactions, which protect the integrity of the body against the action of various pathogens on a daily basis. The inflammation process consists of several key factors that are produced at different levels of this reaction. Each of these levels can be affected by endocrine disruptors, fr

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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

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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. RS

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Shin, Dongyup, and Sang Soo Han. "Design Strategies for Oxygen Evolution Reaction Catalysts: Insights from a Kinetic Perspective via Constrained Ab Initio Molecular Dynamics." ECS Meeting Abstracts MA2024-02, no. 42 (2024): 2848. https://doi.org/10.1149/ma2024-02422848mtgabs.

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Abstract In the pursuit of sustainable energy, the efficient production of green hydrogen through electrochemical water splitting has emerged as a promising strategy.1 Central to this process is the optimization of the Oxygen Evolution Reaction (OER), where the necessity for a high overpotential at the anodic electrode poses a significant barrier. Among the myriad of catalysts studied, iridium oxides (IrOx) have garnered attention for their superior catalytic activity and stability in acidic environments.2 Yet, the quest for unlocking the full potential of IrOx catalysts necessitates a deeper

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Guillamón, Eva, Mónica Oliva, Juan Andrés, et al. "Catalytic hydrogenation of azobenzene in the presence of a cuboidal Mo3S4 cluster via an uncommon sulfur-based H2 activation mechanism." ACS Catalysis 11, no. 2 (2020): 608–14. https://doi.org/10.1021/acscatal.0c05299.

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Azobenzene hydrogenation is catalyzed under moderate conditions by a cuboidal Mo<sub>3</sub>(μ<sub>3</sub>-S)(μ-S)<sub>3</sub> diamino complex via a cluster catalysis mechanism. Dihydrogen activation by the molecular [Mo<sub>3</sub>(μ<sub>3</sub>-S)(μ-S)<sub>3</sub>Cl<sub>3</sub>(dmen)<sub>3</sub>]<sup>+</sup> cluster cation takes place at the μ-S bridging atoms without direct participation of the metals in clear contrast with classical concepts. The reaction occurs with the formation of 1,2-diphenylhydrazine as an intermediate with similar appearance and disappearance

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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 trans

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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 computation

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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

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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 nucleo

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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

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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 inacti

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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 t

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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-

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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

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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,

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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-i

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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 h

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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 p

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Perazzolli, Michele, Noemí Herrero, Lieven Sterck, et al. "Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat." BMC Genomics 17, no. 1 (2016): 838. https://doi.org/10.1186/s12864-016-3174-4.

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<strong>Background: </strong>Soil microorganisms are key determinants of soil fertility and plant health. Soil phytopathogenic fungi are one of the most important causes of crop losses worldwide. Microbial biocontrol agents have been extensively studied as alternatives for controlling phytopathogenic soil microorganisms, but molecular interactions between them have mainly been characterised in dual cultures, without taking into account the soil microbial community. We used an RNA sequencing approach to elucidate the molecular interplay of a soil microbial community in response to a plant patho

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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) b

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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

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Alferova, Vera A., Anna A. Baranova, Olga A. Belozerova, et al. "Molecular Decoration and Unconventional Double Bond Migration in Irumamycin Biosynthesis." Antibiotics 13, no. 12 (2024): 1167. https://doi.org/10.3390/antibiotics13121167.

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Irumamycin (Iru) is a complex polyketide with pronounced antifungal activity produced by a type I polyketide (PKS) synthase. Iru features a unique hemiketal ring and an epoxide group, making its biosynthesis and the structural diversity of related compounds particularly intriguing. In this study, we performed a detailed analysis of the iru biosynthetic gene cluster (BGC) to uncover the mechanisms underlying Iru formation. We examined the iru PKS, including the domain architecture of individual modules and the overall spatial structure of the PKS, and uncovered discrepancies in substrate specif

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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

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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 understa

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Imanishi, Akihito. "(Invited) Surface Local Structure Dependence of Photoinduced Reaction Process on TiO₂ Single Crystal Electrode in Aqueous Solution." ECS Meeting Abstracts MA2024-02, no. 59 (2024): 3988. https://doi.org/10.1149/ma2024-02593988mtgabs.

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Metal oxides such as TiO2 are widely used as electrocatalysts and photo-responsive electrodes in various electrochemical devices, and many researchers have studied them. However, the reaction processes at their interfaces are generally complex, and there are many aspects that remain to be elucidated. Even for TiO2 electrodes, which have been the most widely studied, the mechanism of interfacial reactions still remains unclear, especially the effects of crystal faces and atomic- to nano-level surface structures on electrode reactions. Our group has been investigated how the atomic- to nano-leve

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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 s

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Arbatskiy, Mikhail, Dmitriy Balandin, Ilya Akberdin, and Alexey Churov. "A Systems Biology Approach Towards a Comprehensive Understanding of Ferroptosis." International Journal of Molecular Sciences 25, no. 21 (2024): 11782. http://dx.doi.org/10.3390/ijms252111782.

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Ferroptosis is a regulated cell death process characterized by iron ion catalysis and reactive oxygen species, leading to lipid peroxidation. This mechanism plays a crucial role in age-related diseases, including cancer and cardiovascular and neurological disorders. To better mimic iron-induced cell death, predict the effects of various elements, and identify drugs capable of regulating ferroptosis, it is essential to develop precise models of this process. Such drugs can be tested on cellular models. Systems biology offers a powerful approach to studying biological processes through modeling,

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Johnson, Matthew S., Charles J. McGill, and William H. Green. "Transitory sensitivity in automatic chemical kinetic mechanism analysis." International Journal of Chemical Kinetics, October 21, 2024. http://dx.doi.org/10.1002/kin.21766.

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AbstractDetailed chemical kinetic mechanisms are necessary for resolving many important chemical processes. As the chemistry of smaller molecules has become better grounded and quantum chemistry calculations have become cheaper, kineticists have become interested in constructing progressively larger kinetic mechanisms to model increasingly complex chemical processes. These large kinetic mechanisms prove incredibly difficult to refine and time‐consuming to interpret. Traditional sensitivity analysis on a large mechanism can range from inconvenient to practically impossible without special techn

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